Assembling and Annotating the Genome of the Nematode Caenorhabditis Doughertyi

Total Page:16

File Type:pdf, Size:1020Kb

Assembling and Annotating the Genome of the Nematode Caenorhabditis Doughertyi Date of acceptance Grade Instructor Assembling and annotating the genome of the Nematode Caenorhabditis doughertyi Sinduja Chandrasekaran Helsinki 12/01/16 MSc. Thesis University of Helsinki Department of Computer Science HELSINGIN YLIOPISTO HELSINGFORS UNIVERSITET – UNIVERSITY OF HELSINKI Tiedekunta/Osasto Fakultet/Sektion –Faculty/Section Laitos Institution Department Faculty of Science Department of Computer Science TekijäFörfattare Author Sinduja Chandrasekaran Työn nimi Arbetets titel Title Assembling and annotating the genome of nematode Caenorhabditis doughertyi Oppiaine Läroämne Subject Bioinformatics Työn laji Arbetets art Level Aika Datum Month and year Sivumäärä Sidoantal Number of pages MSc. Thesis January 2016 51+9 pages Tiivistelmä Referat Abstract NGS technologies and the advancement of bioinformatics methodologies have led to the start and success of many projects in genomics. One such project is the Caenorhabditis genome project, aimed at generating draft genomes for all the known and non-sequenced Caenorhabditis species. Except for C. elegans, the model organism responsible for discoveries such as the molecular mechanism of cell death and RNA interference, not much is known about other species in this genus. This hinders our understanding of the evolution of C. elegans and its distinct characteristics. This project is therefore an initiative to understand the Caenorhabditis genus. The aim of my project was to sequence and annotate the genome of Caenorhabditis doughertyi, as a part of the Caenorhabditis Genome Project. C. doughertyi is the sister species of C. brenneri, which is known for its high level of polymorphism among eukaryotes. It was initially found in the regions of Kerala, India by MA Felix in 2007 and consists of both male and female adults. The sequencing of C. doughertyi would pave the way for understanding the evolution of high diversity levels observed in C. brenneri. The raw data of the genome consisted of two paired-end libraries with insert size of 300- and 500 bp, with read lengths of 125 bp. The quality of reads was ensured by quality control measures such as trimming of adaptor sequences, error correction and removal of DNA from non-target organisms. The reads were then assembled using multiple assemblers and ABySS was decided as the best assembly based on metrics such as N50 and biological parameters like CEGMA. The draft genome was then annotated using MAKER pipeline and the orthologs were identified using OrthoMCL. The obtained draft genome can aid in preliminary comparative genomic analyses with other species in the genus. Further work may focus on improving the quality of this draft assembly towards a publication quality genome sequence for this species. ACM Computing Classification System (CCS): Life and medical sciences -> Computational biology Life and medical sciences -> Bioinformatics Avainsanat – Nyckelord Keywords Nematode, Caenorhabditis doughertyi, Genome Assembly, Annotation, Säilytyspaikka Förvaringställe Where deposited Muita tietoja Övriga uppgifter Additional information ii Contents Abbreviations iv 1 Introduction 1 1.1 Caenorhabditis Genome Project............................................................................................2 1.2 Caenorhabditis brenneri........................................................................................................3 1.3 Aims and objectives..............................................................................................................4 2 Methodology 6 2.1 Quality control...................................................................................................................6 2.1.1 FastQC................................................................................................................................6 2.1.2 Adapter trimming.............................................................................................................7 2.1.3 Error correction.................................................................................................................8 2.1.4 Blobology............................................................................................................................9 2.1.4.1 Bowtie.............................................................................................................................10 2.1.5 Filtering reads................................................................................................................11 2.1.6 Insert size estimation......................................................................................................11 2.1.7 Blobology after contamination removal........................................................................11 2.1.8 BLAST against Caenorhabditis briggsae.......................................................................11 2.2 Prior to final assembly....................................................................................................11 2.2.1 Estimating k-mer size.....................................................................................................11 2.3 Final assembly.................................................................................................................12 2.3.1 SPAdes.............................................................................................................................12 2.3.2 Ray...................................................................................................................................12 2.3.3 Velvet...............................................................................................................................12 2.3.4 CLC..................................................................................................................................13 2.3.5 AbySS (Assembly by Short Sequences)..........................................................................13 2.3.6 Trinity..............................................................................................................................14 2.4 Comparison of assemblies...............................................................................................15 2.4.1 Assembly statistics.........................................................................................................15 2.4.2 Biological metrics............................................................................................................15 2.4.2.1 Transcript content.........................................................................................................15 2.4.2.2 Protein content..............................................................................................................15 2.4.2.3 Core Eukaryotic Gene Mapping Approach (CEGMA).................................................15 2.4.3 Statistical metrics...........................................................................................................16 2.4.3.1 Assembly Likelihood Evaluation (ALE).......................................................................16 iii 2.4.3.2 Recognition of Errors in Assembly using Paired Reads (REAPER)...........................17 2.5 Annotation.......................................................................................................................18 2.5.1 Maker pipeline.................................................................................................................18 2.5.1.1 Repeat masking.............................................................................................................18 2.5.1.2 Gene Prediction.............................................................................................................19 2.5.2 Augustus..........................................................................................................................21 2.5.3 OrthoMCL........................................................................................................................22 3 Results 23 3.1 Read data.........................................................................................................................23 3.2 Quality control................................................................................................................23 3.2.1 FastQC.............................................................................................................................23 3.2.2 Adapter trimming...........................................................................................................26 3.2.3 Error correction…............................................................................................................26 3.2.4 Contamination removal...................................................................................................26 3.2.5 Insert size estimation......................................................................................................29 3.2.6 BLAST against Caenorhabditis briggsae.......................................................................30 3.2.7 Estimating k-mer size.....................................................................................................31 3.3 Comparison of assembly.................................................................................................32 3.3.1 Assembly statistics comparison......................................................................................32 3.3.2 Biological metrics comparison........................................................................................34
Recommended publications
  • Incorporating Genomics Into the Toolkit of Nematology
    Journal of Nematology 44(2):191–205. 2012. Ó The Society of Nematologists 2012. Incorporating Genomics into the Toolkit of Nematology 1 2 1,* ADLER R. DILLMAN, ALI MORTAZAVI, PAUL W. STERNBERG Abstract: The study of nematode genomes over the last three decades has relied heavily on the model organism Caenorhabditis elegans, which remains the best-assembled and annotated metazoan genome. This is now changing as a rapidly expanding number of nematodes of medical and economic importance have been sequenced in recent years. The advent of sequencing technologies to achieve the equivalent of the $1000 human genome promises that every nematode genome of interest will eventually be sequenced at a reasonable cost. As the sequencing of species spanning the nematode phylum becomes a routine part of characterizing nematodes, the comparative approach and the increasing use of ecological context will help us to further understand the evolution and functional specializations of any given species by comparing its genome to that of other closely and more distantly related nematodes. We review the current state of nematode genomics and discuss some of the highlights that these genomes have revealed and the trend and benefits of ecological genomics, emphasizing the potential for new genomes and the exciting opportunities this provides for nematological studies. Key words: ecological genomics, evolution, genomics, nematodes, phylogenetics, proteomics, sequencing. Nematoda is one of the most expansive phyla docu- piece of knowledge we can currently obtain for any mented with free-living and parasitic species found in particular life form (Consortium, 1998). nearly every ecological niche(Yeates, 2004). Traditionally, As in many other fields of biology, the nematode C.
    [Show full text]
  • Large Genetic Diversity and Strong Positive Selection in F-Box and GPCR Genes Among
    bioRxiv preprint doi: https://doi.org/10.1101/2020.07.09.194670; this version posted February 17, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 Large genetic diversity and strong positive selection in F-box and GPCR genes among 2 the wild isolates of Caenorhabditis elegans 3 4 Fuqiang Ma, Chun Yin Lau, and Chaogu Zheng* 5 6 School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China 7 *Correspondence: 4S13, Kadoorie Biological Science Building, Pokfulam Road, The 8 University of Hong Kong, Hong Kong, China, Email: [email protected] (C.Z.) 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 Abstract 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.09.194670; this version posted February 17, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 29 The F-box and chemosensory GPCR (csGPCR) gene families are greatly expanded in 30 nematodes, including the model organism Caenorhabditis elegans, compared to insects and 31 vertebrates. However, the intraspecific evolution of these two gene families in nematodes 32 remain unexamined. In this study, we analyzed the genomic sequences of 330 recently 33 sequenced wild isolates of C.
    [Show full text]
  • Evolution and Developmental System Drift in the Endoderm Gene
    fcell-08-00170 March 16, 2020 Time: 15:29 # 1 MINI REVIEW published: 18 March 2020 doi: 10.3389/fcell.2020.00170 Evolution and Developmental System Drift in the Endoderm Gene Regulatory Network of Caenorhabditis and Other Nematodes Edited by: Maike Kittelmann, Chee Kiang Ewe1,2†, Yamila N. Torres Cleuren3*† and Joel H. Rothman1,2,4*† Oxford Brookes University, United Kingdom 1 Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States, 2 Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States, Reviewed by: 3 Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway, 4 Department of Ecology, Morris Maduro, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, United States University of California, Riverside, United States Jose Maria Martin-Duran, Developmental gene regulatory networks (GRNs) underpin metazoan embryogenesis Queen Mary University of London, United Kingdom and have undergone substantial modification to generate the tremendous variety of *Correspondence: animal forms present on Earth today. The nematode Caenorhabditis elegans has been Yamila N. Torres Cleuren a central model for advancing many important discoveries in fundamental mechanistic [email protected] biology and, more recently, has provided a strong base from which to explore the Joel H. Rothman [email protected] evolutionary diversification of GRN architecture and developmental processes in other † ORCID: species. In this short review, we will focus on evolutionary diversification of the GRN for Chee Kiang Ewe the most ancient of the embryonic germ layers, the endoderm. Early embryogenesis orcid.org/0000-0003-1973-1308 Yamila N.
    [Show full text]
  • 5 Molecular Taxonomy and Phylogeny
    5 Molecular Taxonomy and Phylogeny Byron J. Adams1, Adler R. Dillman2 and Camille Finlinson1 1Brigham Young University, Provo, Utah, USA; 2California Institute of Technology, Pasadena, California, USA 5.1. Introduction 119 5.2. The History of Reconstructing Meloidogyne Phylogenetic History 119 5.3. Molecular Phylogenetics: Genetic Markers and Evolutionary Relationships 120 5.4. A Meloidogyne Supertree Analysis 127 5.5. Conclusions and Future Directions 130 5.6. References 135 5.1. Introduction cies descriptions) and, subsequently, phylogenetic analyses. As molecular markers increasingly dem- The genus Meloidogyne contains over 90 described onstrated improved resolving power, they became species and each of these species typically has an more commonplace as diagnostic tools, eventually extremely broad host range (as many as 3000 becoming more prominent as parts of formal plant species; Trudgill and Blok, 2001). In add- taxonomic statements (including descriptions of ition to their host-range diversity, they also exhibit new species) and phylogenetic analyses (e.g. tremendous cytogenetic variation (aneuploidy and Castillo et al., 2003; Landa et al., 2008). With the polyploidy) and mode of reproduction (from incorporation of molecular sources of characters obligatory amphimixis to meiotic and mitotic par- and refinements to phylogenetic theory, the fields thenogenesis) (Triantaphyllou, 1985; see Chitwood of taxonomy and evolutionary biology have now and Perry, Chapter 8, this volume). In current become more completely integrated as a dis- practice, identification of species is based primar- cipline, such that the terms molecular taxonomy ily on the morphological features of females, and phylogenetics are (or should be) subsumed as males and second-stage juveniles (Eisenback and a single research programme (systematics).
    [Show full text]
  • Zootaxa,Comparison of the Cryptic Nematode Species Caenorhabditis
    Zootaxa 1456: 45–62 (2007) ISSN 1175-5326 (print edition) www.mapress.com/zootaxa/ ZOOTAXA Copyright © 2007 · Magnolia Press ISSN 1175-5334 (online edition) Comparison of the cryptic nematode species Caenorhabditis brenneri sp. n. and C. remanei (Nematoda: Rhabditidae) with the stem species pattern of the Caenorhabditis Elegans group WALTER SUDHAUS1 & KARIN KIONTKE2 1Institut für Biologie/Zoologie, AG Evolutionsbiologie, Freie Universität Berlin, Königin-Luise Straße 1-3, 14195 Berlin, Germany. [email protected] 2Department of Biology, New York University, 100 Washington Square E., New York, NY10003, USA. [email protected] Abstract The new gonochoristic member of the Caenorhabditis Elegans group, C. brenneri sp. n., is described. This species is reproductively isolated at the postmating level from its sibling species, C. remanei. Between these species, only minute morphological differences are found, but there are substantial genetic differences. The stem species pattern of the Ele- gans group is reconstructed. C. brenneri sp. n. deviates from this character pattern only in small diagnostic characters. In mating tests of C. brenneri sp. n. females with C. remanei males, fertilization takes place and juveniles occasionally hatch. In the reverse combination, no offspring were observed. Individuals from widely separated populations of each species can be crossed successfully (e.g. C. brenneri sp. n. populations from Guadeloupe and Sumatra, or C. remanei populations from Japan and Germany). Both species have been isolated only from anthropogenic habitats, rich in decom- posing organic material. C. brenneri sp. n. is distributed circumtropically, C. remanei is only found in northern temperate regions. To date, no overlap of the ranges was found.
    [Show full text]
  • Ephemeral-Habitat Colonization and Neotropical Species Richness of Caenorhabditis Nematodes
    bioRxiv preprint doi: https://doi.org/10.1101/142190; this version posted June 1, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Ephemeral-habitat colonization and neotropical species richness of Caenorhabditis nematodes Céline Ferrari1 ([email protected]), Romain Salle1 ([email protected]), Nicolas Callemeyn-Torre1 ([email protected]), Richard Jovelin2 ([email protected]), & Asher D. Cutter2* ([email protected]), Christian Braendle1*([email protected]) 1Université Côte d’Azur, CNRS, Inserm, IBV, Nice, France 2Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada *corresponding authors Key Words Caenorhabditis astrocarya, Caenorhabditis dolens, Caenorhabditis elegans, habitat sharing, morphological crypsis, metapopulations, species co-existence, species richness 1 bioRxiv preprint doi: https://doi.org/10.1101/142190; this version posted June 1, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract Background: The drivers of species co-existence in local communities are especially enigmatic for assemblages of morphologically cryptic species. Here we characterize the colonization dynamics and abundance of nine species of Caenorhabditis nematodes in neotropical French Guiana, the most speciose known assemblage of this genus, with resource use overlap and notoriously similar outward morphology despite deep genomic divergence.
    [Show full text]
  • Downloading the Zinc-Finger Motif from the Gag Protein Must Have Assembly Files and Executing the Ipython Notebook Cells Occurred Independently Multiple Times
    The evolution of tyrosine-recombinase elements in Nematoda Amir Szitenberg1, Georgios Koutsovoulos2, Mark L Blaxter2 and David H Lunt1 1Evolutionary Biology Group, School of Biological, Biomedical & Environmental Sciences, University of Hull, Hull, HU6 7RX, UK 2Institute of Evolutionary Biology, The University of Edinburgh, EH9 3JT, UK [email protected] Abstract phylogenetically-based classification scheme. Nematode Transposable elements can be categorised into DNA and model species do not represent the diversity of RNA elements based on their mechanism of transposable elements in the phylum. transposition. Tyrosine recombinase elements (YREs) are relatively rare and poorly understood, despite Keywords: Nematoda; DIRS; PAT; transposable sharing characteristics with both DNA and RNA elements; phylogenetic classification; homoplasy; elements. Previously, the Nematoda have been reported to have a substantially different diversity of YREs compared to other animal phyla: the Dirs1-like YRE retrotransposon was encountered in most animal phyla Introduction but not in Nematoda, and a unique Pat1-like YRE retrotransposon has only been recorded from Nematoda. Transposable elements We explored the diversity of YREs in Nematoda by Transposable elements (TE) are mobile genetic elements sampling broadly across the phylum and including 34 capable of propagating within a genome and potentially genomes representing the three classes within transferring horizontally between organisms Nematoda. We developed a method to isolate and (Nakayashiki 2011). They typically constitute significant classify YREs based on both feature organization and proportions of bilaterian genomes, comprising 45% of phylogenetic relationships in an open and reproducible the human genome (Lander et al. 2001), 22% of the workflow. We also ensured that our phylogenetic Drosophila melanogaster genome (Kapitonov and Jurka approach to YRE classification identified truncated and 2003) and 12% of the Caenorhabditis elegans genome degenerate elements, informatively increasing the (Bessereau 2006).
    [Show full text]
  • Deep Sampling of Hawaiian Caenorhabditis Elegans Reveals
    RESEARCH ARTICLE Deep sampling of Hawaiian Caenorhabditis elegans reveals high genetic diversity and admixture with global populations Tim A Crombie1, Stefan Zdraljevic1,2, Daniel E Cook1,2, Robyn E Tanny1, Shannon C Brady1,2, Ye Wang1, Kathryn S Evans1,2, Steffen Hahnel1, Daehan Lee1, Briana C Rodriguez1, Gaotian Zhang1, Joost van der Zwagg1, Karin Kiontke3, Erik C Andersen1* 1Department of Molecular Biosciences, Northwestern University, Evanston, United States; 2Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, United States; 3Department of Biology, New York University, New York, United States Abstract Hawaiian isolates of the nematode species Caenorhabditis elegans have long been known to harbor genetic diversity greater than the rest of the worldwide population, but this observation was supported by only a small number of wild strains. To better characterize the niche and genetic diversity of Hawaiian C. elegans and other Caenorhabditis species, we sampled different substrates and niches across the Hawaiian islands. We identified hundreds of new Caenorhabditis strains from known species and a new species, Caenorhabditis oiwi. Hawaiian C. elegans are found in cooler climates at high elevations but are not associated with any specific substrate, as compared to other Caenorhabditis species. Surprisingly, admixture analysis revealed evidence of shared ancestry between some Hawaiian and non-Hawaiian C. elegans strains. We suggest that the deep diversity we observed in Hawaii might represent patterns of ancestral C. elegans *For correspondence: genetic diversity in the species before human influence. [email protected] Competing interests: The authors declare that no Introduction competing interests exist. Over the last 50 years, the nematode Caenorhabditis elegans has been central to many important Funding: See page 21 discoveries in the fields of developmental, cellular, and molecular biology.
    [Show full text]
  • Evolution of Mitotic Spindle Behavior During the First Asymmetric Embryonic Division of Nematodes
    RESEARCH ARTICLE Evolution of mitotic spindle behavior during the first asymmetric embryonic division of nematodes Aurore-CeÂcile Valfort1, Caroline Launay2, Marie SeÂmon2*, Marie Delattre2* 1 Department of Pharmacology & Physiology (Colin Flaveny lab), Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America, 2 UnivLyon, ENS de Lyon, Univ Claude Bernard, Laboratory of Biology and Modelling of the Cell, Lyon University, Lyon, France a1111111111 * [email protected] (MS); [email protected] (MD) a1111111111 a1111111111 a1111111111 a1111111111 Abstract Asymmetric cell division is essential to generate cellular diversity. In many animal cells, the cleavage plane lies perpendicular to the mitotic spindle, and it is the spindle positioning that dictates the size of the daughter cells. Although some properties of spindle positioning are OPEN ACCESS conserved between distantly related model species and different cell types, little is known of Citation: Valfort A-C, Launay C, SeÂmon M, Delattre the evolutionary robustness of the mechanisms underlying this event. We recorded the first M (2018) Evolution of mitotic spindle behavior embryonic division of 42 species of nematodes closely related to Caenorhabditis elegans, during the first asymmetric embryonic division of which is an excellent model system to study the biophysical properties of asymmetric spin- nematodes. PLoS Biol 16(1): e2005099. https:// doi.org/10.1371/journal.pbio.2005099 dle positioning. Our recordings, corresponding to 128 strains from 27 Caenorhabditis and 15 non-Caenorhabditis species (accessible at http://www.ens-lyon.fr/LBMC/NematodeCell/ Academic Editor: Renata Basto, Institut Curie, France videos/), constitute a powerful collection of subcellular phenotypes to study the evolution of various cellular processes across species.
    [Show full text]
  • Caenorhabditis Elegans
    Caenorhabditis elegans From Wikipedia, the free encyclopedia Caenorhabditis elegans (pronounced Caenorhabditis elegans /ˌsiːnoʊræbˈdaɪtɪs ˈɛlɪgænz/) is a free-living, transparent nematode (roundworm), about 1 mm in length, which lives in temperate soil environments. Research into the molecular and developmental biology of C. elegans was begun in 1974 by Sydney Brenner and it has since been An adult hermaphrodite C. elegans worm used extensively as a model organism.[1] Scientific classification Kingdom: Animalia Phylum: Nematoda Contents Class: Secernentea Order: Rhabditida 1 Biology 2 Ecology Family: Rhabditidae 3 Laboratory uses Genus: Caenorhabditis 4 Genome Species: C. elegans 5 Evolution 6 Scientific community Binomial name 7 In the media Caenorhabditis elegans 8 See also Maupas, 1900 9 References 10 Publications 11 Online resources 12 Nobel lectures 13 External links Biology C. elegans is unsegmented, vermiform, bilaterally symmetrical, with a cuticle integument, four main epidermal cords and a fluid- filled pseudocoelomate cavity. Members of the species have many of the same organ systems as other animals. In the wild, they feed on bacteria that develop on decaying vegetable matter. C. elegans has two sexes: hermaphrodites and males.[2] Individuals are almost Movement of Wild-type C. elegans all hermaphrodite, with males comprising just 0.05% of the total population on average. The basic anatomy of C. elegans includes a mouth, pharynx, intestine, gonad, and collagenous cuticle. Males have a single-lobed gonad, vas deferens, and a tail specialized for mating. Hermaphrodites have two ovaries, oviducts, spermatheca, and a single uterus. C. elegans eggs are laid by the hermaphrodite. After hatching, they pass through four larval stages (L1-L4).
    [Show full text]
  • A Phylogeny and Molecular Barcodes for Caenorhabditis, with Numerous
    Kiontke et al. BMC Evolutionary Biology 2011, 11:339 http://www.biomedcentral.com/1471-2148/11/339 RESEARCHARTICLE Open Access A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits Karin C Kiontke1*†, Marie-Anne Félix2†, Michael Ailion3,6, Matthew V Rockman1,4, Christian Braendle5, Jean-Baptiste Pénigault2 and David HA Fitch1 Abstract Background: The nematode Caenorhabditis elegans is a major laboratory model in biology. Only ten Caenorhabditis species were available in culture at the onset of this study. Many of them, like C. elegans, were mostly isolated from artificial compost heaps, and their more natural habitat was unknown. Results: Caenorhabditis nematodes were found to be proliferating in rotten fruits, flowers and stems. By collecting a large worldwide set of such samples, 16 new Caenorhabditis species were discovered. We performed mating tests to establish biological species status and found some instances of semi-fertile or sterile hybrid progeny. We established barcodes for all species using ITS2 rDNA sequences. By obtaining sequence data for two rRNA and nine protein-coding genes, we determined the likely phylogenetic relationships among the 26 species in culture. The new species are part of two well-resolved sister clades that we call the Elegans super-group and the Drosophilae super-group. We further scored phenotypic characters such as reproductive mode, mating behavior and male tail morphology, and discuss their congruence with the phylogeny. A small space between rays 2 and 3 evolved once in the stem species of the Elegans super-group; a narrow fan and spiral copulation evolved once in the stem species of C.
    [Show full text]
  • Molecular Hyperdiversity Defines Populations of the Nematode
    Molecular hyperdiversity defines populations of the nematode Caenorhabditis brenneri Alivia Deya, Cecilia K. W. Chana, Cristel G. Thomasa, and Asher D. Cuttera,b,1 aDepartment of Ecology and Evolutionary Biology and bCentre for the Analysis of Genome Evolution and Function, University of Toronto, ON, Canada M5S 3B2 Edited by Michael Lynch, Indiana University, Bloomington, IN, and approved May 14, 2013 (received for review February 19, 2013) The biology of Sydney Brenner’s eponymous species of nematode, purposes such as identifying and resolving to fine scale the location Caenorhabditis brenneri, is little known to science, despite its fa- and selective pressures on noncoding regulatory elements (18). mous sibling Caenorhabditis elegans. Here we demonstrate that Given the experimental power of Caenorhabditis, this suggests that C. brenneri harbors the most molecular diversity of any eukaryote, higher diversity in outbreeding species like C. brenneri (7) could with its 14.1% of polymorphic synonymous sites between individu- also be leveraged to characterize complementary aspects of the als being 150-fold greater than humans and most comparable to evolutionary process and molecular mechanisms to those that are hyperdiverse bacteria. This diversity is not an artifact of cryptic spe- accessible to the C. elegans model system. Here we interrogate the cies divergence but reflects an enormous pan-tropical population, C. brenneri genome to test for microbe-like within-species diversity confirmed by fully viable genetic crosses between continents, exten- for application to tests of evolutionary theory and the character- sive intralocus recombination, selection on codon use, and only ization of genome function. weak geographic genetic structure. These findings in an animal gal- vanize tests of theory about the evolution of complexity in genomes Results and phenotypes and enable molecular population genetics methods C.
    [Show full text]