8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
ABSTRACTS | INVITED SPEAKERS
EVOLUTION OF GENE REGULATION AMONG DROSOPHILA SPECIES
Patricia Wittkopp, University of Michigan
Genetic dissection of phenotypic differences within and between species has shown that genetic changes affecting the regulation of gene expression are an important source of phenotypic diversity. We have seen this in our own work investigating the genetic basis of pigmentation differences between closely related Drosophila species. To better understand the genetic mechanisms responsible for the evolution of gene expression, we have been investigating the evolution of a specific gene yellow( ) as well as the evolution of gene expression on a genomic scale. Work on both of these topics, with an emphasis on methods adaptable to non-model systems, will be presented.
METAMORPHOSIS AND EVOLUTION OF ARTHROPOD GENOMICS
Judith H. Willis, University of Georgia
I began work on arthropod genomics 50 years ago. At first, I was only interested in the genetic underpinnings of metamorphic transitions, but I have ended up with an increasing orientation toward arthropod evolution. During those 50 years the field itself has evolved (gaining a name in the process) and metamorphosed (witness this meeting). My talk will address both the biology and the history.
I began by testing whether each metamorphic stage was underwritten by a unique set of genes by using cuticular proteins (CPs) as molecular markers. Results, starting with tube gels and progressing to the isolation and characterization of two CP genes and their promoters, demolished that hypothesis. A shift from a giant silkworm to Anopheles gambiae that devotes ~2% of its protein coding genes to structural CPs was accompanied by a larger scale analysis of their activity, including mRNA expression and recovery of authentic CPs from cuticle determined by LC-MS/MS analyses. Collaboration with Stavros Hamodrakas’s group in Athens, Greece has provided homology models that combine structure and function and sequence prediction programs that facilitate cross-species comparisons. CPs have shed light on several aspects of insect evolution: the benefit of gene duplication, importance of concerted evolution, the phylogenetic position of basal arthropods. I have found that fundamental problems can be resolved, and the metamorphosis of models and the evolution of techniques can be followed and summarized by focusing on just one group of proteins of particular importance to arthropods.
11 ABSTRACTS | INVITED SPEAKERS
PHYLOGENY-DRIVEN INITIATIVE ON GENOMIC SEQUENCING
Guojie Zhang 1,2
1. Chinese National Genebank, BGI-Shenzhen, 518083, Shenzhen, China, 2. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.
Comparative genomics has been a powerful and routine tool in revealing the complex evolutionary history and species adaptation. The dramatic development of sequencing technologies has boosted the fast development of genomic studies, from targeting on model organisms to non-model organisms, from single individual genomes to large-scale population genomics, and from single species genome studies to phylogenomic scale studies. In the past few years, we have decoded the genomes of hundreds of animal species, including ~50 arthropod species from 20 different families. However, decoding the genomes with high repetitive contents and high heterozygosity has not been fully resolved with current technologies. Therefore, my group has given the top priority to organisms with simple genome structure, and developed several projects within the phylogenetic framework for eusocial insects and birds. The avian phylogenomic project is one of projects we recently accomplished. In this project, we have collected genomes of 48 bird species, representing nearly all of the major groups of living birds, and applied information from the entire genome to resolve the deep avian phylogenetic relationships, which has been a challenge to biologists for centuries. With the newly reconstructed phylogenetic tree, our analyses also revealed that the genomic biodiversity across birds covaries with diverse adaptations to different lifestyles. We have learned a lot of lessons from this large-scale international coordinating project that could be useful for the i5k group.
AUTOMATED ANNOTATION OF I5K GENOMES
Dan Hughes, Genome Sequencing Center at Baylor College of Medicine
We are using a combination of MAKER and an extended version of the Cegma pipeline to perform automated annotation of the various i5k genomes. Heuristics are used to post-process tophat/cufflinks RNASeq predicted transcripts to systematically limit the presence of fusion transcripts. MAKER is then used to run alignments of ~1M non-redundant Metazoan peptide sequences and synthesize the results of RNASeq analysis and ab initio predictions. Further heuristics are used to choose between MAKER and Cegma derived models and each locus and tweak models where necessary to generate the final gene set. Gene names are assigned via a synthesis of OrthoMCL and reciprocal BLAST analysis and InterProScan5 is run on the resulting proteome prior to public release.
12 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
THE I5K WORKSPACE@NAL – ENABLING GENOMIC DATA ACCESS, VISUALIZATION AND CURATION FOR THE I5K COMMUNITY
Monica Poelchau, USDA Maryland
Genomic data access and visualization – in particular, the establishment of ‘genome portals’ - is a critical, yet often overlooked component of genome sequencing projects. Genomic data should be visualized to assess and improve the quality of genome assemblies and annotations, both at the pre- and post-release steps of a genome’s life cycle. In addition, gene model curation, during which a community manually inspects and improves computationally predicted gene models, is a critical step in the maturation of a genome project. Existing or preconfigured genome portals facilitate data access and community building, but not all research groups have the means or connections to host a dedicated portal for their sequenced organism. The National Agricultural Library (NAL), as part of our broader mission to enable access to genomic information for arthropod genomes and the agricultural community, has implemented a genome portal for such ‘orphaned’ i5k genomes (http://i5k.nal.usda.gov/). We provide access to genomic information via organism and gene pages, data downloads, a Blast interface, and the JBrowse genome browser. We also provide the Web Apollo manual annotation editor for these species. In this talk, I will describe the post-gene prediction life cycle of a typical i5k genome, and the NAL’s plan/vision to support i5k genomes at this stage via the i5k Workspace@NAL and other services.
13 ABSTRACTS | INVITED SPEAKERS
CHROMOSOME ORGANIZATION AND EVOLUTION OF THE YELLOW FEVER MOSQUITO GENOME
Maria V. Sharakhova, Department of Entomology, Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA
The yellow fever mosquito Aedes aegypti has a large 1.37 Gb genome with a high density of repetitive elements. Physical genome mapping in Ae. aegypti is difficult due to the poor quality of polytene chromosomes. As a result, chromosome organization and evolution of the yellow fever mosquito genome remain largely unexplored. We developed an approach for physical mapping of genomic supercontigs based on the banding pattern of mitotic chromosomes of Ae. aegypti. Using fluorescentin situ hybridization, we assigned 624 Mb of the genome assembly (45%) to specific bands of chromosome idiograms. Chromosome and genome maps were integrated with the linkage genetic map by direct placement of 100 BAC clones carrying major genetic markers. As a result, 12 QTLs related to the pathogen transmission were also anchored to the chromosome positions. These QTLs were combined into five major clusters on the chromosome map. In addition, we analyzed the distribution of genes, tandem repeats and transposable elements along the chromosomes and explored the patterns of chromosome homology and rearrangements between Ae. aegypti and An. gambiae. The study demonstrated that the q arm of the sex-determining chromosome 1 has the lowest gene content and the highest density of minisatellites. A comparative genomic analysis with An. gambiae determined that the previously proposed whole-arm synteny is not fully preserved; a number of pericentric inversions have occurred between the two species. The sex-determining chromosome 1 had a higher rate of genome rearrangements than observed in autosomes 2 and 3 of Ae. aegypti. The research tools and information generated by this study contribute to a more complete understanding of the genome organization and evolution in mosquitoes.
14 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
GENOME STUDIES OF THE LYME DISEASE TICK, IXODES SCAPULARIS: FACILITATING RESEARCH ON TICK AND MITE VECTORS OF DISEASE
Catherine A. Hill 1, Monika Gulia-Nuss 1, Jyothi Thimmapuram 2, Jason M. Meyer 1, the Ixodes scapularis Genome Consortium and VectorBase 3
1. Purdue University, Department of Entomology, 901 West State Street, West Lafayette, IN, 47907, USA. 2. Purdue University, Purdue Bioinformatics Core, 155 South Grant Street, West Lafayette, IN, 47907, USA. 3. Eck Center for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.
Ticks and mites (subphylum Chelicerata: subclass Acari) are notorious ectoparasites and vectors of human and animal pathogens. The Lyme disease tick, Ixodes scapularis (family Ixodidae) is the most important arthropod vector of human disease in North America and transmits the pathogens that cause Lyme disease, granulocytic anaplasmosis and babesiosis. The assembled genome of I. scapularis (IscaW1), funded by the U.S. National Institutes of Health, is the first for a medically important species within the entire diverse lineage of Acari and a non-insect arthropod vector. Annotation of the 2.1 Gbp nuclear genome revealed 20,486 protein-coding genes, expansions of gene families associated with tick-host interactions, neurological, developmental and chemoreception processes likely unique to ticks, and proteins tied to pathogen uptake. Repetitive DNA accumulation in the genome represents an extreme amongst sequenced arthropods. Fluorescent in situ-based hybridization (FISH) was used to study the distribution of classes of tandem repeats on the I. scapularis chromosomes and develop a FISH-based physical map. Restriction-site Associated DNA sequencing (RADseq) was employed for genome-wide single nucleotide polymorphism (SNP) discovery in I. scapularis collected from geographically isolated regions across North America. These markers are being used to assess genetic diversity within and between I. scapularis populations and to create the first high-density linkage map for this tick. These resources are expected to facilitate much needed research on the biology of I. scapularis and other species of tick and mite vectors from the molecular to whole-organism level.
15 ABSTRACTS | INVITED SPEAKERS
WHAT ANTS CAN TEACH US ABOUT EPIGENETICS
Roberto Bonasio, Epigenetics Program, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania
Ants live in sophisticated societies in which morphologically and behaviorally distinct types of individuals (castes) arise from a single genome, carry out different tasks, and respect societal boundaries so that colonies can thrive. Female embryos become either reproductive queens or various types of workers, and these profound differences in developmental trajectory are usually independent of their genetic make-up. Hence, the molecular information that specifies the phenotypic differences among castes must be provided at an epigenetic level, that is, without changes in the DNA sequence.
We have sequenced the genome and obtained genome-wide DNA methylation and chromatin structure profiles for the antsCamponotus floridanus and Harpegnathos saltator. Camponotus ants live in large colonies, where only the long-lived queen lays fertilized eggs. In contrast, Harpegnathos queens can be replaced by one or few workers, which acquire behavioral and physiological phenotypic traits typical of the queen. This phenomenon offers unparalleled opportunities to study the epigenetic reprogramming of behavioral and physiological traits in the context of an adult organism that can be manipulated in the laboratory.
Our results show that ant castes differ in their chromatin structure and that the reprogramming of Harpegnathos workers into pseudo-queens is accompanied by transcriptional changes in genes involved in the regulation of longevity and neurophysiology. I will discuss the implications of these findings for epigenetic research and the potential of ants,Harpegnathos in particular, to serve as genetic models for epigenetic experiments in social insects
16 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
GENOMIC SIGNATURES OF REPEATED EUSOCIAL EVOLUTION IN BEES
(Co-First Authors) Karen M. Kapheim (Illinois), Cai Li (BGI), Jun Wang (BGI), Gene E. Robinson (Illinois), Guojie Zhang (BGI)
Most of the relatively few origins of eusociality have occurred within the bees, an important group of pollinators with exceptionally diverse social organization. Most are solitary, but some show basic or complex eusociality, the latter with intricate caste systems and up to tens of thousands of colony members. The evolutionary processes underlying repeated evolution of eusociality are unknown, because genome sequences from closely related solitary and social species have been heretofore unavailable. We analyzed draft genome sequences of ten species from three families differing in social organization. Here we show that independent origins of basic eusociality from solitary ancestors share common genomic features despite being separated by over 50 million years, while elaborations of complex eusociality among more closely related species involve disparate features. We found genes associated with increasingly complex social organization with signatures of convergent evolution, positive selection, negative selection, and non- adaptive evolution. Genes showing positive selection include those involved in carbohydrate metabolism and genes showing convergent evolution include those that encode highly conserved transcription factors, including several in the homeobox family. The dominant signal of eusocial evolution in bees is constrained protein evolution coupled with increased regulatory capacity, involving increases in promoter region transcription factor binding sites and gene body methylation. This pattern is similar to that described for human brain evolution, suggesting eusocial evolution is associated with increasingly complex networks of genes.
17 ABSTRACTS | INVITED SPEAKERS
THE GENOMICS OF ECOLOGICAL DIVERGENCE IN SYMPATRY: THE APPLE MAGGOT FLY, RHAGOLETIS POMONELLA
Jeffrey L. Feder, Dept. of Biological Sciences Univ. of Notre Dame, Notre Dame IN, USA 46556
Darwin argued that natural selection is the major force driving the formation of new species. If true, then a pronounced footprint of divergent selection should be seen between the genomes of speciating organisms. Here, we test for this footprint between hawthorn and apple host races of the fruit flyRhagoletis pomonella (Diptera: Tephritidae), a model for sympatric ecological speciation with gene flow. We report that the response of 32,455 SNPs in a selection experiment on diapause depth, a key adaptive trait between host plants, was highly predictive of the genome-wide pattern of genetic divergence between the fly races in nature. Thus, as divergent natural selection drives even the earliest stages of speciation, it can produce a large and predictable effect on genome-wide divergence.
18 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
THE GENOMICS AND ECOLOGY OF ADAPTATION AT A BUTTERFLY SUPERGENE
Mathieu Joron, Institute of Systematics, Evolution and Biodiversity, UMR CNRS 7205, Muséum National d’Histoire Naturelle, Paris, France
Butterfly mimicry is characterised by powerful selection shaping extraordinary wing pattern convergence between species, as well as a rich diversity of distinct mimicry groups. Within increasing genomic resources for butterflies, mimicry is therefore an excellent system to explore the genomic basis of adaptation and diversification. My talk will focus on the maintenance of adaptive polymorphism in an Amazonian butterfly,Heliconius numata, in which multiple wing pattern forms coexist and mimic the diversity of local mimicry groups in every locality. Polymorphism is controlled by a supergene, a coadapted cluster of loci locked together by polymorphic inversions. Population genomics now allow us to study the origins of this architecture and its evolutionary consequences. We studied the differentiation of allelic blocks using population genomics and whole-genome resequencing of populations of H. numata and closely related species, to reveal how the structure of recombination is set by the precise location of inversion breakpoints. Shared polymorphisms with a non-sister species show that this supergene was probably initiated through ancient introgression. Genotype-phenotype association helps pinpointing the few co-adapted genes within the cluster, and reveal that many other genes seem to follow by mere hitchhiking, suggesting that coadaptation here could have direct evolutionary consequences for neighbouring genes. Experiments reveal disassortative mating based on inversion genotypes, suggesting sexual selection on inversions may influence the stability of adaptive polymorphisms. Our results suggest that an initial inversion kick-started the formation of a complex genomic architecture with multiple evolutionary outcomes, and far- reaching consequences in terms of demographics, population differentiation, cladogenesis and community ecology.
19 ABSTRACTS | INVITED SPEAKERS
EVOLUTION OF ANOPHELES IN RELATION TO MALARIA
Nora J. Besansky and the Anopheles Genomes Cluster (AGC) consortium
Anophelines are the only mosquitoes capable of transmitting human malaria, but only a handful of them do so—for reasons that are poorly understood. The recently completed 16 Anopheles genomes project was undertaken to provide annotated genome assemblies and associated genetic resources as a foundation to resolve this mystery, through exploration of the molecular basis of behavioral and physiological traits that contribute to “vectorial capacity”. The project was anchored by the pre-existing reference genome assembly of Anopheles gambiae, and includes five of its close relatives in the eponymousAn. gambiae complex—sibling species that diversified recently and rapidly yet differ dramatically in vectorial efficiency. Many if not most malaria vectors belong to sibling species complexes, but none are as well studied as the An. gambiae complex, which is a case study and potential model for cryptic speciation and the nature of genomic features that limit or augment vectorial capacity. Outside of this species complex, twelve additional species were sampled at increasing evolutionary distances across the three most speciose subgenera of Anopheles and an estimated 100 MY divergence time. Ongoing comparative genomic analysis of these mosquitoes by the scientific community has focused on biological themes of particular relevance to their roles as human disease vectors, including reproduction and sex biased gene expression, immunity, chemosensation, insecticide resistance, molecular and chromosomal evolution, and species complex evolution. Insights emerging from these investigations include the observation of an overall higher rate of gene gain and loss in Anopheles relative to Drosophila, notably with respect to gene families critical to survival under potentially stressful environmental conditions, such as cuticle protein genes and immunity genes. Additionally, using new approaches that distinguish shared ancestral polymorphism from genetic introgression, we find evidence of massive autosomal introgression between the two most important malaria vectors in the An. gambiae complex, An. gambiae and An. arabiensis, despite the fact that they are not each other’s closest relatives, suggesting that ongoing genetic exchange between different malaria vectors may be an important means of rapid evolution.
20 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
EXPLORING THE MOSQUITO GUT MICROBIOME FOR MALARIA AND DENGUE TRANSMISSION MODULATORS
Saurabh Sinha, Associate Professor, Dept. of Computer Science, University of Illinois at Urbana-Champaign
I will present how we are using the wealth of cis-regulatory information available for Drosophila to study highly diverged insects such as honey bee, mosquito, beetle and wasp. In one study, transcription factor (TF) - DNA binding motifs characterized in Drosophila were used to computationally predict regulatory targets of TFs in the honey bee and nine other bee genomes. Comparative analysis of these targets suggested regulatory elements correlated with the evolution of social behavior. In another study, experimentally validated enhancers from Drosophila were used as training data to predict novel developmental enhancers in other insects, leading to glimpses of cis-regulatory evolution at the binding site level across hundreds of million years. I will discuss the opportunities for and limitations of this general paradigm of using Drosophila data to study cis-regulation and its evolution in other insects.
EXPLORING THE MOSQUITO GUT MICROBIOME FOR MALARIA AND DENGUE TRANSMISSION MODULATORS
George Dimopoulos, PhD MBA
The microbiota of the insect gut has been shown to play a pivotal role in influencing the development and transmission of human pathogens by their mosquito vectors. Using common laboratory strains of bacteria, and less-characterized bacteria isolated from wild mosquito populations, we have shown that the composition of the mosquito midgut microbiota can determine the vector’s competence for dengue viruses and Plasmodium parasites through direct antagonistic and agonistic activities mediated by microbe-produced factors, and by the stimulation of the mosquito’s innate immune system. We are characterizing these interactions, thereby providing critical information for developing novel vector-borne disease control strategies that rely on the natural field mosquito microbiome.
21 ABSTRACTS | INVITED SPEAKERS
GENOMICS OF GUT MICROBIAL COMMUNITIES IN HONEY BEES AND BUMBLE BEES
Nancy A. Moran (University of Texas at Austin), Philipp Engel (University of Lausanne), Waldan Kwong (Yale University and University of Texas at Austin), Eli Powell (University of Texas at Austin)
A central role of microbial partners, particularly gut bacteria, in animal ecology and evolution is increasingly evident. Honey bees and bumble bees have characteristic bacterial species in their guts most of which are absent from most other bees or other insects. Unlike gut communities in many insects, these communities are composed of specialists, not found in other environments. In honey bees, gut communities are dominated by 6 to 8 bacterial species, each consisting of numerous strains that differ in gene repertoires. Three of these species are Gram negative bacteria that have recently been described as Gilliamella apicola, Snodgrassella alvi, and Frischella perrera; these dominate in the ileum region of the hindgut. Experiments show that these bacteria are transmitted through social interactions, and that each honey bee worker is fully colonized before leaving the hive for the first time. Related bacteria occur in bumble bees, in which they have been shown to confer protection against trypanosome parasites. Another similarity to the human gut microbiota is the existence of extensive strain diversity within particular species in the community: analyses both from metagenomic sequencing and from single cell genomics indicate that a single honey bee colony can harbor numerous divergent strains within S. alvi and within G. apicola. One gene category for which gene sets differ extensively is that associated with sugar and carbohydrate metabolism by G. apicola. Since honey bees encounter a wide variety of plant-produced carbohydrates, these differences among symbiont capabilities may impact the host nutrition and ability to use or detoxify different dietary components. Genomic analyses and experimental assays indicate that a subset of strains of G. apicola is able to digest pectin, suggesting a possible role in pollen wall digestion. Newly emerged adult bees lack the microbiota and can be inoculated experimentally with known strains, enabling further experiments on their effects on host biology and potentially enabling the development of probiotics for honey bees. The full extent of favorable or harmful effects of these bacteria is not yet known.
22 ABSTRACTS | ORAL PRESENTATIONS
THE GLANVILLE FRITILLARY BUTTERFLY HAS RETAINED THE ANCESTRAL LEPIDOPTERAN KARYOTYPE FOR 140 MY
Toby Fountain, University of Helsinki, The Melitaea cinxia consortium
The most common chromosome numbers in Lepidoptera are n=29-31, and the putative ancestral chromosome number has been conjectured to be 31, but until recently this has been difficult to confirm due to lack of comprehensive phylogenies. The Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae) is the first butterfly species for which the genome and high- density linkage map are available, and which has the putative ancestral lepidopteran karyotype n = 31. The genome of the Glanville fritillary (393Mb) consists of 1,453 superscaffolds (N50=331 kb) covering 72% of the genome and which have been assigned to the linkage map, and 4,846 other scaffolds without consistent linkage information.
Phylogenetic analyses of Nymphalidae (312 species) and of other Lepidoptera, together with ortholog-level comparisons of chromosomes, suggest that the ancestral lepidopteran karyotype has been retained for at least 140 My. We show that chromosomal fusions in Lepidoptera are not random events, but rather favor chromosomes with higher evolutionary rate and higher transposable element content. Furthermore, the same, shortest ancestral chromosomes have participated in fusion events in species with smaller karyotypes, such as the silk moth. The exceptionally high stability of chromosomal content and constrained fusions in Lepidoptera offer practical advantages for genomic research and highlight distinctive features of the evolutionary dynamics of butterfly and moth genomes.
24 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
LONG NON-CODING RNA IN THE PEA APHID; IDENTIFICATION AND COMPARATIVE EXPRESSION IN SEXUAL AND ASEXUAL EMBRYOS Legeai F 1, Derrien T 2, Wucher V 1, David A 1, Le Trionnaire G 1 and Tagu D 1
1. IGEPP INRA 2. IGDR CNRS
Long non coding RNA (lncRNA) have been shown to be involved in multiple mechanisms in particular in epigenetic regulation such as control of DNA methylation patterns or chromatin remodeling. Aphids have the ability to produce extremely divergent phenotypes in response to environmental stimuli. Reproductive modes are condition-dependent in aphids since they are able to switch from asexual to sexual reproduction in response to autumnal photoperiod shortening. This means that aphids produce embryos developing into either sexual adults or asexual parthenogenetic females. Our group already deciphered the transcriptomic and post- transcriptomic regulations associated with this process and as a general understanding of epigenetic regulatory mechanisms potentially mediating phenotypic plasticity, we investigated the role of lncRNA in sexual and asexual embryos of the pea aphid. We established a new bioinformatics pipeline for the detection of lncRNAs from RNA-Seq data, and produced the first pan-genomics catalogue of aphids lncRNAs. Among 2,172 identified lncRNAs, 24 are differentially expressed between sexual and asexual embryos at different stages. Furthermore, we asserted for each lncRNA a classification of putative cis-interactions based on its genomic distance to neighboring mRNAs. Besides the identification of microRNAs and their putative targets, these results allow the constitution of a broad gene regulation network of the aphid phenotypic plasticity at the embryo level.
This workflow is available in Galaxy on the BioInformatics Platform for Arthopods of Agroecosystems (www.inra.fr/bipaa) and can be applied to any organism for which an annotated genome sequence and RNA-Seq data are provided.
25 ABSTRACTS | ORAL PRESENTATIONS
ODORANT AND GUSTATORY RECEPTORS IN THE TSETSE FLY GLOSSINA MORSITANS MORSITANS George F. O. Obiero, Paul O. Mireji, Steven R. G. Nyanjom, Alan Christoffels, Hugh M. Robertson, Daniel K. Masiga
Glossina morsitans morsitans genome ORs and GRs were annotated using homologs of these genes in Drosophila melanogaster and an ab initio approach based on OR and GR specific motifs in G. m. morsitans gene models coupled to gene ontology (GO). Phylogenetic relationships among the ORs or GRs and the homologs were determined using Maximum Likelihood estimates. Relative expression levels among the G. m. morsitans ORs or GRs were established using RNA-seq data derived from adult female fly. Overall, 46 and 14 putativeG. m. morsitans ORs and GRs respectively were recovered. These were reduced by 12 and 59 ORs and GRs respectively compared to D. melanogaster. Six of the ORs were homologous to a single D. melanogaster OR (DmOr67d) associated with mating deterrence in females. Sweet taste GRs, present in all the other Diptera, were not recovered in G. m. morsitans. The GRs associated with detection of CO2 were conserved in G. m. morsitans relative to D. melanogaster. RNA-sequence data analysis revealed expression of GmmOR15 locus represented over 90% of expression profiles for the ORs. TheG. m. morsitans ORs or GRs were phylogenetically closer to those in D. melanogaster than to other insects also assessed. We found the chemoreceptor repertoire in G. m. morsitans smaller than other Diptera, and we postulate that this may be related to the restricted diet of blood-meal for both sexes of tsetse flies. However, the clade of some specific receptors has been expanded, indicative of their potential importance in chemoreception in the tsetse.
26 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
DOPAMINE RECEPTORS AS TARGETS IN A “GENOME-TO-LEAD” INSECTICIDE DISCOVERY PIPELINE
Nuss A.B., Ejendal K.F. K., Meyer J.M., Conley J.M., Doyle T.B., Lang E.G., Watts V.J., Hill C.A.
Resistance to commercial insecticides among arthropod vectors of infectious disease necessitates the development of new mode-of-action chemistries for vector control. Biogenic amine-binding G protein-coupled receptors (GPCRs) are promising targets for insecticide discovery because of their critical role in the neurological processes of arthropods. The Purdue Invertebrate Receptor Group (PIRG) was created to pursue target-based insecticide discovery around these receptors. The research group has mined multiple arthropod vector genomes to identify candidate GPCR targets. In proof of concept studies, D1-like dopamine receptors (DARs) from the Lyme disease tick, Ixodes scapularis, the yellow fever mosquito, Aedes aegypti, the malaria mosquito, Anopheles gambiae and the northern house mosquito, Culex quinquefasciatus, were expressed in reporter cell lines and pharmacological profiles in response to biogenic amines and a panel of human DAR antagonists and agonists were evaluated. The arthropod D1-like DAR, DOP2, from these four vectors exhibits pharmacological properties distinct from the human ortholog, hD1. On the basis of strong signal-to-noise ratio, the Ae. aegypti AaDOP2 and I. scapularis IsDOP2 targets were selected for high-throughput chemical library screening to identify small molecule antagonists. The most potent antagonist hits were validated via in vitro confirmation assays, and molecules with >10-fold selectivity for the invertebrate target versus the human DAR ortholog, hD1, were identified that caused significant mortality ofAe. aegytpi and C. quinquefasciatus larvae and Ae. aegypti adults in vivo. Our results demonstrate the utility of the PIRG strategy for identification of novel, vector-specific insecticidal leads that are broadly effective against key vector species.
POSSIBLE INVOLVEMENT OF MICRORNA EDITING IN HONEY BEE DIVISION OF LABOUR
Eirik Søvik, Guy Bloch, and Yehuda Ben-Shahar
MicroRNAs are evolutionary-conserved short non-coding RNAs that regulate mRNA stability and translation. We, and others, have shown that the expression of specific microRNAs differs between honey bees performing foraging and brood care activities. Our new preliminary data indicate that in addition to the variation in expression levels, some miRNAs are also edited post- transcriptionally. Editing of microRNAs has been reported for other species, but its physiological functions are not understood. It has been suggested that RNA editing increases microRNA diversity with potentially altered targets. We found several microRNAs that are differentially edited between nurses and foragers collected from colonies in the field. Our findings suggest that both qualitative and quantitative aspects of the miRNAome are associated with the social regulation of behavior in honey bees.
27 ABSTRACTS | ORAL PRESENTATIONS
STAMPING THE ROYAL SEAL WITH DNA METHYLATION
Welch M, Edwards O, Millar H, Lister R, Baer B
Female honeybees have two distinctly separate castes that either work (workers) or reproduce (queens). Phenotypically the two castes are highly divergent and exhibit caste-specific morphological traits, yet they both originate from fertilised eggs. Queen-destined individuals are fed royal jelly and this nutritional stimulus initiates queen development. Epigenomic modifications allow phenotypically plastic shifts in response to external stimuli such as dietary cues, by tethering the genome to the environment.
Epigenome dynamics are facilitated in-part by DNA methylation, which is known to be critical for caste determination during early larval development. Our aim is to identify the initial molecular response to royal jelly in larvae that are yet to commit to their developmental fate, in order to unravel the very first and most critical genetic and epigenomic changes that underlie caste determination in honeybees.
Study Design: We collected young larvae prior to the caste determination and provided them with royal jelly to artificially initiate queen development. To determine the initial trigger(s), we placed age-matched (+/-1 hr) 1 day old larvae in either worker comb (control) or artificial queen cells with fresh royal jelly. Pooled larvae (n=6) were then collected 0, 2, 4, 6 and 8 hrs after placement and for a total of 4 biological replicates. Each of these replicates were used to make independent transcriptome and methylome libraries and sequenced on an Illumina Hiseq 2000. Results about the initial molecular responses to royal jelly feeding will be presented and discussed in a broader context of caste determination in social insects.
28 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
FINE SCALE MAPPING OF QTL ASSOCIATED WITH REPRODUCTIVE DIAPAUSE WITHIN THE CULEX PIPIENS COMPLEX USING A RADTAG GENOMIC APPROACH Roberta Engel & David W. Severson, Dept. of Biological Sciences & Eck Institute for Global Health, Univ. of Notre Dame
Culex pipiens is a broadly distributed species complex that transmits human diseases (e.g., West Nile Virus, Lymphatic Filariasis). Cx. p. pipiens, one member of the complex, is found across temperate zones of the world while Cx. p. quinquefasciatus is restricted to subtropical and tropical regions. One physiological trait that distinguishes Cx. p. pipiens from its sister taxon is its ability to enter reproductive diapause. Photoperiod is the primary trigger of this complex life history trait. Previous work using markers developed with traditional methods inferred four quantitative trait loci (QTL) in an F2 mapping population. The ability to generate informative Single Nucleotide Polymorphic markers (SNPs) and infer QTL has increased dramatically with the advent of massively parallel sequence technology (e.g., Illumina HiSeq2000). In addition, a published reference genome for Cx. p. quinquefasciatus is available. An advanced intercross line (Cx. p. quinquefasciatus Johannesburg x Cx. p. pipiens South Bend) was established.
First instar larvae collected from the F6 generation were exposed to diapause inducing conditions (i.e., 8:16 light:dark cycle and 18°C). Follicle size in ten-day old adult females was used to score phenotype. Only the extreme phenotypes were sampled to construct a reduced representation paired-end library. Using a RADtag approach, each of the 100 samples had a unique identifier. SNPs were generated in silico; a filtered subset of 2000 SNPs was used to infer linkage groups. Linkage groups with at least 15 markers were assigned to chromosomes. Marker density on the linkage map is an order of magnitude greater than on the map used in an earlier study. Presently we are mapping QTL regions on a fine scale. This has positioned us to advance our understanding of what genes and genetic pathways regulate reproductive diapause.
29 ABSTRACTS | ORAL PRESENTATIONS
USING HIGH-THROUGHPUT QUANTITATIVE GENOMICS TO IDENTIFY HYBRID INCOMPATIBILITIES BETWEEN TWO MALARIA VECTORS Raissa G. Green, David Turissini, Stephanie G. Truong, Bradley J. White
Despite the central importance of the Dobzhasnky-Muller model to diversification, identification of genes causing hybrid dysfunction has been primarily limited to model species. Anopheles gambiae, the principal vector of malaria in Africa, belongs to a complex of about nine isomorphic species.
In accordance with Haldane’s rule, reciprocal crosses between An. gambiae and its sister species Anopheles merus produces sterile males, but fertile females. When we backcrossed F1 hybrid females to their maternal parental males, the resulting male progeny displayed a range of phenotypes from completely sterile to completely fertile. This phenotypic range provides us with the foundation for quantitative trait locus (QTL) mapping. We performed reciprocal backcrosses, phenotyped ~2500 males from those backcrosses, and genotyped each male using a total of ~12,000 markers across the genome using a reduced representation sequencing approach. Our uniquely large quantitative genomics data set, when combined with testes-specific expression analysis, has allowed us to identify a small number of hybrid-sterility candidate genes. Identification and characterization of these candidate genes will not only provide insights into how postzygotic reproductive isolation barriers evolve, but they could also be important in the development of advanced sterile-insect control strategies aimed at reducing the role of the Anopheles gambiae complex in the African malaria transmission cycle.
30 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
THE GENOMIC BASIS OF ECOLOGICAL ADAPTATION IN A DROSOPHILA AGRICULTURAL PEST
Sukanya Ramasamy, Santosh Revadi, Kaur Rupinder, Teun Dekker, Gianfranco Anfora, Omar Rota Stabelli
Drosophila suzukii is one of the few fruit flies capable of laying eggs and feed on fresh fruit. Its recent outbreak in western countries from Asia, and its peculiar ecological behaviour makes it an emerging model in pest management and evolutionary biology. To understand the molecular basis behind the switch from fermenting to fresh fruit reproductive habit, we mined D. suzukii genome(s) and performed thorough comparative studies of its repertoire of chemosensory genes against genomes of 21 other Drosophila.
Although odorant and gustatory receptors in D. suzukii follows a typical birth-and-death model of evolution, there are local significant expansion and contractions in receptors associated with fruit detection and oviposition choice. Odorant receptors that are responsible for fresh fruit detection and oviposition site choice in D. melanogaster experience duplication in D. suzukii, and even show significant signals of adaptation. On the other hand genes involved in detecting fermentation in D. melanogaster are either pseudogenes or experienced neofucntionalisation. Notably, these genes are extremely different in the genomes of European and American populations, suggesting that ancient adaptive losses of function have been followed by separation of population in Asia. These results are being validated by targeted PCR in different populations, and are finding pleasing reciprocal confirmations with chemical ecological and neurobiological experiments.
Our comparative analyses reveal key genomic adaptations responsible for the building of a new ecological behavior, and unveil key genes which may become target of field chemical control strategies.
31 ABSTRACTS | ORAL PRESENTATIONS
COMPARATIVE GENOMICS OF INSECT IMMUNITY, FROM WHOLE GENOMES TO INDIVIDUAL RESEQUENCING
William J Palmer, Joseph Harvey, Punita Juneja, Ho Y Shwen, Arnab Pain, Francis M Jiggins
The insect innate immune system is highly complex and capable of responding to viral, prokaryotic, and eukaryotic pathogens. A clear understanding of its function and evolution are key to tackling arthropod vectored diseases, agricultural pests, and deepening our knowledge of evolution in the mammalian immune system. Many individual proteins, pathways and molecules that contribute to the immune response have been functionally and genetically characterised in the model fruit flyDrosophila melanogaster. Recent annotation of other whole genomes has greatly extended this work. However it remains largely unclear to what extent individual genes and their evolutionary patterns are conserved beyond higher insects, and what (if any) are the general rules of immune system evolution. The recent assembly of many near complete arthropod genomes provides an unprecedented opportunity to address these questions in a deeper evolutionary context.
Firstly, using multiple whole genome sequences from distant arthropod groups spanning insects, crustaceans, myriapods, and chelicerates, we time key innovations in the insect innate immune gene repertoire. Secondly, using whole genome and exome captured resequencing data from wild populations of mosquitoes and butterflies, we reveal the pattern and process of immune evolution in these groups, which, taken with previous studies, suggest signatures of selection common to all arthropods.
32 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
DYNAMIC RECRUITMENT OF AMINO ACID TRANSPORTERS TO THE INSECT-SYMBIONT INTERFACE Duncan RP, Husnik F, Van Leuven JT, Gilbert DG, Davalos LM, McCutcheon JP, Wilson ACC
Symbiosis is well known to influence bacterial symbiont genome evolution, and has recently been shown to shape eukaryotic host genomes. Intriguing patterns of host genome evolution, including remarkable numbers of gene duplications, have been observed in the pea aphid, a sap-feeding insect that relies on a bacterial endosymbiont for amino acid provisioning.
Previously, we proposed that gene duplication has been important for the evolution of symbiosis based on aphid-specific gene duplication in amino acid transporters (AATs), with some paralogs highly expressed in the cells housing symbionts (bacteriocytes). Here, we use a comparative approach to test the role of gene duplication in enabling recruitment of AATs to bacteriocytes. Using genomic and transcriptomic data, we annotate AATs from sap-feeding and non sap- feeding insects and find that, like aphids, AAT gene families have undergone independent large- scale gene duplications in three out of four additional sap-feeding insects. RNA-seq differential expression data indicate that, like aphids, the sap-feeding citrus mealybug possesses several lineage-specific bacteriocyte-enriched paralogs. Further, differential expression data combined with quantitative PCR support independent evolution of bacteriocyte enrichment in sap-feeding insect AATs. Although these data indicate that gene duplication is not necessary to initiate host/ symbiont amino acid exchange, they support a role for gene duplication in enabling AATs to mediate novel host/symbiont interactions broadly in the sap-feeding suborder Sternorrhyncha. In combination with recent studies on other symbiotic systems, gene duplication is emerging as a general pattern in host genome evolution.
33 ABSTRACTS | ORAL PRESENTATIONS
CHARACTERIZATION AND DISRUPTION OF DERMACENTOR ANDERSONI BACTERIAL MICROBIOME Cory A. Gall 1, Glen A. Scoles 2 and Kelly A. Brayton 1
1. Department of Veterinary Microbiology and Pathology 2. USDA-ARS, Animal Disease Research Unit, Washington State University, Pullman, Washington 99163
Ticks are obligate hematophagous ecoparasitic arthropods that feed on terrestrial vertebrates and are of medical-veterinary importance due to their ability to inflict harm to humans and animals. The Rocky Mountain wood tick, Dermacentor andersoni, is the principal vector of bovine anaplasmosis, caused by Anaplasma marginale, which is the most widespread tick- borne pathogen of livestock worldwide. Although ticks are host to pathogenic bacteria, they harbor several non-pathogenic species. These endosymbionts have been shown to have a role in physiology, survival, and pathogen acquisition. The goal of this study is to characterize the bacterial microbiome and then to examine the impact disruption of this microbiome has on pathogen acquisition.
We have characterized the bacterial microbiome of two populations of D. andersoni ticks with differing vector competence for A. marginale: Burns, Oregon had a high rate (60%) and Lake Como, Montana a low rate (20%). We used Pacific Bioscience SMRT sequencing platform to amplify 16S rRNA in order to examine the microbiome. After bacterial characterization, we exposed ticks from both locations to antibiotics to disrupt the bacterial microbiome. The role that the bacterial microbiome plays in pathogen acquisition was then analyzed in several pathogen competence experiments.
We have characterized the bacterial microbiomes of Burns and Lake Como D. andersoni ticks. Our study has shown that the bacterial composition is both location-specific as well as tissue- specific. Additionally, the disruption of the microbiome has shown to influence the ability ofD. andersoni to acquire pathogens.
34 ABSTRACTS | i5k
1. KEY RESPONSE TRANSCRIPTS OF THE INVASIVE BROWN MARMORATED STINK BUG, HALYOMORPHA HALYS (STÅL) (HETEROPTERA: PENTATOMIDAE) Michael E. Sparks, Kent S. Shelby, Daniel Kuhar, and Dawn E. Gundersen-Rindal (USDA-ARS- IIBBL, Beltsville, MD)
The Brown marmorated stink bug (BMSB), Halyomorpha halys (Stål) (Heteroptera: Pentatomidae), is an invasive agricultural and nuisance pest rapidly and aggressively expanding its geographic incidence in North America. This voracious pest poses significant threats to both rural and urban agriculture, especially to specialty crops such as apples, grapes and ornamental plants, as well as to staple crops including soybean and corn. The main objective of this study was to generate the BMSB transcriptomic sequence data necessary to annotate the BMSB genome currently in queue for the i5k. RNA-seq libraries derived from BMSB insects representing developmental stages and sexes were sequenced on an Illumina HiSeq 1000. We assembled 439,615,225 quality RNA-Seq reads using the Trinity RNA-Seq assembler into a total of 248,569 putatively unique transcripts (PUTs). PUTs were segmented into three disjoint tiers of varying reliability, with 4,794 classified as gold tier, 16,878 as silver, and 14,357 as bronze. The gold-tier PUTs were associated with 2,580 distinct non-redundant protein sequences obtained from the NCBI NR database; 1,785 of these NR proteins (69%) could be mapped to annotated proteins in the Swiss-Prot subset of the UniProtKB database, from which 1,273 unique Pfam families and 459 unique GO terms from the Molecular Function aspect were encountered. Of the silver tierís 6,527 unique GI numbers, 4,193 mapped to UniProtKB entries (64%), from which 1,941 and 640 unique Pfam and Molecular Function-specific GO terms were extracted. PUTs similar to hypothetical proteins of Nosema ceranae, a honeybee parasite, were more abundantly expressed in adults versus nymphs. Collectively these resources for BMSB can be utilized to develop novel control methodologies to disrupt insect-specific life processes, such as defense against entomopathogenic biopesticides, endocrinology, cuticle formation, reproduction, alleleochemical detoxification, and insecticide resistance management.
36 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
2. ANNOTATING THE GENOME OF VARROA DESTRUCTOR
Darren E. Hagen 1, Colin M. Diesh 1, Deepak Unni 1, Jay D. Evans 2 and Christine G. Elsik 1,3,4
1. Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA 2. Bee Research Laboratory, USDA-Agricultural Research Service, Beltsville, MD 20705, USA 3. Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA 4. MU Informatics Institute, University of Missouri, Columbia, MO 65211, USA The ectoparasitic mite Varroa destructor is the most detrimental parasite of domestic honey bees (Apis mellifera). Widespread colony declines can be explained in part by the direct effects of this mites as well as its ability to transmit harmful RNA viruses. Characterization of genes in the Varroa genome will advance our understanding of Varroa biology and provide new avenues for mite control. With over 200 million years divergence between Varroa and the western predatory mite (Metaseiulus occidentalis), the closest relative with a sequenced genome, homology-based gene prediction will likely miss many divergent genes. Here we report progress in developing a comprehensive gene list for Varroa, leveraging paired-end RNAseq data from eight tissues/stages. Our pipeline includes de novo repeat detection and repeat masking, maximum intron size estimation, de novo gene prediction, protein homolog and transcript alignment, and providing manual annotation tools to the research community. We use a combination of reference-based, de novo and hybrid RNAseq assembly methods. The RNASeq data is also used to generate training and test sets for gene prediction, create scores for weighted gene prediction, serve as input data in a combined gene set, and generate a comprehensive transcriptome database. Genome browsers and BLAST are available at the Bee Pests and Pathogens web site (http://hymenopteragenome.org/beebase/?q=bee_pathogens). This gene set is a key component of the Varroa Genome Sequencing Consortium’s effort to develop tools for understanding and controlling this key honey bee pest.
3. GENOME SIZE DIVERSITY IN ORTHOPTERA Shawn Hanrahan, J. Spencer Johnston; Department of Entomology, Texas A&M University
Genome size diversity among Arthropods remains poorly sampled, with far less than one percent of species surveyed. To date, the genome size for these species has ranged from 98 Mbp for a midge (Chironomidae) all the way up to 18,000 Mbp for a shorthorn grasshopper (Acrididae). This variation is the equally distributed among orders. The largest genome sizes are almost exclusively found within the Orthoptera, with many acridid species surpassing 10,000 Mbp. The size of these genomes has limited complete sequencing efforts. We surveyed genome size in a number of orthopteran species and families in an effort to find exceptions. Here we report 40 genome size estimates from two orthopteran subfamilies in which genome sizes are not always large. Outliers smaller than 2,000 Mbp were found in both Ensifera and Caelifera. One example, a Tetrigidae (pygmy grasshopper) has an estimated genome size of 870 Mb.
37 ABSTRACTS | i5k
4. THE RATE AND PATTERN OF GENOME SIZE EVOLUTION IN DROSOPHILIDAE AND FORMICIDAE Carl E. Hjelmen & J. Spencer Johnston, Department of Entomology, Texas A&M University, College Station, TX
Genome size variation across species has been found to be 18,900 fold in arthropods to date. Even though much data has been accumulated about genome sizes, the ever present variation has been largely ignored from a phylogenetic standpoint. This has resulted in a lack of knowledge about how the changes in genome sizes have occurred throughout evolutionary history. Here, we address the question, Where during the phylogenetic process does genome size change? Does it change during speciation when species effective population size is small and drift drives the process? Alternatively, is it a very gradual process due to equilibrium between insertion and deletion rates? Lastly, is it different for different taxa, with each taxa evolving at its own rate in response to different environmental conditions? Fundamentally, the first two hypotheses provide the possibilities of finding phylogenetic signal in genome size, whereas the third hypothesis only has low potential for this phylogenetic signal.These hypotheses were analyzed by constructing Bayesian phylogenies of Drosophilidae and Formicidae with taxa that are represented in the genome size database. Genome size is then analyzed comparatively using BayesTraits to determine the presence of a continuous or variable rate in genome size evolution. The approach is demonstrated here with genome size data for Drosophilidae and Formicidae. As larger sets of genome size estimates become available for additional arthropod species, this approach will provide a powerful tool for comparison of genome size evolution rates and trends among an even wider range of taxa.
5. USING BNG WHOLE GENOME RESTRICTION MAPS TO COMPARE TRIBOLIUM SPECIES GENOMES
Jennifer Shelton 1, Nic Herdon 1, DJ Yuhn 1, Susan J Brown 1
1. Division of Biology, Ackert Hall, Kansas State University
Genome assemblies based on NGS technologies are often high fragmented. We are using a novel technology developed by BioNano Genomics (bionanogenomics.com) to generate whole genome restriction maps based on images of ultra long molecules of DNA. We use these maps to validate the computational genome assembly and extend scaffolds. For the red flour beetle, Tribolium castaneum, we have validated the assembly, reoriented scaffolds on chromosomes, drawn unanchored scaffolds into chromosome builds and increased scaffold length from an N50 of ~1Mb, to over 3Mb. Addtional species include Tribolium freemani and Tribolium madens.
38 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
6. HYMENOPTERA GENOME DATABASE 2014 UPDATE
Christine G. Elsik 1,2,3, Colin M. Diesh 1, Deepak Unni 1 and Darren E. Hagen 1
1. Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA 2. Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA 3. MU Informatics Institute, University of Missouri, Columbia, MO 65211, USA
The Hymenoptera Genome Database (HGD; http://HymenopteraGenome.org) is a genome informatics resource for hymenopteran insect species. HGD includes genomic data of three honey bee species (Apis mellifera, A. dorsata and A. florea), two bumble bee species (Bombus terrestris and B. impatiens), a sweat bee (Lasioglossum albipes), nine ant species (Acromyrmex echinatior, Atta cephalotes, Camponotus floridanus, Cardicondyla obscurior, Harpegnathos saltator, Linepithema humile, Pogonomyrmex barbatus, Solenopsis invicta, Wasmannia auropunctata) and a parasitoid wasp (Nasonia vitripennis). Users may access data through genome browsers (GBrowse and JBrowse), BLAST searching and data download. Datasets include genome assemblies, computed and manually-annotated genes, protein homologs, cDNA sequences, non-coding RNA sequences, RNAseq data and genetic markers. Pre-computed orthologs are linked across GBrowse sites. We have also deployed Jbrowse/WebApollo for several species. Jbrowse enables users to view annotations, RNAseq, and genome re- sequencing data. WebApollo, which is accessible to registered users, combines the Jbrowse viewer with annotation tools. An example use case for the Apis Mellifera Jbrowse/WebApollo instance is comparison of the new (OGSv3.2) and old (OGSv1.0) gene sets. When investigators, in the course of their research, come across OGSv3.2 gene predictions that appear to have been incorrectly split or merged, they may view both gene sets along with other evidence tracks to determine which gene model is correct and make corrections if necessary. We are in the process of deploying Jbrowse/WebApollo for all of the species in HGD, so that research community members can continue to improve genome annotations.
39 ABSTRACTS | i5k
7. ACCURACY AND COMPLETENESS OF AN ARTHRO-TRIPOD OF GENOMES, DEER TICK, HONEY BEE, AND WATER FLEA, FROM MRNA- ASSEMBLED AND GENOME-MODELLED GENES
Gilbert, Don, Indiana University, Biology, Bloomington, IN 47405
Gene sets of three species spanning the arthropod phylum are examined with recent mRNA assemblies and genome gene predictions. Apis mellifera, Daphnia magna, and Ixodes scapularis now have genes discovered from both approaches. Each approach has values and problems for biologically accurate knowledge of genes. mRNA assemblies can produce species-complete sets of orthologs, unique genes, and alternate transcripts from direct gene evidence, without artifacts from other sources. Such assemblies surpass genome gene models in accuracy for new species projects, but with trade-offs in detail. This is evident for transposon-fragmented genomes like Ixodes, and paralog-rich genomes of Daphnia, versus more complete mRNA-gene assemblies. For the more mature Apis genome assembly and gene set, mRNAassembly adds to accuracy of genes.
RNA-seq assembly struggles with too little or too much data for some genes, may err in discriminating alternates from high identity paralogs, and have other problems due to missing genome locations. Accurate genome assembly remains a harder problem, with modeling inaccuracies and ortholog biases adding to gene inaccuracy. Combining both approaches is best, when errors of both are addressed. Find informatics software and recent arthropod gene sets at http://arthropods.eugenes.org/EvidentialGene/Changing the dogma of genome discovery projects is warranted, to first discover genes via mRNA assembly, adding genome assembly where cost-effective. Standards of quality for mRNA assembly can be improved, with better methods information, along with better assessment of errors from both approaches, to ensure high quality gene sets.
40 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
8. GENOME SEQUENCING OF LEPTOTROMBIDIUM PALLIDUM, A MAJOR VECTOR MITE FOR SCRUB TYPHUS
Ju Hyeon Kim 1, Jong Yul Roh 2, Seungil Yoo 3, Seung-Jae Noh 3, Junhyung Park 3, E-hyun Shin 2, Mi-Yeoun Park 2 and Si Hyeock Lee 1,4
1. Department of Agricultural Biotechnology, Seoul National University, 151-921, Seoul, Korea 2. Division of Medical Entomology, National Institute of Health, 363-951, Osong, Korea 3. Deparment of Research, Codes Division, Insilicogen, Inc., Suwon, 441-813, Korea 4. Research Institute of Agriculture and Life Sciences, Seoul National University, 151-921, Seoul, Korea
Leptotrombidium pallidum is the major vector mite for Orientia tsutsugamushi, the causative agent of scrub typhus, in Asian countries, including Korea. Prior to genome sequencing, the genome size was estimated by a method based on quantitative real-time PCR (qPCR). The genome size estimated using qPCR was 191 ± 7 Mb. For sequencing, genomic DNA (gDNA) was extracted from a single female mite of inbred L. pallidum (9 generations) and used for whole genome amplification (WGA). The resulting amplified gDNA was used for the construction of paired-end and mate-pair libraries and sequenced using Illumina HiSeq2000 platform. An unamplified gDNA sample extracted from 20 female mites was also processed for library construction and used for sequencing. The k-mer analysis-based genome size was estimated to be 175 Mb, confirming that the estimates from these two independent methods were mutually complementary and within a similar range to those of other Acariform mites. More than 100 Gb sequence reads from both paired-end and mate-pair libraries of the WGA gDNA were trimmed and further processed using the CLC Asembly Cell v.4.0 for de novo contig assembly and SSPACE for scaffolding. Initial assembly generated approximately 30,067 scaffolds with the N50 value of 45,061 and total size of ~173Mb. Further assembly and gene prediction is currently in progress.
41 ABSTRACTS | i5k
9. GENOME ASSEMBLY OF THE I5K PILOT SPECIES
Shwetha C. Murali, Daniel S.T. Hughes, Jiaxin Qu, Yue Liu, Kim C. Worley, Donna Muzny, Richard A Gibbs and Stephen Richards
The i5K is an initiative to sequence the genomes of 5,000 arthropods of medical, agricultural and scientific importance. As a pilot project to identify potential problems and challenges in areas like species selection, identification and acquisition, DNA isolation, sequencing strategies and assembly, annotation and analysis, the HGSC is sequencing ~30 arthropods, selected by the i5K selection committee. We describe the sequencing plan and assembly of 28 species. Most genome sizes of the insects from the pilot are less than 3Gb and assembled using our standard pipeline: using the short-read assembler ALLPATHS-LG for the initial assembly, and further improvement using in-housetools- Atlas Link and Atlas Gap-fill. Our assembly results vary with the amount of polymorphism in the input DNA sample. For example, inbred hymenoptera gave very good assemblies (high contig N50), but multiple individuals from the gall psyllid gave a bad assembly. Although single inbred individuals are preferred, the small size of some insects limits the quantity of DNA obtained (as in the case of the Blackfly). Bigger and more polymorphic genomes pose challenges to the assembler requiring greater compute resources.
A deeper understanding of specific compute resource requirements enabled us to optimally match the demands of individual steps to different types of hardware configurations.The pilot has successfully identified and developed methods to address the challenges of scalingde novo genome sequencing and assembly from one animal at a time to projects with thousands of new species genomes.
42 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
10. PROGRESS ON INSECT GENOME SEQUENCING AT UNIVERSITY OF ILLINOIS
Kimberly Walden and Hugh Robertson, Department of Entomology, University of Illinois at Urbana-Champaign
We will update our efforts to sequence the genomes of 10 insects of particular interest to members of our department using ILLUMINA-only strategies. The species are six Hymenoptera (the alfalfa leafcutter bee Megachile rotundata, the wheat stem sawfly,Cephus cinctus, a trap-jaw ant, Odontomachus brunneus, and two parasitoid wasps Microplitis demolitor and Diachasma alloeum), two moths (the navel orange worm Amyelois transitella and the parsnip webworm Depressaria pastinacella), one fly (the apple maggot flyRhagoletis pomonella), and one beetle (the corn rootworm Diabrotica virgifera). While most of the assemblies are complete and gene modelling and analysis is underway, the last three genomes are particularly large and difficult. We are exploring the use of MOLECULO long reads from ILLUMINA to help complete these larger genomes.
43 ABSTRACTS | VECTOR BIOLOGY
11. TRANSCRIPTIONAL REGULATION OF DIAPAUSE INDUCTION IN THE FEMALE ASIAN TIGER MOSQUITO, AEDES ALBOPICTUS Xin Huang and Peter Armbruster, Department of Biology, Georgetown University
Precise induction of photoperiodic diapause, a developmental arrest in response to a token photoperiodic cue, is essential for survival of many insects through the winter. However, knowledge of the molecular mechanisms regulating diapause induction is still extremely limited. In Ae. albopictus, short day length induces the female to produce offspring in which the pharate larva enters diapause inside the chorion of the egg. We have investigated the global transcriptional profiles of adult females before and after a blood meal to elucidate transcriptional regulation of diapause induction in Ae. albopictus. Paired-end mRNA sequencing of biologically replicated libraries was performed on whole body adult females exposed to diapause or non-diapause conditions with or without a blood meal. Before blood feeding, cell proliferation was down-regulated under diapause conditions, whereas synthesis of juvenile hormone and ecdysteroids was up-regulated. These changes are interpreted to relate to preparing the female for enhanced vitellogenesis after taking a blood meal. After blood feeding, precursor metabolites, energy production and fatty acid synthesis were up-regulated under diapause conditions. These results suggest that offspring provisioning increases under diapause conditions, consistent with previous results that diapausing eggs are bigger and contain more total lipids relative to non-diapausing eggs. The circadian clock genes timeless and cryptochrome 1 were up-regulated before blood feeding under diapause conditions, suggesting a potential role for these genes in photoperiodic time measurement. This study provides candidate genes and pathways for studying diapause induction in other insects.
44 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
12. DOSAGE COMPENSATION IN THE AFRICAN MALARIA MOSQUITO, ANOPHELES GAMBIAE
Graham Rose, Elzbieta Krzywinska, Loic Revuelta, Jaroslaw Krzywinski
Dosage compensation is the fundamental process, by which gene expression from the monosomic X chromosome in males and from the two X chromosomes in females is balanced. Various molecular mechanisms have evolved in different organisms to achieve this task. In Drosophila, genes on the male X chromosome are expressed two-fold higher compared to females. To test whether the same mechanism is operating in mosquitoes, we analyzed global gene expression in Anopheles gambiae pupae using RNA-seq approach. Total RNA was isolated from pupae collected at three different time points (4, 10 and 20 h after pupation) and sequenced using the Illumina platform, generating three pairs of male and female transcriptomes. A mean 346 million high quality 101-bp-long reads obtained per sample were used in a reference- based assembly to capture the transcript landscape at an unprecedented depth. These data were complemented with testes transcriptome generated by 454 RNA-sequencing. Male to female comparisons revealed that the great majority of genes from the X chromosome are fully compensated. Moreover, X-linked (X) to autosomes (A) expression ratios between the male and female pupae were near to 1:1, with no statistical difference between the distributions of ratios between the sexes. This result, indicative of dosage compensation driven by overexpression of X-linked genes in males, was independent of normalisation methods used to calculate RNA- seq expression. Transcript levels of selected genes were validated by quantitative RT-PCR. In conclusion, our data support dosage compensation in A. gambiae males, similar to the dosage effects in Drosophila.
45 ABSTRACTS | VECTOR BIOLOGY
13. THE INFLUENCE OF THE CIRCADIAN CLOCK AND LIGHT/DARK CYCLE ON RNA EXPRESSION IN AEDES AEGYPTI
Matthew T Leming, Samuel SC Rund, Giles E Duffield, Joseph EO’Tousa
Biological rhythms regulate many behaviors and physiological processes underlying disease transmission, survivability, and fitness. The circadian clock regulation of RNA expression influences daily physiological and behavioral output. TheAedes aegypti mosquito is the major vector of both yellow fever and dengue fever, and exhibits 24 hr rhythms in biting, flight, and oviposition. To better understand the patterns of specific gene expression controlled by the daily light/dark (LD) cycle or the circadian clock in Ae. aegypti, we undertook a microarray analysis (>90% transcriptome) of adult female mosquito heads collected every 4 hr over 2 days maintained under LD or constant dark (DD) conditions. Data were subjected to cosine wave analysis (JTK_CYCLE) to determine ~24 hr rhythmicity. From this, we developed a searchable database with gene expression profiles and accompanying statistical analysis allowing examination of potential rhythmicity of the expression profile for each gene. We identified 4 classes of genes present within the transcriptome: rhythmic only under LD cycle conditions, rhythmic only under DD conditions, rhythmic under both conditions, and non-rhythmic.
Genes relating to vision, olfaction, metabolism and detoxification were examined and compared to published expression profiles inAnopheles gambie. Ae. aegypti genes involved in vision, metabolism and detoxification are under circadian control or non-rhythmic, as predicted by studies of An. gambiae. However, genes relating to olfaction demonstrate differences in expression patterns through both LD and DD conditions. These Ae. aegypti studies allow for comparisons of transcriptional regulation with different mosquito species, and show temporal modulation of sensory system and metabolic processes.
46 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
14. A PHYSICAL GENOME MAP FOR THE EUROPEAN MALARIA VECTOR ANOPHELES ATROPARVUS Gleb Artemov, Maria Sharakhova, Anastasia Naumenko, Dmitri Karagodin, Elena Baricheva, Vladimir Stegniy, Igor Sharakhov
Anopheles atroparvus is one of the dominant malaria vectors from Maculipennis group in Europe. Cytogenetic analysis based on salivary gland chromosomes have been used for taxonomic and population genetic studies of mosquitoes from this group. However, a high-resolution cytogenetic map that could be useful for physical genome mapping in An. atroparvus is still lacking. In this study we developed a high-quality photomap for the polytene chromosomes from ovarian nurse cells of An. atroparvus. Using fluorescentin situ hybridization, we localized 16 genes from 8 largest genomic supercontrigs on the polytene chromosome and anchored 48% of the genome to the cytogenetic map. Our study established chromosome arm homology between An. atroparvus and the major African malaria vector An. gambiae suggesting a whole arm translocation between autosomes of these two species. A standard photomap for ovarian nurse cell chromosomes of An. atroparvus constructed by this study is shown to be useful for routine physical mapping. This map will assist in developing a fine-scale chromosome-based genome assembly for this species and will also facilitate comparative and evolutionary genomics studies in the genus Anopheles.
47 ABSTRACTS | VECTOR BIOLOGY
15. VECTORBASE AND THE POPULATION BIOLOGY BROWSER (POPBIO)
Gloria I. Giraldo-Calderón, Daniel Lawson, Scott J. Emrich, Frank H. Collins and the members of the VectorBase Consortium
The VectorBase database is updated and expanded every two months. In 2013 we have updated the gene builds, the assemblies or both for Glossina morsitans, Aedes aegypti, Rhodnius prolixus, Anopheles stephensi and An. darlingi. We have also almost tripled the number of hosted genomes from 11 to 30. These new genomes include the two sandfliesLutzomyia longipalpis and Phlebotomus papatasi, 16 new Anopheles species, and the snail Biomphalaria glabrata, an intermediate host of Schistosoma mansoni. Based on user feedback and internal discussions, all of our tools and resources have had multiple interface and performance improvements. A new tool, the Population Biology Browser (PopBio), which we had presented initially under a beta version, was also released. This new tool is part of our ongoing efforts to integrate genomic, phenotypic (including insecticide resistance) and population data, as a strategy to integrate basic and applied research. Also under development is the new “sample picker”, this tool in the VectorBase genome browser will display the data from PopBio. The sample picker will allow users to select samples, these samples will display single-nucleotide polymorphisms (SNPs) data; come to our poster to show you how. In the past, the large number of samples in the variation database made selecting samples for display a difficult process both because the list of samples is very long, and because useful descriptions of the samples were missing. We have attempted to address these issues by providing two different sample selection pathways via the “configure this page” option: 1) Selected individuals and 2) Individual metadata. If you have any questions or were not able to visit our poster for a demo, please send us your comments to [email protected].
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16. RAD SEQUENCING OF SNPS IN THE IXODES SCAPULARIS GENOME: TOWARD AN INTEGRATED GENETIC AND PHYSICAL MAP
Monika Gulia-Nuss 1, Jyothi Thimmapuram 2, Catherine Hill 1
1. Department of Entomology, Purdue Univeristy 2. Bioinformatics core, Purdue University
Hard ticks (family Ixodidae) are the primary vectors of multiple pathogenic viruses, bacteria and protozoa. Increasing evidence suggests the existence of different populations of the Lyme disease vector tick, Ixodes scapularis, across North America with differences in host preference, vector competence, environmental tolerance and morphology, yet little is known regarding the genetic diversity of theis vector. In order to answer this question, we are utilizing Restriction- site Associated DNA sequencing (RADseq) approach to identify single nucleotide polymorphism (SNP) to evaluate genetic diversity in multiple I. scapularis populations collected from across North America.
We have constructed 66 RADseq libraries, consisting of 6 geographic locations (Indiana, Maine, Massachusetts, New Hampshire, North Carolina, and Wisconsin) and Wikel reference strain, using DNA extracted from individual female. DNA samples were digested with the restriction enzyme SbfI, each sample was subsequently given a barcode via ligation of a P1 adapter, and pooled for library construction and sequencing. Using process_radtags.pl wrapper from Stacks, reads were cleaned, clustered and de-multiplexed. Sequences with a single error were corrected and those with an average quality score below 90% (Phred score less than 10) were discarded. Reads from each sample were aligned separately to the I. scapularis reference genome assembly using the end-to-end mode with default parameters of Bowtie2 v 2.1.0. SNPs were called by using the mpileup function of Samtools and variants and per-sample genotypes were called by using max-likelihood (Bayesian) inference. Maximum read depth was set to 250. On an average, each sample had about 10 million raw reads of which about 80% of the reads were retained after demultiplexing and trimming of low quality bases. About 78% of these retained reads were mapped to the reference genome. About 71K SNPs were predicted for each sample. Efforts are underway to use this information to develop the first high density genetic map for I. scapularis.
49 ABSTRACTS | VECTOR BIOLOGY
17. DEVELOPMENT OF AN INTEGRATED CHROMOSOME, GENETIC LINKAGE, AND GENOME MAP FOR THE SOUTHERN HOUSE MOSQUITO CULEX QUINQUEFASCIATUS
Anastasia N. Naumenko, Vladimir A. Timoshevskiy, Becky S. deBruyn, David W. Severson, Igor V. Sharakhov, Maria V. Sharakhova
Culex quinquefasciatus, a southern house mosquito, is a member of geographically widespread mosquito complex species with high variation in behavioral patterns and ability to transmit diseases, including lymphatic filariasis and West Nile fever. Only 10.4 % of the 579 Mb genome is currently assigned to the chromosomes based on genetic linkage mapping. Although cytogenetic maps for the polytene chromosomes for this mosquito were developed, their utilization for the genome mapping remains difficult because of the low number of high quality spreads in chromosome preparations. We constructed idiograms for mitotic chromosomes of Cx. quinquefasciatus based on their banding patterns at early metaphase. These idiograms represent the first cytogenetic map developed for mitotic chromosomes ofCx. quinquefasciatus. Genetic contigs associated with 14 major genetic markers and 10 largest contigs were anchored to the exact positions on Cx. quinquefasciatus chromosomes using fluorescentin situ hybridization. The order of genetic markers was consistent with the previously developed genetic linkage map. Our study in progress linked chromosome and genetic linkage maps with 4.8% of the Cx. quinquefasciatus genome.
50 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
18. CUTICULAR PROTEINS IN JOHNSTON’S ORGAN OF ANOPHELES GAMBIAE
Vannini, Laura; Zhou, Yihong; Reed, Tyler; Willis, Judith H
Department of Cellular Biology, University of Georgia, Athens, GA 30602 USA
Johnston’s organ (JO) is a mechanosensory structure located in the second antennal segment that interprets vibrations of antennal flagella from the wing-beats of nearby mosquitoes. JO has an elaborate cuticular organization that connects its sensory cells to the flagella.
Anopheles gambiae assigns almost 2% (~250) of its protein coding genes to structural cuticular proteins (CPs). We wanted to identify the proteins in JO with LC-MS/MS and learn the precise roles played by four of them (CPF3, CPLCG3/4, CPR152 and CPAP3-C) using EM immunolocalization. Analysis with RT-qPCR had found only one CP (CPR152) that had predominantly male expression. In situ hybridization revealed that its mRNA was localized exclusively in JO. Over 40 CPs were detected in JO by LC-MS/MS; almost all had been identified in other structures.
Immunolabeling revealed that CPR152 was the only one of the four CPs tested that was localized in the basal plate, the structure that transduces vibration frequency. CPR152 and CPAP3-C, implicated in tracheal formation in Drosophila, were found in the caps, scolopidia lumen and network of the fine filaments that keep the scolopidia firmly anchored when the basal plate vibrates. CPF3 was localized only in caps. Only CPLCG3/4 was localized in the pedicel wall.
The data we obtained provide the first record of CPs localized in the JO. The clear association of different CPs to different functional parts of this organ underlined its complex organization as well as why An. gambiae devotes so many genes to structural CPs.
51 ABSTRACTS | VECTOR BIOLOGY
19. PROTEOMICS ANALYSIS OF CUTICULAR PROTEINS IN ANOPHELES GAMBIAE: AFFINITY FOR CHITIN AND PRESENCE IN DIFFERENT STRUCTURES
Zhou, Yihong 1; Badgett, Majors 2; Reed, Tyler 1; Vannini, Laura 1; Orlando, Ron 2; Willis, Judith H 1
1. Department of Cellular Biology, University of Georgia, Athens, GA 30602 USA 2. Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
Genes for ~250 cuticular proteins (CPs) have been identified inAnopheles gambiae. It is still unknown how these CPs interact with chitin and each other to form the cuticle, and whether different CPs are used to build specific structures. We undertook a proteomics approach (LC- MS/MS) to investigate these issues.
We used serial extraction with increasing concentrations of urea to test: 1) Whether different CPs are released as concentration rise; 2) If yes, whether different chitin-binding capabilities of identified CPs are associated with different sequences in their chitin-binding domains; 3) Whether CPs with no evidence for chitin-binding domains were more readily soluble. Our preliminary data showed that a few CPs were totally extracted from pulverized whole animals with urea solutions. Most CPs were insoluble in urea and were identified from the final body debris. We are also investigating release by calcofluor which should be more specific for chitin- protein interaction.
In situ hybridization had revealed that many CPs were associated with the cells that secrete the eye lens and transcripts for some CPs appeared to be restricted to specific structures. In order to learn if these transcripts were actually translated and secreted into these structures, we performed LC-MS/MS analysis on dissected eye lens, antennae, Johnston’s organs, legs and wings. We found that many distinct CPs or protein groups were used to build each structure. These structures had most CPs in common, but each had some unique ones. We also discovered some previously unannotated CPs.
52 ABSTRACTS | SOCIAL INSECTS
20. GENOMIC AND PHYSIOLOGICAL MECHANISMS UNDERPINNING DIAPAUSE IN BUMBLE BEE QUEENS Etya Amsalem 1, Jonathan Cnaani 2, David Galbraith 1, Peter Teal 3, Christina Grozinger 1
1. Department of Entomology, Center for Pollinator Research, Center for Chemical Ecology, The Pennsylvania State University, University Park, PA 16802 U.S.A. 2. BizBee, Ein-Yahav, 86820, Israel 3. Chemistry Research Unit, 1600-1700 SW, 23rd Drive, Gainesville, FL 32608, USA
Bumble bees provide critical commercial and wild pollination services throughout the world. However, populations of many wild bumble bee species are declining while commercial mass rearing operations are also reporting reduced survival, fertility and health. In wild populations, the majority of the losses occur during the winter-diapause, a sensitive period during life cycle associated with physiological changes in hormones, fats, metabolism and immunity. Similarly, treatment of managed bumblebees with CO2 to bypass diapause results in variable losses and there is evidence for negative effects on queen performance and survival. The underlying molecular mechanisms associated with diapause or the impacts of CO2 on queens have not been characterized.
Here we examined the behavior, physiology and genome-wide gene expression patterns of bumblebee queens as they transition through mating, diapause and colony founding, via either artificial diapause or CO2 treatment. Genes involved in core nutrient storage and metabolic pathways, including insulin signaling, play a major role in the process, similar to other non- social insects, despite differences in social organization and patterns of diapause. However, pathways that have been modified during the evolution of eusociality, such as vitellogenin and juvenile hormone, do not show a typical pattern of expression. CO2 treatment affected gene expression and was associated with higher JH levels, lower lipid mass in fat body, higher activity and mortality.
The mechanisms regulating diapause are highly conserved across different insect taxa. However, very little is known on the regulation of diapause in social insects, where diapause is assumed to be an important element in the transition from solitary to sociality. Bumblebees are excellent models for examining diapause regulation in social insects. Furthermore, understanding the regulatory processes underlying diapause and CO2 treatment can lead to recommendation to improve commercial and wild bumblebee management.
54 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
21. ACUTE AND CHRONIC EFFECTS OF TRANSPORTATION STRESS IN THE HONEY BEE, APIS MELLIFERA Anna Bennett, George Yocum, Joseph Rinehart, William Kemp, Stephen Peterson
Owing to the continued impact of colony collapse disorder (CCD) on the beekeeping industry, numerous stressors including nutrition, pests and pathogens and biocides are being investigated as potential contributors to what appears to be a multi-factorial disorder. Because honey bee hives are transported across the U.S. for pollination services in numerous crops throughout the growing season, we believe that it is important to understand how transportation may contribute as an additional stressor. Nurse bees were collected from hives prior to transportation from North Dakota then one week and three weeks after field placement in California bee yards. Hive strength was recorded as frame numbers of bees prior to and at multiple time points after shipment. Two lanes of paired-end Illumina sequencing was performed on RNA from three bees from each of three hives for each of the three time points for a total of 27 biological samples.
Transcript assembly and differential gene expression analyses were carried out using the Tuxedo Suite. Transcripts were aligned to NCBI’s NR protein database, with annotation and ontology analysis performed using BLAST2GO. Genes were differentially regulated between hives at each time point suggesting between hive variability, which was reflected in frame count number and Nosema prevalence. Genes differentially regulated between time points appear to show both acute and chronic patterns of expression. Preliminary results suggest these data have the potential to yield biomarkers for pre-shipment and transportation stress that may allow us to predict the likelihood of hive failure if exposed to transportation stress.
55 ABSTRACTS | SOCIAL INSECTS
22. JUVENILE HORMONE SIGNALING PATHWAYS AND THE SOCIAL PHYSIOLOGY OF THE BUMBLEBEE BOMBUS TERRESTRIS Hagai Shpigler 1,2, Yang Li 2, Adam J. Siegel 1, Mira Cohen 1, Zachary Y. Huang 3, Jian Ma 2, Gene E. Robinson 2, Mark Band 4, and Guy Bloch 1
1. Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel 2. Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America 3. Department of Entomology, Michigan State University, East Lansing, Michigan, United States of America 4. Roy J. Carver Biotechnology Center, University of Illinois, Urbana, Illinois
The evolution of advanced sociality in bees was apparently associated with significant modifications in juvenile hormone (JH) functions. By contrast to most insects in which JH is a gonadotropin regulating female fertility, in the highly eusocial honey bee (Apis mellifera) JH has lost its gonadotropic function in adult females and instead it regulates age-related division of labor among worker bees. This variation in JH function provides an excellent model system for understanding major evolutionary changes that are mediated by modifications in endocrine signaling pathways. We manipulated JH levels in workers of the “primitively eusocial” bumble bee Bombus terrestris by removing the sole JH producing glands, the corpora allata (CA). Allatectomized bees showed strong reduction in several behavioral, physiological, and molecular systems: egg laying, egg-cell construction, ovarian development, vitellogenin expression levels, and wax secretion. These effects were partially reversed by treating the allatectomized bees with JH-III, the natural JH homolog of bees. By combining these manipulations with RNA-seq transcriptomic analyses we identified hundreds of brain transcripts that are regulated by JH and studied the influence of JH on RNA editing. The list of differentially expressed transcripts includes krüppel homolog 1, genes associated with the insulin/ insulin-like signaling pathway, oxidation, and ribosomal functions. JH also influenced the splicing pattern of several dozen transcripts. These results reveal the molecular processes regulated in the bumblebee brain by JH as a gonadotropin. Finally, comparing our results to those from a previously published study on the influence of the JH-analog methoprene on brain gene expression in the honey bee, we found several dozen brain transcripts that are regulated by JH in the two bee species. The influence of JH had a similar direction for some of the genes, but opposite for others. Our study starts revealing the molecular substrates underlying a remarkable evolutionary modification in JH functions in bees.
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23. RECIPROCAL AND CONTEXTUALLY DEPENDENT RELATIONSHIPS BETWEEN BRAIN TRANSCRIPTOME AND BEHAVIOR IN THE HONEY BEE A.R. Hamilton (Neuroscience, UIUC) & G.E. Robinson (Neuroscience, Institute for Genomic Biology, Entomology, UIUC)
Although a great deal is known about the strong connection between neurotranscriptomic and behavioral states in the honey bee Apis mellifera, the regulatory mechanisms underlying this relationship are far less understood. Elucidating whether and how transcriptional modules associated with distinct behavioral states mediate those behaviors could lead to fundamental insights into the organization of behavior.
Results from a previous honey bee brain transcriptional regulatory network (TRN) and computational scans for cis-regulatory motifs predict that a small number of transcription factors (TFs) regulate discrete gene modules associated with one or more specific types of behavior (behavioral maturation, aggression or foraging). To determine whether these TFs and their putative targets influence behavior in a specific and causal manner, we performed RNAi knockdowns of broad and ftz-f1 in the brains of adult worker bees and examined their effects on behavioral maturation and aggression. Broad and Ftz-F1 are integral components of ecdysone and juvenile hormone signaling in insects, and Broad has been shown to regulate Ftz-F1 in prior studies of Drosophila melanogaster development. We found the same hierarchical relationship by modulating expression in the adult bee brain, and yet despite this intrinsic connection Broad and Ftz-F1 have dissociable influences on behavioral state (as predicted by the aforementioned TRN). Although broad knockdown impacted both behavioral maturation and aggression, reducing ftz-f1 expression influenced only behavioral maturation, suggesting that Broad may exert its effects on aggressive behavior through an Ftz-F1 independent mechanism.
Consistent with this modularity, predicted Broad targets were regulated only by RNAi against broad but not ftz-f1, and vice versa. Moreover, preliminary results indicate that the expression of Broad and its targets are modulated by exposure to aggression-inducing stimuli. By contrast, these stimuli do not affect Ftz-F1 or its targets, suggesting that a reciprocal and contextually dependent relationship exists between Broad and aggressive behaviors. Together, these results provide a basic framework for how distinct neurotranscriptomic states might influence, and be influenced by, behavior.
57 ABSTRACTS | POPULATION/ECOLOGICAL GENOMICS
24. GENOME-WIDE SNP DATA IN BACTROCERA DORSALIS ELUCIDATES GEOGRAPHIC SOURCES OF INTERCEPTED FLIES Scott Geib, Sheina Sim, Nicholas Manoukis, USDA-ARS-PBARC, Hilo HI
The oriental fruit fly, Bactrocera dorsalis, while not established, is a species of concern in California and the mainland United States. Each year, flies are intercepted or trapped in California as part of the Tephritid fruit fly detection and exclusion program. We used genome-wide SNPs derived from RAD-Seq analysis of populations from throughout the native and established range of the oriental fruit fly to screen flies intercepted in California from 2005-2012. From this analysis we explore the origins of the intercepted flies, as well as test hypotheses on the establishment and movement of this species in southern California.
25. GENOME SIZE EVOLUTION IN DROSOPHILA MELANOGASTER J. Spencer Johnston, Carl E. Hjelmen & Aaron M. Tarone
Genome size evolution is ubiquitous, and even after decades of research mysterious. Numerous correlations between genome size and fitness-related phenotypes have been documented, suggesting selection could play a role in genome size evolution. Unfortunately, many of the effects in those studies are confounded with factors that could provide alternative explanations. In order for selection to drive genome size evolution (either directly or indirectly), variation in genome size must occur within a species and be connected to a phenotype that impacts fitness. Genome size estimates for 211 Drosophila melanogaster sequenced inbred strains from the Drosophila Genetic Reference Panel (DGRP) reveal significant conspecific and intrapopulation variation in genome size that is skewed toward larger genomes, and varies with chromosomal inversion type. To test whether this variation is connected to a phenotype that impacts fitness, we compared several life history traits in three thermal environments for 25 DGRP lines with large and 25 DGRP lines with small genomes. Genome size accounted for up to 23% of the variation in developmental phenotypes, but the contribution of genome size to variation in life history traits was plastic and varied according to the thermal environment. Gene expression analyses suggest a role for differences in metabolism between strains with large and small genomes.
Thus, there is genetic variation in genome size within D. melanogaster that is connected to variation in both genetic and environmentally dependent life history traits. These observations indicate that selection is indeed a potential mechanism by which genome size can evolve.
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26. ECOLOGICAL GENOMICS AND PLASTICITY OF GENETIC REGULATION FOR SALTWATER TOLERANCE Hilary A. Smith, Changde Cheng, Nora J. Besansky
Evolution of osmoregulatory systems is a key factor in the transition of species between fresh- and saltwater. Here we use RNA-Seq to investigate gene expression differences between an obligate freshwater (Anopheles coluzzii) and euryhaline malaria vector (An. merus). After rearing in freshwater (FW), both young and old larval instars of each mosquito species were briefly (6 h) exposed to either saltwater (SW) or FW to test the impact of water salinity on mRNA levels.
We aimed to address three questions: What is the transcriptomic response of anophelines to water salinity? How does this response differ between An. merus and An. coluzzii? How does the response differ with age? Our results are congruent with the ability of gene induction to mediate SW tolerance, with the intolerant An. coluzzii exhibiting little difference in gene expression (<2% of the transcriptome), in contrast to greater plasticity by An. merus. In the latter, >16% of the11,025 genes assayed responded to saltwater exposure. The impact of age at exposure was less dramatic than species identity, with 567 genes significantly differentially expressed in response to water type between young and old An. merus. Besides effector genes with putative roles in ion transport, we also report differential expression by genes involved in general stress responses such as heat shock proteins, and potential cross-talk between the immune response and osmoregulation. Finally, we report on gene co-expression networks.
59 ABSTRACTS | COMPARATIVE GENOMICS
27. IDENTIFICATION OF OPEN CHROMATIN REGIONS IN MALES AND FEMALES INDIVIDUALS WITHIN THE PEA APHID G. Le Trionnaire, G. Richard, J. Jaquiery, N. Leterme-Prunier, S. Hudaverdian, F. Legeai, A. Breteaudeau, D. Tagu
In aphids, the sex of individuals is genetically determined by the number of X chromosome copies, females being XX whereas males are X0. A recent report in the team (JaquiÈry et al., 2013) surprisingly demonstrated that X chromosome global gene expression was significantly higher in males (that carry only one X chromosome) compared to females (that carry two X chromosome copies). In other organisms, global gene expression on sex chromosomes is often regulated by specific mechanisms to compensate for gene dose between sexes (e.g. X chromosome inactivation, down- or up-regulation of X-linked gene expression), so we suspect that such specific regulation mechanisms might be involved in aphids. As chromatin accessibility to transcription is globally linked to the observed expression patterns, we make the hypothesis that X-chromosome sex-specific expression patterns in the pea aphid are associated with different patterns in global chromatin accessibility and thereby epigenetic regulations. To test that, we developed the FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements) methodology to isolate open chromatin regions from males and females aphid samples. We first validated the method by quantitative-PCR on selected candidate genomic regions, e.g transcription start sites regions from highly expressed genes in both samples. We then sequenced open chromatin regions from males and females samples at a genome scale using NGS approaches with the aim of looking for differences in chromatin accessibility on the X chromosome between sexes.
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28. MULTI-SPECIES GENOMIC ANALYSIS REVEALED AN EXTREMELY HIGH RATE OF THE X CHROMOSOME EVOLUTION IN MALARIA MOSQUITOES Igor Sharakhov, Ashley Peery, Atashi Sharma, Xiaofang Jiang, Brantley Hall, Maria Sharakhova, Zhijian Tu, The AGC Consortium
To understand the pattern and mechanism of the nonuniform distribution of chromosomal inversions, we developed genome maps for Anopheles atroparvus, An. funestus and An. stephensi. Comparison of the aforementioned species with An. gambiae demonstrated highly nonuniform rates of gene order reshuffling among the chromosomes. The X chromosome had about 4 times more breaks per 100 genes than the autosomes exceeding the rates observed in Drosophila. We found a high abundance of simple tandem repeats in the X chromosome suggesting their role in genomic plasticity. The rates of autosomal evolution and distribution of common polymorphic inversions positively correlate with the densities of genes and microsatellites. Genes functioning as drivers of adaptation could be expected to occur in greater densities in chromosomal arms with higher numbers of polymorphic inversions.
While rapid generation and fixation of inversions on the X chromosome may facilitate speciation in Anopheles. To test the latter assumption, we mapped multiple satellite DNA probes with respect to bands of pericentric heterochromatin of the mitotic X chromosome in the M and S forms of An. gambiae. Satellite Ag53A hybridized next to the rDNA locus in both forms.
However, satellites AgY53B and AgY477 hybridized at the base of the proximal band in the M form but at the tip of the proximal band in the S form indicating an inversion. Our results revealed that the rapid evolution of the X chromosome is not restricted to species with the postmating reproductive isolation but could also play a role in initial diversification of malarial vectors.
61 ABSTRACTS | COMPARATIVE GENOMICS
29. INSIGHTS FROM DISCOVERY AND COMPARISON OF REGULATORY ELEMENTS IN EVOLUTIONARILY DISTANT HOLOMETABOLOUS INSECT SPECIES
Kushal Suryamohan 1,2, Majid Kazemian 3,4, Saurabh Sinha 3,5, Molly Duman Scheel 6,7 and Marc S. Halfon 1,2,8,9
1. Department of Biochemistry and 8 Department of Biological Sciences University at Buffalo- State University of New York, Buffalo, NY 14203, USA 2. NY State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY 14203, USA 3. Department of Computer Science and 5 Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA 4. Laboratory of Molecular Immunology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20824, USA 6. Department of Medical and Molecular Genetics, Indiana University School of Medicine, South Bend, IN 42602, USA 7. Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA 9. Molecular and Cellular Biology Department and Program in Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
Insects are by far the most diverse and ecologically important group of animals in the animal kingdom, with more than a million species described to date. With the completion of sequencing of most insect genomes (as part of the i5K project), comprehensive genome annotation—including regulatory regions—is imperative if we are to understand development, pathophysiology and other biological processes in these organisms. Regulatory element discovery in non-model organisms (the majority of insects) remains a major challenge as regulatory sequences rapidly diverge past the point of recognition by standard sequence alignment methods.
Here, we demonstrate methods we developed for computational cis-regulatory module (CRM) discovery in highly diverged (250-350 Mya) insect species such as Aedes aegypti, Anopheles gambiae, Tribolium castaneum, Apis mellifera, and Nasonia vitripennis using Drosophila melanogaster CRMs to guide the search for functionally related CRMs in these species. We show that we can leverage our extensive knowledge of Drosophila CRMs to enable CRM discovery in species where there is little or no functional annotation, suggesting that extensive regulatory sequence annotation will be possible in newly-sequenced species without recourse to costly and labor-intensive genome-scale experiments. We have currently validated in vivo 18 new CRMs from the aforementioned species in transgenic Drosophila. Examination of these validated CRMs indicates deep underlying homology among putatively orthologous pairs despite a complete lack of overall sequence homology. Our work provides the basic information needed to elucidate key gene regulatory networks in insects and subsequently identify the regulatory mechanisms leading to the diverse morphogenetic differences between insects.
62 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
We also show that we can successfully predict CRMs that drive expression of target genes in a specific tissue. Using these tissue-specific CRMs, we have started to elucidate changes in the regulatory mechanisms governing nervous system development in D. melanogaster compared to Ae. aegypti.
63 ABSTRACTS | MICROBIOME
30. USING ENDOSYMBIONT GENOMES TO UNDERSTAND GLOBAL SPREAD OF THE RED GUM LERP PSYLLID
Jeff Garnas (Forestry and Agricultural Biotechnology Institute [FABI], Entomology) and Bernard Slippers (FABI, Genetics)
The red gum lerp psyllid, Glycaspsis brimblecombei, native to Australia and introduced into 20 countries on four continents, was recently detected in South Africa causing considerable damage to commercial Eucalyptus plantations. Work is underway to understand patterns of global movement and spread in G. brimblecombei, part of the larger goal of examining pathways of invasion in the growing assemblage of nonnative forest pests in Africa and worldwide. Due to the large projected genome size of Glycapsis (~700mB, based on psyllid relatives) we are using a marker-based and selective sequencing approach to assess patterns of population diversity in global collections of the insect. We further ask whether genomic variation in the primary endosymbiont, Carsonella ruddii, likewise carries useful information about introduction history and spread. The genome of this obligate bacterium was sequenced recently in a related host, but genomic variability of this and other endosymbionts is not well characterized at the population level. We are currently sequencing fifteenC. ruddii genomes from bacteriocytes of selected global populations of G. brimblecombei to examine whether enhanced reconstructions of global movement can be obtained using whole symbiont genomes relative to using insect markers alone. This project will provide baseline understanding of patterns of genomic diversity and variation across native and invasive symbiont populations. Additionally, we ask whether Illumina sequencing of pooled bacteriocytes can provide sufficient coverage of insect and microbial DNA to facilitate candidate SSR marker discovery or the identification of facultative endosymbionts. Future work on comparative genomics of endosymbionts is discussed, particularly in the context of global invasion.
64 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
31. ANALYSIS OF THE GUT-SPECIFIC MICROBIOME OF FIELD- CAPTURED TSETSE FLIES, AND ITS POTENTIAL RELEVANCE TO HOST TRYPANOSOME VECTOR COMPETENCE
Bridget C Griffith, Brian LWeiss, Emre Z Aksoy, Serap Aksoy
The tsetse fly Glossina( sp.) gut is colonized by maternally transmitted and environmentally acquired bacteria. Maternally transmitted symbionts are well characterized, but little is known about the origin and function of environmentally acquired bacteria that inhabit this niche. To address this shortcoming, culture dependent and independent methods were used to characterize and quantify bacterial communities that reside within the midgut of tsetse flies collected at five geographically isolated locations in Kenya and Uganda. Bacteria were isolated from 83.33% of flies using culture dependent methods. In total, 38 strains were isolated. We used Illumina-based deep-sequencing of the V4 hypervariable region of the bacterial 16S ribosomal RNA (rRNA) gene to determine the relationship between the type and number of bacteria present in midguts of G. pallidipes individuals that were collected from distinct geographic locations and were either infected or uninfected with pathogenic African trypanosomes. Tsetseís midgut was dominated by the obligate endosymbiont Wigglesworthia, but we also observed a diversity of other microbiota in individuals that were unique to each location.
This was consistent between trypanosome infected and uninfected samples. The results of this study will increase our understanding of the breadth and depth of tsetse’s midgut bacterial communities as they relate to the environmental acquisition of the fly’s microbiota and its correlation to trypanosome vectorial capacity. Future studies can then be performed to determine the specific molecular mechanisms that underlie bacteria-mediated trypanocidal immunity in tsetse’s gut.
65 ABSTRACTS | MICROBIOME
32. THE EVOLUTIONARY POTENTIAL OF DIVERSE SPIROPLASMA STRAINS IN DROSOPHILA NEOTESTACEA
Tammy Haselkorn, John Jaenike
Spiroplasma are the second most common type of heritable bacterial endosymbiont, behind Wolbachia and they can function either as reproductive parasites or as strong mutualists. Seventeen species of Drosophila are infected with diverse Spiroplasma strains whose characterized effects, so far, include male-killing, resistance to wasp parasitism, and tolerance to nematode parasitism. For many strains, their effects are unknown. We infected five Spiroplasma strains from three divergent phylogenetic clades into D. neotestacea, host to its own native Spiroplasma, to test the ability of these different strains of Spiroplasma to establish and infection and spread in a non-native, phylogenetically distant host. In doing this we also sought to unravel whether the Spiroplasma phenotype was determined by the host species or Spiroplasma strain, as well as shed light on other phenotypic effects of Spiroplasma in Drosophila and the mechanisms underlying these effects.
Generally, the effects of Spiroplasma in Drosophila are due to the bacterial strain. Artificial infections could be established with varying levels of success, and in cases where a phenotypic effect is known, such as male-killing and wasp protection, that phenotypic effect could be transferred to D. neotestacea. No other strain of Spiroplasma, however, could restore fertility to nematode-parasitized flies, suggesting that this phenotypic effect is strain-specific. Furthermore, the nematode protective strain could also provide protection against a parasitic wasp, providing more evidence for the possibility that Spiroplasma strains could have multiple effects that allow them to persist in Drosophila populations.
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33. THE EVOLUTIONARY PSYLLID MICROBIOME AS A POOL FOR HGT BETWEEN INSECT SYMBIONTS AND PLANT PATHOGENS
Eva Novakova and Vaclav Hypöa
Horizontal gene transfer (HGT) is considered the main driver of bacterial evolution and adaptation to diverse environments. In the domain of Bacteria, HGTs have in most cases been discussed for the groups with similar ecology, e.g. pathogenic or symbiotic bacteria, mainly those with large and dynamic genomes. Recently, Nakabachi and colleagues highlighted a possible evolutionary importance of HGT between two distinct ecological types ofbacteria: plant pathogen, Liberibacter asiaticus (Alphaproteobacteria), and an obligate symbiont of its insect vector, Profftella armatura (Betaproteobacteria) possessing an extremely reduced and conservative genome.
Here, we investigate all available Liberibacter genomes and report number of gene clusters horizontally transferred from facultative symbionts of the Liberibacter psyllid vectors, e.g. Sodalis, Arsenophonus or related bacteria. The extent of the HGT in some Liberibacter species is substantial and includes core gene clusters expanding metabolic and transfer capacity of the bacteria with e.g. tryptophan biosynthesis or iron acquisition through ABC transporters. Our results point out the importance of psyllid host microbiome as a functional pool for HGT.
67 ABSTRACTS | MICROBIOME
34. EXPRESSION PROFILES OF ASTAKINE GENES IN LYGUS LINEOLARIS (PALISOT DE BEAUVOIS) EXPOSED TO FUNGAL SPORES OF BEAVERIA BASSIANA
Omaththage P. Perera, Gordon L. Snodgrass, and Kent S. Shelby
Astakines are cytokines originally isolated from crustaceans which mediate the circadian regulation of hematopoiesis. Lygus lineolaris, the tarnished plant bug (Heteroptera: Miridae), is a piercing sucking polyphagous mirid pest found throughout North America. In this study we demonstrate the genomic and transcriptomic cloning of two astakines from the L. lineolaris transcriptome, LlAst-1 and LlAst-2. To confirm the validity of the assembled transcripts, each putative astakine was cloned from L. lineolaris tissues and sequenced. The 342 bp LlAst-1 sequence encoded a predicted 113 aa peptide sequence homologous to astakine variant-1 of Penaeus monodon containing a 108 residue prokineticin-like domain. A second 399 bp LlAst-2 sequence encoded an 132 aa peptide homologous to astakine variant-2 of P. monodon with a prokineticin-like domain. The predicted molecular weight was 14266.4 D while a pI of 4.23 was predicted from the aa sequence. Alignment of LlAst-1 andLlAst-2 with other homologs from the Arthropoda revealed the characteristic prokineticin domain pattern of ten conserved Cys residues. Real-time PCR measurements demonstrated expression of both astakines in legs, antenna, heads, fat bodies and guts of adult males and females. LlAst-1 was expressed most strongly in the fat bodies of females, while LlAst-2 expression was highest in the fat bodies of both males and females. Inoculation with a fatal dose of the entomopathogenic spores of Beauveria bassiana significantly elevated LlAst-1 expression 24 and 48 hours post inoculation in both males and females. In contrast, the expression of LlAst-2 was significantly downregulated by B. bassiana inoculation in males and females.
68 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
35. MICROBIOME OF THE DISEASE VECTOR IXODES SCAPULARIS ACROSS LIFE STAGES AND INFECTION WITH HUMAN PATHOGENS
Christine P. Zolnik, Robert. J. Prill, Richard C. Falco, Thomas J. Daniels, and Sergios-Orestis Kolokotronis
Research on the human microbiome suggests that the microbial community of a species may play important regulatory roles or impact susceptibility to infection. Higher microbial diversity may also promote stability of the microbial community and decrease a species’ susceptibility to large environmental disturbances. However, lack of microbial species identification and community profiling in most organisms prevents an understanding of microbial community composition, diversity, relationship dynamics, and functional roles.
This study explores the microbiome of the blacklegged tick (Ixodes scapularis), the most important arthropod disease vector in the United States. We determined the diversity of bacterial taxa within blacklegged ticks across all three life stages and determined whether specific microbes were associated with infectious agents that cause Lyme disease, anaplasmosis, and babesiosis in humans. Blacklegged ticks were collected in southern New York State, where this species is prevalent, during each life stage’s respective activity periods in 2013. Additionally, newly hatched larvae, reared in the laboratory, were collected to determine baseline microbial community structure. Nymphs and female adults were tested for each of three human disease agents: Borrelia burgdorferi, Anaplasma phagocytophilum, and Babesia microti. DNA from infected and uninfected ticks and each developmental stage was amplified for the prokaryotic 16S rRNA gene, and amplicon sequencing was carried out using 2x300bp paired- end reads on an Illumina MiSeq. Our results on internal bacterial diversity and associations across tick developmental stages and infection status provide a seminal baseline for future directions that will identify and assess complex ecological and functional interactions between microbes and this disease vector.
69 ABSTRACTS | OTHER
36. THE CHEMOSENSORY TRANSCRIPTOME OF THE COTTON LEAFWORM SPODOPTERA LITTORALIS
Emmanuelle Jacquin-Joly 1, Erwan Poivet 1, Aurore Gallot 1,2, Fabrice Legeai 2, Nicolas Montagnè 3
1. INRA, UMR iEES-Paris, Institute of Ecology and Environmental Sciences, Versailles, France 2. IRISA, BIPAA Platform, Campus universitaire de Beaulieu, Rennes, France 3. UPMC Universitè Paris 6, UMR iEES-Paris, Institute of Ecology and Environmental Science, Paris, France
The sense of smell is determinant for vital insect behaviours, including mate and food seeking, oviposition and predator avoidance. To decipher the underlying mechanisms in the cotton leafworm, Spodoptera littoralis, we sequenced its chemosensory transcriptome. Among the ~ 77000 annotated expressed contigs, we described a large repertoire of candidate odorant- binding and chemosensory proteins, ionotropic receptors and olfactory receptors. Comparison between adults and larvae revealed different but somewhat overlapping expression of the chemosensory genes in the different developmental stages.
The transcriptome was also used to investigate the transcriptional changes induced by 24h starvation in the chemosensory tissues of S. littoralis caterpillars, using RNAseq expression profiling. Among the up- and down-regulated transcripts upon starvation, we identified genes potentially involved in olfaction. These approaches establish the use of transcriptomic sequencing for the identification of divergent chemosensory receptors in a species for which no genomic data are available, and for investigating olfactory plasticity via digital gene-expression profiling.
70 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
37. HEMOLYMPH SERINE PROTEASES AND PROTEASE INHIBITORS IN THE GENOME OF MANDUCA SEXTA
Michael R. Kanost, Department of Biochemistry and Molecular Biophysics, Kansas State University, Xiaolong Cao, Department of Entomology and Plant Pathology, Oklahoma State University
Manduca sexta is a useful species for studies on insect innate immunity, because its large size permits sufficient samples for thorough biochemical analysis of plasma proteins and hemocytes. Now its genome sequence is available for identifying a full spectrum of immune- related proteins. Serine protease cascade pathways stimulate activation of immune responses, including melanization and synthesis of antimicrobial peptides. Biochemical studies have led to understanding of some protease cascades and their regulation by protease inhibitors in the hemolymph. However, current knowledge of function is available for only a small subset of the proteases and inhibitors in M. sexta hemolymph. Analysis of the M. sexta genome revealed genes for 35 clip domain serine proteases and 7 clip domain serine protease homologs (SPH) (catalytically inactive proteins that can modulate function of proteases). Currently the functions of 6 clip domain proteases and 2 SPHs are known in M. sexta, in activation of phenoloxidase and the Toll ligand spaetzle. The genome contains 6 modular serine proteases, containing multiple putative regulatory/interaction domains (but no clip domain). Only one of these modular proteases, HP14, has a known function, initiation of the prophenoloxidase activation pathway. Hemolymph serine proteases are regulated by protein inhibitors, including members of the serpin and Kunitz superfamilies. The genome contains 32 serpin genes and 13 genes encoding small secreted proteins composed of one or two Kunitz domains. Analysis of expression patterns of the proteases and inhibitors will provide clues for hypotheses regarding their functions, and availability of the sequences will facilitate functional studies of the complete protease systems in M. sexta hemolymph.
71 ABSTRACTS | OTHER
38. INTEGRATING THE RESOURCES OF A LIVING COLLECTION WITH ADVANCEMENTS IN GENOME BIOLOGY AT THE DROSOPHILA SPECIES STOCK CENTER
Maxi Polihronakis Richmond and Therese A. Markow
The Drosophila Species Stock Center at UC San Diego is a critical resource for researchers integrating comparative genomics with studies of morphological evolution, behavior, ecological specialization, adaptation, reproductive isolation, cytogenetics, human diseases, and genome evolution. As part of its mission to maintain and distribute living cultures of Drosophila species, the Drosophila Species Stock Center has the source cultures of 23 Drosophila species with publicly available genome sequences.
These cultures include 11 of the 12 species from the original 12 Genomes Consortium, as well as eight species sequenced for the modENCODE Project. The phylogenetic relationships of these sequenced species are well resolved and provide the necessary backbone to complete comparative analyses in a range of disciplines. The utility of the known phylogenetic diversity of the sequenced species is coupled with additional information regarding feeding habits, reproductive biology, mating behavior, and appealing morphological characters for phenotypic analysis. We also have stock sets of several species that have been resequenced for investigations of genomic variation in natural populations. These resequencing projects provide an avenue to study large-scale patterns of intraspecific variation and population genetics. To facilitate use of the increasing number of Drosophila genomes becoming available, the DSSC is working with the research community to develop a BLAST component to our existing website to increase access to unpublished Drosophila genome data. The entire living collection of Drosophila species at the Center comprises 250 species represented by over 1500 stocks. In order to facilitate familiarity between the research community and the diversity in our collection, the Center hosts an annual workshop where researchers learn to identify, culture, and experiment with over 100 Drosophila species.
72 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
39. DYNAMIC ASSEMBLY OF CUTICULAR PROTEINS INTO THE ELYTRAL PROCUTICLE OF TRIBOLIUM CASTANEUM
Li, Beibei; Jasrapuria, Sinu; Chaudhari, Sujata S; Arakane, Yasuyuki; Moussian, Bernard; Mezendorfer, Hans; Specht, Charles A; Beeman, Richard W; Kramer, Karl J and Muthukrishnan, Subbaratnam
(BL, SJ, SSC, KJK, SM) Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, (YA) Chonnam National University, Gwangju, South Korea, (BM) University of Tubingen, Tubingen Germany, (HM) University of Osnabrueck, Osnabrueck, Germany, (CAS) University of Massachusetts Medical School, Boston, MA and (RWB, KJK) USDA- ARS-CGAHR, Manhattan, KS
This study is focused on the functional characterization of several Tribolium castaneum genes that encode Cuticular Proteins Analogous to Peritrophins (CPAP) and their assembly into the developing cuticle. These proteins contain one or three copies of the chitin-binding domain, ChtBD2, with its six characteristically spaced cysteine residues. CPAP genes are expressed exclusively in cuticle-forming tissues and have been classified into two families,CPAP1 and CPAP3. The CPAP1 family has 10 members, each with one ChtBD2 domain, while the CPAP3 family has eight members, each with three ChtBD2 domains. Individual members of the CPAP1 and CPAP3 gene families have distinct developmental patterns of expression. Many of these genes are essential for development, molting, cuticle integrity or proper locomotion and fecundity. RNA interference (RNAi) targeting TcCPAP1-C, TcCPAP1-H, TcCPAP1-J or TcCPAP3-C transcripts results in death at the pharate adult stage of development. RNAi for other CPAP3 genes results in different developmental defects, including abnormal elytra or hindwings, abnormal gait, and/or adult/embryonic mortality. Immunohistochemistry and confocal microscopic analysis of multiple developmental stages of wild type insects shows that TcCPAP3-C protein is confined to the assembly zone near the cell surface. These results provide experimental support for specialization in the functions of several CPAP proteins in T. castaneum and provide a biological rationale for the conservation of orthologs within these CPAP families of proteins in insects of different orders. Many of these proteins serve essential and non-redundant functions in maintaining the structural integrity of the cuticle. Supported by grants from the National Science Foundation (IOS-1022227) and Kansas Idea Network for Biomedical Research Excellence (P20RR016475, P20GM103418).
73 ABSTRACTS | OTHER
40. GENE SILENCING OF ARGININE KINASE IN TISSUES OF ANASA TRISTIS (DE GEER) (HETEROPTERA: COREIDAE)
Kent S. Shelby (USDA-ARS-BCIRL, 1503 S. Providence Rd., Columbia, MO), and Joseph A. Ringbauer (USDA-ARS-BCIRL)
The Squash bug, Anasa tristis (De Geer), is a major pest of squash, pumpkin, and other cucurbits throughout North America. A. tristis is a piercing/sucking feeder which causes extensive foliar wilting, fruit scarring, and in addition transmits plant pathogens. Current biological control agents available for control of A. tristis infestations are extremely limited in efficacy, thus newer control methods must be developed. Gene silencing by application of double stranded RNA to insects, or RNA interference (RNAi) is a recently introduced technology with the potential to reach pest insects via either the food plant (in planta RNAi expression) or by field applications of encapsulated RNA. In order to determine whetherA. tristis is a suitable candidate for control via RNAi we undertook an examination of insect-specific gene silencing in this pest by injection of dsRNAi against arginine kinase (ATP: L-arginine phosphotransferase, EC2.7.3.3) which catalyzes the reversible phosphorylation of Arg by ATP yielding phosphoarginine. A. tristis arginine kinase (AtAK) transcript was identified within the recently completed survey of immune-stimulated A. tristis transcripts (Genbank Accession NCBI#JQ266746.1). Expression of AtAK is significantly upregulated inA. tristis adults and nymphs following bacterial elicitation with a septic puncture. As a control for activation of the immune response upregulated expression of the antibacterial peptide anasin (KF578378.1) was concurrently measured. An AtAK dsRNAi-producing amplimer was constructed for generation of dsRNAi by in vitro transcription. Injection of up to 1 ug AtAK RNAi into A. tristis adults and nymphs resulted in significant reduction inAtAK transcripts compared to water injected control insects.
74 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
41. GENOME-WIDE ECDYSONE RECEPTOR BINDING CHANGES AFTER EXPOSURE TO THE JUVENILE HORMONE MIMIC METHOPRENE
Rebecca F. Spokony 1, Robert Arthur 1, Christopher D. Brown 2, Nicholas Bild 1, Jennifer Zieba 1, Matthew Slattery 1, Jesse Cohen 1, Kevin P. White 1
1. Institute for Genomics and Systems Biology, University of Chicago, Chicago IL 60637 2. Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104
Drosophila melanogaster development is controlled by two main hormones, ecdysone and juvenile hormone (JH). Ecdysone controls developmental transitions and acts primarily through a heterodimer of two nuclear receptors, Ecdysone Receptor (EcR) and Ultraspiracle (USP). Juvenile hormone controls the type of transitions and acts through two bHLH proteins, Methoprene-tolerant (MET) and Germ cell-expressed (gce). In the presence of JH, MET has been shown to bind Taiman (TAI) and FTZ-F1, two nuclear receptors also involved in the ecdysone pathway. Ectopic juvenile hormone can disrupt normal ecdysone mediated processes and is used as an insecticide. Known ecdysone mediated process that are disrupted include polytene puffing and morphogenesis of the central nervous system and salivary glands. Drosophila melanogaster is most sensitive to ectopic juvenile hormone at the larval to prepupal transition (pupariation). We exposed white prepupae (WPP) to the juvenile hormone mimic, methoprene at WPP for 4-5 hours. Using ChIP-seq, we characterized EcR binding sites in the absence and presence of methoprene.
Using 100 bp windows, there are 186 locations with 4-fold more EcR binding after exposure to methoprene and 825 locations with 4-fold less EcR binding after exposure to methoprene. Differential binding was found at many JH targets’ loci, such as Eip75B, ftz-f1, Kr-h1, and tai, as well as differentially expressed genes under ectopic JH or methoprene exposure. EcR binding increases are enriched for TAI binding sites (characterized by late wandering third larval binding pattern, when JH is normally present). We predict that the lost EcR binding sites required TAI or FTZ-F1 that has been removed due to binding with MET. In order to test if these binding sites are responsible for the differential expression, we are constructing reporters using 1 kb intact- EcR binding regions and mutated-EcR binding regions and testing their responsiveness to methoprene.
75 ABSTRACTS | OTHER
42. GENOME-WIDE SEQUENCING & OPEN READING FRAME ANALYSIS OF DDT SUSCEPTIBLE 91-C & RESISTANT 91-R DROSOPHILA MELANOGASTER STRAINS
Steele, L.D., Muir, W.M., Seong, K.M., Valero, M.C., Rangesa, M., Sun, W., Clark, J.M., Coates, B., & B.R. Pittendrigh
The Drosophila melanogaster 91-R and 91-C strains are of common origin, however, 91-R has been intensely selected for dichlorodiphenyltrichloroethane (DDT) resistance over six decades while 91-C has been maintained as the non-selected control strain. These fly strains represent a unique genetic resource to understand the accumulation and fixation of mutations under laboratory conditions over decades of pesticide selection. Considerable research has been done to investigate the differential expression of genes associated with the highly DDT resistant strain 91-R, however, with the advent of whole genome sequencing we can now begin to develop an in depth understanding of the genomic changes associated with this intense decades-long xenobiotic selection pressure. Here we present the first whole genome sequencing analysis of the 91-R and 91-C fly strains to identify genome-wide structural changes within the open reading frames. Between-strain changes in allele frequencies revealed a higher percent of new alleles going to fixation for the 91-R strain, as compared to 91-C (P< 0.0001). These results suggest that resistance to DDT in the 91-R laboratory strains could potentially be due primarily to new mutations, as well as being polygenic rather than the result of a few major mutations, two hypotheses that remain to be tested.
76 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
43. IMPLICATIONS OF SEASON AND MANAGEMENT PROTOCOL ON THE GENE EXPRESSION LANDSCAPE DURING DIAPAUSE DEVELOPMENT IN THE ALFALFA LEAF
George Yocum, Anna Bennett, Joseph Rinehart, William Kemp, Theresa Pitts-Singer, Julia Bowsher
The alfalfa leaf cutting bee, Megachile rotundata, is the world’s most intensively managed solitary bee for commercial pollination. It is the primary pollinator for alfalfa seed production. Managed bees are subjected to thermal regimes for overwintering and subsequent adult emergence in time for alfalfa bloom. Mating, foraging and nesting occurs in the field and larvae develop in brood cells provisioned by the mother. In nature, larval development is typically completed by the fall when bees undergo diapause, a period of suppressed metabolism and development, and overwinter as prepupa.
Management practices during the prepupal stage affect the physiology of the adult bee and likewise have implications for overwintering survival. Therefore, an understanding of how diapause is regulated could lead to better management practices. Diapausing prepupae produced early and late in the season were removed from nests on September 1, 2010 and divided between two management groups, those kept at a constant 4-5°C and those kept outdoors. Each of these four treatment groups was sampled monthly from October to July. Samples from four months were chosen to span the course of diapause development. Illumina sequencing was performed on RNA from three bees from each treatment group from each of the four months (48 samples). Distinctly different gene expression landscapes underlie each treatment group with uniquely expressed genes found in each group. This unprecedented characterization of diapause will provide a foundation for understanding the sequence of gene expression during diapause and will aid in commercial management decisions for M. rotundata.
77 ABSTRACTS | OTHER
44. RIGHT DOSE FOR EACH SEX? RNASEQ AND A FUSED SEX CHROMOSOME YIELD INSIGHTS INTO DOSAGE COMPENSATION AND CHROMOSOME EVOLUTION IN LEPIDOPTERA
Aloy Gu, Department of Entomology, Cornell University
In diploid species, there are primarily two types of sex determination systems. The heterogametic sex is male in XX/XY systems and female in ZZ/ZW systems. Since the Y chromosome of XY males and the W chromosome of ZW females are usually degenerate, the dosage of functional sex linked genes is different between two sexes. Dosage compensation is a mechanism to equalize the expression of sex linked genes, thereby ensuring the health of the individuals. Observations and mechanisms of dosage compensation differ between the two systems, and at present most studies have focused on XX/XY system, leaving the ZZ/ZW world poorly understood. Among insects, the sibling orders of Lepidoptera and Trichoptera stand out as the only orders having the ZZ/ZW system. In the quest to address dosage compensation and its relationship to chromosome evolution in Lepidoptera, we resort to the codling moth, Cydia pomonella. C. pomonella belongs to a phylogenetically basal group, Tortricidae, with intriguingly a neo-Z sex chromosome that originated from translocation of an autosome to the ancestral Z chromosome. Using Illumina RNAseq data and bioinformatics tools, we performed de nove assembly of the first C. pomonella transcriptome, and compared the expression abundance in relation to autosome/sex-chromosome linkage within individuals, as well as sex-specificity between males and females. We also specifically compared the pattern of expression between the ancestral Z and ancestral 15 segments of the neo-Z chromosome, further inferring possible scenarios regarding sex chromosome evolution in Lepidoptera.
78 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
45. WIDESPREAD EXPRESSION OF ANCIENT SMALL RNAS IN SMALL INSECT SYMBIONT GENOMES
Allison K. Hansen 1, Patrick H. Degnan 2
1. Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA (current institution) 2. Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
The smallest microbial genomes known are found in insect endosymbionts, and are generally dedicated to provisioning their insect host with essential nutrients. Given their small size it is unsurprising that genome architecture of these mutualistic microbes changed dramatically after their transition from free-living lifestyles to symbiotic associations within eukaryotic cells. Symbiont genomes experience numerous rearrangements and massive gene loss, which is expected to radically alter gene regulatory networks compared to free-living relatives. As such, it remains unclear if and how these small symbiont genomes regulate gene expression. Here, employing a label-free mass-spec quantification approach we found that differential protein regulation occurs in Buchnera, a model aphid symbiont with a reduced genome, when it transitions between two distinct life stages. However, differential mRNA expression could not be detected between Buchnera life stages, despite the presence of a small number of transcriptional regulators. Instead a comparative analysis of small RNA expression profiles among five divergentBuchnera lineages, which span a variety of Buchnera lifestages, reveal 140 novel small RNAs and 517 untranslated regions that were significantly expressed, some of which have been conserved for over 65 million years. Additionally, the majority of these small RNAs exhibit both sequence covariation and thermodynamic stability, indicators of a potential structural RNA role. Together these data suggest that gene regulation at the post- transcriptional level in Buchnera is of greater importance. Ultimately post-transcriptional regulation may shape metabolic complementation between Buchnera and its aphid host, thus impacting the animal’s ecology and evolution.
79 ABSTRACTS | OTHER
46. CHARACTERIZING THE GENETIC BASIS OF MIGRATION IN THE MONARCH BUTTERFLY, DANAUS PLEXIPPUS, USING POPULATION GENOMICS
Shuai Zhan, Wei Zhang, Steve Reppert, Sonia Altizer, Jacobus de Roode, Marcus Kronforst
Every year in late summer, millions of monarch butterflies fly from the northern United States and southern Canada to overwinter in enormous colonies in Mexico and southern California. A largely unappreciated aspect of this system is that not all monarchs migrate. In fact, the geographic distribution of Danaus plexippus extends far beyond North America and it does not migrate across most of its range. Despite decades of study, we know relatively little about the underlying genetic basis of migratory behavior in the monarch butterfly. To examine this within a comparative genomic context, we sequenced the genomes of monarch butterflies from across their range and then searched for signatures of divergent selection associated with migratory behavior. Our analysis, based on genome-wide SNP data, allowed us to reconstruct the monarch’s evolutionary origin and history of dispersal. Furthermore, we found that approximately 2% of the genome showed signatures of divergent natural selection associated with migration, encompassing genes enriched for functional categories likely to play an important role in mediating this complex behavioral adaptation. Our work is motivated by the fact that our ability to explore monarch migration will soon come to an end. Each year the number of migrating monarchs is reduced by a substantial margin, and this past winter’s overwintering colony in Mexico reached an all-time low. While the monarch butterfly itself is unlikely to go extinct, it appears the days are numbered for its iconic migratory behavior.
80 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
47. CHEMOSENSORY CONSEQUENCES FOLLOWING THE LOSS OF HEMATOPHAGY IN MOSQUITOES: THE DE NOVO ASSEMBLY OF THE CHEMORECEPTIVE REPERTOIRE OF TOXORHYNCHITES AMBOINENSIS
David Rinker 1,2, Xiaofan Zhou 1, R Jason Pitts 1, Rokas A 1, LJ Zwiebel 1,2
1. Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA. 2. Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN, USA
Hematophagy (blood-feeding) is a phenotype shared among most mosquito species and is primarily olfactory driven. Among those rare mosquito genera that do not blood feed, the species belonging to Toxorhynchites represent the most taxonomically and geographically expansive representation of non-blood feeding mosquitoes in the world. Here we examine whether or not the principle chemosensory organs (antenna and maxillary palp) of Toxorhynchites differ from hematophagous mosquitoes in their expressed chemosensory repertoire. To this end, we have conducted a whole transcriptome sequencing and comprehensive, assembly, annotation and quantitation of mRNA isolated from the whole body, antennae and maxillary palp of female To. amboinensis. Our analysis allowed for the subsequent construction of a robust phylogeny that placed To. amboinensis as a sister taxa to the hematophagous human disease vector Aedes aegypti, leading us to conclude that hematophagy was lost in this species. Nevertheless, despite the divergence in blood feeding phenotype between these two taxa the profile of expressed chemosensory genes inTo. amboinensis chemosensory appendages proved remarkably similar to that seen in Ae. Aegypti. Therefore, despite the dramatic phenotypic and morphologic differences that exist between To. amboinensis and Ae. Aegypti, the putative, peripheral chemoreceptive receptive range of To. amboinensis appears largely intact relative to the common ancestor of these two taxa.
81 ABSTRACTS | OTHER
48. THREE’S A CROWD-SOURCE: THE COLLABORATIVE NATURE OF GENOME ANNOTATION
Monica C Munoz-Torres 1, Eduardo Lee 1, Colin Diesh 2, Chris Mungall 1, Seth Carbon 1, Heiko Dietze 1, Deepak Unni 2, Ian Holmes 3, Christine G Elsik 2, Suzanna E Lewis 1
1. Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA 2. Divisions of Animal and Plant Sciences, University of Missouri, Columbia, MO USA 3. Department of Bioengineering, University of California Berkeley, Berkeley, CA USA
Automated genome annotations must be curated to resolve discrepancies, providing clarity and validation. Unlike earlier genome projects, which had the advantage of more highly polished genomes, recent projects usually have lower coverage. Therefore researchers now face additional work correcting for more frequent assembly errors and annotating genes split across multiple contigs. It is impossible for a single individual to fully curate a genome with precise biological fidelity. Beyond the problem of scale, curators need second opinions and insights from colleagues with domain and gene family expertise, an inherently collaborative task. Understanding this need, the i5K community has successfully begun to implement Web Apollo, a collaborative genome annotation editor that allows researchers real-time interactivity. Breaking down large amounts of data into manageable portions and mobilizing groups of researchers to extract the most accurate representation of the biology from all available data distills invaluable knowledge from genome analysis. Continuing to improve genomic annotation and curation will involve increasing researchers’ efficiency by providing a suite of integrated curation tools, and increasing the effective population of researchers by providing universally accessible tools. To this end we are creating a federated environment that combines gene structural and functional data, transcriptomic, proteomic, and phenotypic data. We are also focused on training the next generation of researchers reaching out to educators to make these tools available as part of curricula via workshops and webinars, and through widely applied systems such as iPlant and DNA Subway. Here we offer details of our progress.
82 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
49. METABOLIC PATHWAYS UNDERLYING AGGRESSION IN DROSOPHILA BRAIN
Hongmei Li-Byarlay, Barry R. Pittendrigh, Gene E. Robinson
Social behavior such as aggression is common across different species in animal kingdom. Aggression is a complex behavior with a complicated biological basis. Understanding the molecular mechanism underlining aggression will help to will provide input for the evolution of social behavior. Previous functional transcriptomic comparison of honey bees has indicated metabolic genes in the brain were associated with the regulation of aggression behavior. We tested this hypothesis in Drosophila melanogaster by genetically silencing the expression of candidate metabolic genes in oxidative phosphorylation pathway by utilizing the GAL4-UAS system. Silencing metabolic genes of ND20-like (CG2014) recapitulate its effect on aggression displayed in honey bee. Elevated aggressiveness was detected in genetically neuron-silenced flies when comparing to wild type control, but not in genetically glia-silenced flies. Our results are indicating the evolutionary common ground of animal aggression behavior on the molecular basis. The significance of our study is possibly decoding the metabolic pathways underlying aggressive behavior.
83 ABSTRACTS | OTHER
50. BUSCOS: BENCHMARKING SETS OF UNIVERSAL SINGLE-COPY ORTHOLOGS
Felipe Simao 1,2, Robert M. Waterhouse 1,2,3,4, Panagiotis Ioannidis 1,2, Evgenia V. Kriventseva 1,2, Evgeny M. Zdobnov 1,2,5
1. Department of Genetic Medicine and Development, University of Geneva Medical School, Rue Michel-Servet 1, 1211, Geneva 4, Switzerland. 2. Swiss Institute of Bioinformatics, Rue Michel-Servet 1, 1211, Geneva 4, Switzerland. 3. Computer Science and Arti¬ficial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA. 4. The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. 5. Division of Molecular Biosciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
With ever-lowering sequencing cots, genome sequencing projects have been initiated for a wide range of organisms spanning every domain of life. Although many projects have yielded what are considered complete genome assemblies, the vast majority of genomes currently exist in the form of draft assemblies. Considering that an important driving force behind genome projects is the acquisition of a complete catalogue of genes, an important task lies in assessing the integrity and completeness of the genomic assembly. Despite this, current approaches for assessing the completeness of genome assemblies are scarce and the most popular method relies on a relatively small set of core eukaryotic genes that are thought to be present in low copy numbers in eukaryotes. As such, our goal is to make use of phylogenetic information to generate larger and lineage-focused benchmarking sets and a benchmarking pipeline. Universal single-copy orthologous groups identified from major phylogenetic lineages of OrthoDB are expected to be present in single-copy in the genome of any species from the lineage and thus comprise our benchmarking sets of universal single-copy orthologs - BUSCOs. This approach provides a novel and complementary metric to assess a genome assembly’s quality, integrity and completeness that can be easily employed on assemblies of both model and non-model organisms even in the absence of any gene prediction or annotation. Due to its use of phylogenetic information the BUSCOs dataset is both larger and more speci¬fic than existing alternatives for benchmarking new genome assemblies.
84 8th Annual ARTHROPOD GENOMICS SYMPOSIUM (AGS)
51. PHYLOGENETIC ANALYSIS OF CHEMOSENSORY GENE FAMILIES AND DETECTION OF POSITIVE SELECTION ACROSS SEVEN ANT GENOMES
Xiaofan Zhou 1, Berger, S.L. 2, Bonasio, R. 2, Liebig, J. 3, Ray, A. 4, Reinberg, D. 5, Antonis Rokas 1, LJ. Zwiebel 1
1. Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA. 2. Departments of Cell and Developmental Biology, Genetics and Biology, University of Pennsylvania, Philadelphia, PA, USA. 3. School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA. 4. Department of Entomology, University of California, Riverside, CA, 92521, USA. 5. Department of Molecular Pharmacology and Biochemistry, New York University School of Medicine, New York, NY, 10016, USA.
Ants are highly successful social insects, and their complex social behaviors heavily depend on chemosensation. Therefore, it has been hypothesized that chemosensory genes have played essential roles in the origin and evolution of sociality in ants. Previous studies in four ant species have revealed extremely dynamic copy number changes of ant chemosensory genes. In particular, one olfactory receptor subfamily has expanded from one single gene in the common ancestor of hymenoptera to more than 100 copies in ants. However, it remains less clear whether this pattern holds true for other ants, and to what extend these rapidly expanded chemosensory gene families have experienced functional divergence. In this study, we first extended the phylogenetic analysis of chemosensory genes to all seven currently available ant genomes. While overall similar numbers of chemosensory genes and patterns of gene gain- and-loss were found in the three newly included ants, we identified an exceptional expansion of a gustatory receptor subfamily in the red imported fire ant. Furthermore, we detected signatures of positive selection in multiple chemosensory gene subfamilies, including genes in all seven ants, suggestive of ample divergence in their chemosensory functions. Moreover, we performed similar analyses in two non-social insect lineages (Drosophila and Anopheles) where abundant genomic resources are available. The comparison among the three social and non-social insect lineages revealed several unique features of chemosensory gene evolution in ants. Our results provide valuable information to guide future characterization of ant chemosensory gene functions and their roles in the social behavior of ants.
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