DOCSLIB.ORG

Genome Consortium Supplementary Information

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Genome Consortium Supplementary Information Milkweed Bug (Oncopeltus fasciatus) Genome Consortium [Logo by Chiaki Ueda] Supplementary Information Table of Contents 1. Genome and transcriptome sequencing and assembly ............................................ 4 1.1 Source materials, DNA and RNA purification ..................................................... 4 1.2 Library preparation ............................................................................................... 4 1.3 Sequencing ............................................................................................................ 5 2. Genome characteristics, quality control, expression analyses ................................ 6 2.1 Genome size .......................................................................................................... 6 2.1.a Flow cytometry estimation ..................................................................... 6 2.1.b k-mer estimation .................................................................................... 8 2.2 Lateral gene transfer events and bacterial contamination ................................... 13 2.3 Repeat content ..................................................................................................... 19 2.4 Comparative transcriptomic assessments of hemipteroid reproductive biology 23 3. Automated gene annotation using a Maker 2.0 pipeline tuned for arthropods ..... 26 4. Community curation and generating the official gene set .................................... 28 1 5. Curation and comparative analysis of specific gene families ............................... 33 5.1 Developmental regulation: transcription factors and signaling pathways .......... 33 5.1.a Anterior-posterior body axis: terminal patterning system and segmentation .................................................................................................... 34 5.1.b Hox and other homeobox transcription factors .................................... 36 5.1.c Iroquois Complex (Iro-C) cluster ......................................................... 39 5.1.d T-box transcription factors and heart determinants ............................. 42 5.1.e Nuclear receptors.................................................................................. 44 5.1.f Dorsal-ventral body axis: BMP/TGF- pathway ................................. 46 5.1.g Dorsal-ventral body axis: Toll/ NFB pathway ................................... 48 5.1.h Innate immunity ................................................................................... 51 5.1.i Notch, Hedgehog, and Torso RTK pathways ....................................... 53 5.1.j Wnt pathway ......................................................................................... 55 5.1.k Appendage patterning .......................................................................... 59 5.1.l Germline genes ..................................................................................... 61 5.1.m Eye development ................................................................................. 63 5.2 Structural and differentiation genes .................................................................... 65 5.2.a Bristle and neural development ............................................................ 65 5.2.b Molting and metamorphosis genes ...................................................... 72 5.2.c Structural cuticular proteins and pigmentation .................................... 74 5.3 Environmental adaptations .................................................................................. 77 5.3.a Stress response ..................................................................................... 77 5.3.b Cytochrome P450s ............................................................................... 79 5.3.c Insecticide resistance ............................................................................ 80 2 5.3.d Neuropeptides and their receptors........................................................ 81 5.3.e Visual genes and light detection........................................................... 82 5.3.f Chemoreceptors .................................................................................... 85 5.4 Molecular machinery .......................................................................................... 95 5.4.a Gene silencing machinery (RNAi, miRNA, piRNA) ........................... 95 5.4.b Sex determination and dosage compensation ...................................... 97 5.4.c Epigenetic machinery ........................................................................... 99 5.4.d Repressive C2H2 zinc finger effectors (KAP-1/ TRIM proteins) ..... 107 6. Post-OGS v1.1 pipeline analyses ........................................................................ 109 6.1 Protein gene orthology assessments via OrthoDB and BUSCO ....................... 109 6.2 Transcription factor classifications and orthology assignments ....................... 112 6.3 Gene structure evolution ................................................................................... 113 6.4 Interspecific comparisons of metabolic enzymes ............................................. 116 7. References ........................................................................................................... 117 3 1. Genome and transcriptome sequencing and assembly Contributors: Stephen Richards, Daniel S.T. Hughes, Shwetha C. Murali, Jiaxin Qu, Shannon Dugan, Sandra L. Lee, Hsu Chao, Huyen Dinh, Yi Han, HarshaVardhan Doddapaneni, Kim C. Worley, Donna M. Muzny, Richard A. Gibbs, Kristen A. Panfilio, Stefan Koelzer The milkweed bug Oncopeltus fasciatus is one of thirty arthropod species sequenced as a part of a pilot project for the i5K arthropod genomes project at Baylor College of Medicine Human Genome Sequencing Center. For all of these species, an enhanced Illumina-ALLPATHS-LG (v. 35218) sequencing and assembly strategy enabled multiple species to be approached in parallel at reduced costs. For most species in the pilot, including O. fasciatus, we sequenced four libraries of nominal insert sizes 180 bp, 500 bp, 3 kb and 8 kb. The amount of sequence generated from each of these libraries is noted in Table S 1.1, with NCBI SRA accessions. 1.1 Source materials, DNA and RNA purification Genomic DNA was extracted from an individual adult male to construct the main sequencing libraries: 180-bp, 500-bp paired end and 3-kb mate pair libraries. A fourth, larger mate pair library with 8-10 kb inserts was constructed with DNA extracted from an individual adult female, due to the higher amount of starting DNA required for this library. Additionally, to aid in genome assembly and gene prediction, RNA was extracted from three samples representing three different life history samples: an individual adult male, an individual adult female, and pooled, mixed- instar nymphs. 1.2 Library preparation To prepare the 180-bp and 500-bp libraries, we used a gel-cut paired end library protocol. Briefly, 1 µg of the DNA was sheared using a Covaris S-2 system (Covaris, Inc. Woburn, MA) using the 180-bp or 500-bp program. Sheared DNA fragments were purified with Agencourt AMPure XP beads, end-repaired, dA-tailed, and ligated to Illumina universal adapters. After adapter ligation, DNA fragments were further size selected by agarose gel and PCR amplified for 6 to 8 cycles using Illumina P1 4 and Index primer pair and Phusion® High-Fidelity PCR Master Mix (New England Biolabs). The final library was purified using Agencourt AMPure XP beads and quality assessed by Agilent Bioanalyzer 2100 (DNA 7500 kit) determining library quantity and fragment size distribution before sequencing. The long mate pair libraries with 3-kb or 8-kb insert sizes were constructed according to the manufacturer’s protocol (Mate Pair Library v2 Sample Preparation Guide art # 15001464 Rev. A PILOT RELEASE). Briefly, 5 µg (for 2 and 3-kb gap size library) or 10 µg (8-10 kb gap size library) of genomic DNA was sheared to desired size fragments by Hydroshear (Digilab, Marlborough, MA), then end repaired and biotinylated. Fragment sizes between 3-3.7 kb (3 kb) or 8-10 kb (8 kb) were purified from 1% low melting agarose gel and then circularized by blunt-end ligation. These size selected circular DNA fragments were then sheared to 400 bp (Covaris S- 2), purified using Dynabeads M-280 Streptavidin Magnetic Beads, end-repaired, dA- tailed, and ligated to Illumina PE sequencing adapters. DNA fragments with adapter molecules on both ends were amplified for 12 to 15 cycles with Illumina P1 and Index primers. Amplified DNA fragments were purified with Agencourt AMPure XP beads. Quantification and size distribution of the final library was determined before sequencing as described above. 1.3 Sequencing Sequencing was performed on Illumina HiSeq2000s generating 100-bp paired end reads. Reads were pre-processed using cutadapt for adapter removal and sickle-trim for quality trimming (- min length 20bp). Subsequently, reads were assembled using ALLPATHS-LG (v35218) [1] on a large memory computer with 1 TB of RAM and further scaffolded and gap-filled using in-house tools Atlas-Link (v.1.0) and Atlas gap-fill (v.2.2) (https://www.hgsc.bcm.edu/software/). This yielded an assembly of 1.099 Gb (774 Mb without gaps within scaffolds), with a contig N50 of 4.0 kb and scaffold N50 of 340 kb, which has been deposited in GenBank (assembly accession GCA_000696205.1). Table S 1.1: Sequencing, assembly, annotation statistics and accession numbers in Excel Supplement 5 2. Genome
Load more

Recommended publications
  • Evolution of Olfaction in Lepidoptera and Trichoptera Gene Families and Antennal Morphology Yuvaraj, Jothi Kumar
    Evolution of olfaction in Lepidoptera and Trichoptera Gene families and antennal morphology Yuvaraj, Jothi Kumar 2017 Document Version: Publisher's PDF, also known as Version of record Link to publication Citation for published version (APA): Yuvaraj, J. K. (2017). Evolution of olfaction in Lepidoptera and Trichoptera: Gene families and antennal morphology. Lund University, Faculty of Science, Department of Biology. Total number of authors: 1 Creative Commons License: CC BY-NC-ND General rights Unless other specific re-use rights are stated the following general rights apply: Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal Read more about Creative commons licenses: https://creativecommons.org/licenses/ Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. LUND UNIVERSITY PO Box 117 221 00 Lund +46 46-222 00 00 JOTHI KUMAR YUVARAJ KUMAR JOTHI தாமிꟍ ꯁ쟁வ鏁 உலகிꟍ ꯁற埍க迍翁 கா믁쟁வ쏍 க쟍றறிꏍ தா쏍. olfaction of volution in Lepidoptera and Trichoptera - தி쏁埍埁ற쿍 399 E When the learned see that their learning contributes Evolution of olfaction in to make all the world happy, They are pleased and pursueWhen their the learninglearned more.see that their learning contributes Lepidoptera and Trichoptera to make all the world happy, They are pleased and pursue their learning more.
    [Show full text]
  • Helobdella Robusta Sp.Nov., and Comparison with Helobdella Triserialis on the Basis of Morphology, Embryology, and Experimental Breeding
    Description of the Californian leech Helobdella robusta sp.nov., and comparison with Helobdella triserialis on the basis of morphology, embryology, and experimental breeding MARTYSHANKLAND Department of Anatomy and Cellular Biology, Harvard Medical School, Boston, MA 021 15, U.S. A. SHIRLEYT. BISSEN Department of Biology, University of Missouri, St. Louis, MO 63121, U.S.A. AND DAVIDA. WEISBLAT Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, U.S. A. Received August 2, 199 1 Accepted December 18, 199 1 SHANKLAND,M., BISSEN,S. T., and WEISBLAT,D. A. 1992. Description of the Californian leech Helobdella robusta sp. nov., and comparison with Helobdella triserialis on the basis of morphology, embryology, and experimental breeding. Can. J. Zool. 70: 1258 - 1263. This paper describes the leech Helobdella robusta, which was collected from the Sacramento delta of California. This new species is generally similar to another species found in California, Helobdella triserialis, and the two were compared in detail. In the adult, we observed reliable differences in the relative dimensions of the body, the size of the dorsal papillae, the pattern of cutaneous pigmentation, and the structure of the gut. In the embryo, we observed differences in the appearance of the yolk platelets and the size of the adhesive gland. We also observed differences in the rate of embryonic development. All of these differences persist in breeding populations that have been maintained in the laboratory over many generations. Experimental studies indicate that H. robusta and H. triserialis have little or no proclivity for interbreeding, supporting their distinction as separate species.
    [Show full text]
  • Intermediate Filament Genes As Differentiation Markers in the Leech Helobdella
    Dev Genes Evol (2011) 221:225–240 DOI 10.1007/s00427-011-0375-3 ORIGINAL ARTICLE Intermediate filament genes as differentiation markers in the leech Helobdella Dian-Han Kuo & David A. Weisblat Received: 12 August 2011 /Accepted: 8 September 2011 /Published online: 22 September 2011 # Springer-Verlag 2011 Abstract The intermediate filament (IF) cytoskeleton is a evolutionary changes in the cell or tissue specificity of CIFs general feature of differentiated cells. Its molecular compo- have occurred among leeches. Hence, CIFs are not suitable nents, IF proteins, constitute a large family including the for identifying cell or tissue homology except among very evolutionarily conserved nuclear lamins and the more closely related species, but they are nevertheless useful diverse collection of cytoplasmic intermediate filament species-specific differentiation markers. (CIF) proteins. In vertebrates, genes encoding CIFs exhibit cell/tissue type-specific expression profiles and are thus Keywords Cell differentiation . Intermediate filament . useful as differentiation markers. The expression of Gene expression pattern . Helobdella . Leech . Annelid invertebrate CIFs, however, is not well documented. Here, we report a whole-genome survey of IF genes and their developmental expression patterns in the leech Helobdella, Introduction a lophotrochozoan model for developmental biology re- search. We found that, as in vertebrates, each of the leech The intermediate filament (IF) cytoskeleton is a structural CIF genes is expressed in a specific set of cell/tissue types. component that provides mechanical support for the cell. In This allows us to detect earliest points of differentiation for keeping with the large variety of cellular phenotypes, the IF multiple cell types in leech development and to use CIFs as cytoskeleton exhibits a high level of structural diversity and molecular markers for studying cell fate specification in is assembled from a much larger family of proteins leech embryos.
    [Show full text]
  • The Asymmetric Cell Division Machinery in the Spiral-Cleaving Egg and Embryo of the Marine Annelid Platynereis Dumerilii Aron B
    Nakama et al. BMC Developmental Biology (2017) 17:16 DOI 10.1186/s12861-017-0158-9 RESEARCH ARTICLE Open Access The asymmetric cell division machinery in the spiral-cleaving egg and embryo of the marine annelid Platynereis dumerilii Aron B. Nakama1, Hsien-Chao Chou1,2 and Stephan Q. Schneider1* Abstract Background: Over one third of all animal phyla utilize a mode of early embryogenesis called ‘spiral cleavage’ to divide the fertilized egg into embryonic cells with different cell fates. This mode is characterized by a series of invariant, stereotypic, asymmetric cell divisions (ACDs) that generates cells of different size and defined position within the early embryo. Astonishingly, very little is known about the underlying molecular machinery to orchestrate these ACDs in spiral-cleaving embryos. Here we identify, for the first time, cohorts of factors that may contribute to early embryonic ACDs in a spiralian embryo. Results: To do so we analyzed stage-specific transcriptome data in eggs and early embryos of the spiralian annelid Platynereis dumerilii for the expression of over 50 candidate genes that are involved in (1) establishing cortical domains such as the partitioning defective (par) genes, (2) directing spindle orientation, (3) conveying polarity cues including crumbs and scribble, and (4) maintaining cell-cell adhesion between embryonic cells. In general, each of these cohorts of genes are co-expressed exhibiting high levels of transcripts in the oocyte and fertilized single-celled embryo, with progressively lower levels at later stages. Interestingly, a small number of key factors within each ACD module show different expression profiles with increased early zygotic expression suggesting distinct regulatory functions.
    [Show full text]
  • Especie Nueva De Sanguijuela Del Género Helobdella (Rhynchobdellida: Glossiphoniidae) Del Lago De Catemaco, Veracruz, México
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Acta Zoológica Mexicana (nueva serie) Acta Zoológica MexicanaActa Zool. (n.s.)Mex. 23(1):(n.s.) 23(1)15-22 (2007) ESPECIE NUEVA DE SANGUIJUELA DEL GÉNERO HELOBDELLA (RHYNCHOBDELLIDA: GLOSSIPHONIIDAE) DEL LAGO DE CATEMACO, VERACRUZ, MÉXICO Alejandro OCEGUERA-FIGUEROA City University of New York (CUNY), Graduate School and University Center y Division of Invertebrate Zoology, American Museum of Natural History. Central Park West at 79th Street, Nueva York, Nueva York, 10024, EUA. [email protected] RESUMEN Se describe una especie nueva de sanguijuela del género Helobdella del Lago de Catemaco, Veracruz, México con base en 23 ejemplares. Los organismos se encontraron adheridos a piedras y raíces a las orillas del lago. La especie nueva carece de placa quitinoide dorsal y se diferencia del resto de las especies del género por presentar la superficie dorsal del cuerpo obscura con manchas blancas de tamaño y distribución muy variable; de tres a cinco hileras dorsales de papilas; glándulas salivales difusas en el parénquima; buche con seis pares de ciegos, el último par forma post-ciegos o divertículos. Palabras Clave: Hirudinea, Glossiphoniidae, Helobdella, Catemaco, México, sanguijuela. ABSTRACT A new leech species of the genus Helobdella from Catemaco Lake, Veracruz, Mexico is described based on the examination of 23 specimens. Leeches were found attached to submerged rocks and plants. The new species lacks a nuchal scute and is distinguishable from other species of the genus by the presence of a obscure dorsal surface with white spots of different size and irregularly arranged; three or five longitudinal rows of dorsal papillae; salivary glands diffused in the parenchyma; six pairs of crop caeca, the posterior pair forming post-caeca or diverticula.
    [Show full text]
  • Evolutionary Crossroads in Developmental Biology: Annelids David E
    PRIMER SERIES PRIMER 2643 Development 139, 2643-2653 (2012) doi:10.1242/dev.074724 © 2012. Published by The Company of Biologists Ltd Evolutionary crossroads in developmental biology: annelids David E. K. Ferrier* Summary whole to allow more robust comparisons with other phyla, as well Annelids (the segmented worms) have a long history in studies as for understanding the evolution of diversity. Much of annelid of animal developmental biology, particularly with regards to evolutionary developmental biology research, although by no their cleavage patterns during early development and their means all of it, has tended to concentrate on three particular taxa: neurobiology. With the relatively recent reorganisation of the the polychaete (see Glossary, Box 1) Platynereis dumerilii; the phylogeny of the animal kingdom, and the distinction of the polychaete Capitella teleta (previously known as Capitella sp.); super-phyla Ecdysozoa and Lophotrochozoa, an extra stimulus and the oligochaete (see Glossary, Box 1) leeches, such as for studying this phylum has arisen. As one of the major phyla Helobdella. Even within this small selection of annelids, a good within Lophotrochozoa, Annelida are playing an important role range of the diversity in annelid biology is evident. Both in deducing the developmental biology of the last common polychaetes are marine, whereas Helobdella is a freshwater ancestor of the protostomes and deuterostomes, an animal from inhabitant. The polychaetes P. dumerilii and C. teleta are indirect which >98% of all described animal species evolved. developers (see Glossary, Box 1), with a larval stage followed by metamorphosis into the adult form, whereas Helobdella is a direct Key words: Annelida, Polychaetes, Segmentation, Regeneration, developer (see Glossary, Box 1), with the embryo developing into Central nervous system the worm form without passing through a swimming larval stage.
    [Show full text]
  • Australian Entomolog
    Volume 44, Part 3, 29 September 2017 THE AUSTRALIAN ENTOMOLOGIST ABN#: 15 875 103 670 The Australian Entomologist is a non-profit journal published in four parts annually by the Entomological Society of Queensland and is devoted to entomology of the Australian Region, including New Zealand, New Guinea and islands of the south-western Pacific. The journal is produced independently and subscription to the journal is not included with membership of the society. The Publications Committee Editor: Dr D.L. Hancock Assistant Editors: Dr G.B. Monteith, Dr F. Turco, Dr L. Popple, Ms S. Close. Business Manager: Dr G.B. Monteith ([email protected]) Subscriptions Subscriptions are payable in advance to the Business Manager, The Australian Entomologist, P.O. Box 537, Indooroopilly, Qld, Australia, 4068. For individuals: A$33.00 per annum in Australia. A$40.00 per annum in Asia-Pacific Region. A$45.00 per annum elsewhere. For institutions: A$37.00 per annum in Australia. A$45.00 per annum in Asia-Pacific Region. A$50.00 per annum elsewhere. Electronic Subscriptions: A$25 individuals, A$30 institutions. Please forward all overseas cheques/bank drafts in Australian currency. GST is not payable on our publication. ENTOMOLOGICAL SOCIETY OF QUEENSLAND (www.esq.org.au) Membership is open to anyone interested in Entomology. Meetings are normally held at the Ecosciences Precinct, Dutton Park, at 1.00pm on the second Tuesday of March-June and August-December each year. Meetings are announced in the Society’s News Bulletin which also contains reports of meetings, entomological notes, notices of other Society events and information on Members’ activities.
    [Show full text]
  • Similarities Between Decapod and Insect Neuropeptidomes
    A peer-reviewed version of this preprint was published in PeerJ on 26 May 2016. View the peer-reviewed version (peerj.com/articles/2043), which is the preferred citable publication unless you specifically need to cite this preprint. Veenstra JA. 2016. Similarities between decapod and insect neuropeptidomes. PeerJ 4:e2043 https://doi.org/10.7717/peerj.2043 Similarities between decapod and insect neuropeptidomes Jan A Veenstra Background. Neuropeptides are important regulators of physiological processes and behavior. Although they tend to be generally well conserved, recent results using trancriptome sequencing on decapod crustaceans give the impression of significant differences between species, raising the question whether such differences are real or artefacts. Methods. The BLAST+ program was used to find short reads coding neuropeptides and neurohormons in publicly available short read archives. Such reads were then used to find similar reads in the same archives and the DNA assembly program Trinity was employed to construct contigs encoding the neuropeptide precursors as completely as possible. Results. The seven decapod species analyzed in this fashion, the crabs Eriocheir sinensis, Carcinus maenas and Scylla paramamosain, the shrimp Litopenaeus vannamei, the lobster Homarus americanus, the fresh water prawn Macrobrachium rosenbergii and the crayfish Procambarus clarkii had remarkably similar neuropeptidomes. Although some neuropeptide precursors could not be assembled, in many cases individual reads pertaining to the missing precursors show unambiguously that these neuropeptides are present in these species. In other cases the tissues that express those neuropeptides were not used in the construction of the cDNA libraries. One novel neuropeptide was identified, elongated PDH (pigment dispersing hormone), a variation on PDH that has a two amino acid insertion in its core sequence.
    [Show full text]
  • Joint Genome Institute PROGRESS REPORT 2006 JGI’S Mission
    U.S. DEPARTMENT OF ENERGY Joint Genome Institute PROGRESS REPORT 2006 JGI’s Mission The U.S. Department of Energy Joint Genome Institute (JGI), supported by the DOE Office of Science, is focused on the application of Genomic Sciences to support the DOE mission areas of clean energy generation, global carbon management, and environmental characterization and clean-up. JGI’s Production Genomics Facility in Walnut Creek, California , provides integrated high-throughput sequencing and compu- tational analysis that enable systems-based scientific approaches to these challenges. In addition, the Institute engages both technical and scientific partners at five national laboratories, Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest, along with the Stanford Human Genome Center. U.S. DEPARTMENT OF ENERGY Joint Genome Institute PROGRESS REPORT 2006 table of contents Director’s Perspective + + + + + + + + + + + + + + + + + + + + + iv JGI History + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 6 JGI Departments and Programs + + + + + + + + + + + + + + 8 JGI Users + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 11 The Benefits of Biofuels + + + + + + + + + + + + + + + + + + + 14 The JGI Sequencing Process + + + + + + + + + + + + + + + 1 6 Science Behind the Sequence Highlights: Biomass to Biofuels + + + + + + + + + + + + + + 18 Carbon Cycling + + + + + + + + + + + + + + + + + + + + + + + + + + 22 Bioremediation + + + + + + + + + + + + + + + + + + + + + + + + + + 24 Exploratory Sequence-Based
    [Show full text]
  • The Genome of Medicinal Leech (Whitmania Pigra) and Comparative Genomic Study for Exploration of Bioactive Ingredients
    The Genome of Medicinal Leech (Whitmania pigra) and comparative genomic study for Exploration of Bioactive Ingredients Lei Tong Kunming University Shao-Xing Dai Kunming University of Science and Technology De-Jun Kong Kunming University Peng-Peng Yang Kunming University of Science and Technology Xin Tong Kunming University of Science and Technology Xiang-Rong Tong Kunming University Xiao-Xu Bi Kunming University Yuan Su Kunming University Yu-Qi Zhao University of California Los Angeles Zi-Chao Liu ( [email protected] ) Kunming University https://orcid.org/0000-0002-7509-6209 Research article Keywords: Whitmania pigra, Genome, Bioactive Ingredients, Helobdella robusta, Hirudo medicinalis Posted Date: October 12th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-31354/v2 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/20 Abstract Background Leeches are classic annelids that have a huge diversity and closely related to people, especially medicinal leeches. Medicinal leeches have been widely utilized in medicine based on the pharmacological activities of their bioactive ingredients. Comparative genomic study of these leeches enables us to understand the difference among medicinal leeches and other leeches and facilitates the discovery of bioactive ingredients. Results In this study, we reported the genome of Whitmania pigra and compared it with Hirudo medicinalis and Helobdella robusta. The assembled genome size of W. pigra is 177 Mbp, close to the estimated genome. Approximately about 23% of the genome was repetitive. A total of 26,743 protein-coding genes were subsequently predicted. W. pigra have 12346 (46%) and 10295 (38%) orthologous genes with H.
    [Show full text]
  • Milkweed Bug (Oncopeltus Fasciatus)
    Milkweed Bug (Oncopeltus fasciatus) Genome Consortium [Logo by Chiaki Ueda] Supplementary Information Table of Contents 1. Genome and transcriptome sequencing and assembly ............................................ 4 1.1 Source materials, DNA and RNA purification ..................................................... 4 1.2 Library preparation ............................................................................................... 4 1.3 Sequencing ............................................................................................................ 5 2. Genome characteristics, quality control, expression analyses ................................ 6 2.1 Genome size .......................................................................................................... 6 2.1.a Flow cytometry estimation ..................................................................... 6 2.1.b k-mer estimation .................................................................................... 8 2.2 Lateral gene transfer events and bacterial contamination ................................... 13 2.3 Repeat content ..................................................................................................... 19 2.4 Comparative transcriptomic assessments of hemipteroid reproductive biology 23 3. Automated gene annotation using a Maker 2.0 pipeline tuned for arthropods ..... 26 4. Community curation and generating the official gene set .................................... 28 1 5. Curation and comparative analysis of specific gene families
    [Show full text]
  • Multifunctional Neuropeptides and Hormones in Insects and Other Invertebrates
    International Journal of Molecular Sciences Review Leucokinins: Multifunctional Neuropeptides and Hormones in Insects and Other Invertebrates Dick R. Nässel 1,* and Shun-Fan Wu 2 1 Department of Zoology, Stockholm University, S-10691 Stockholm, Sweden 2 College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; [email protected] * Correspondence: [email protected] Abstract: Leucokinins (LKs) constitute a neuropeptide family first discovered in a cockroach and later identified in numerous insects and several other invertebrates. The LK receptors are only distantly related to other known receptors. Among insects, there are many examples of species where genes encoding LKs and their receptors are absent. Furthermore, genomics has revealed that LK signaling is lacking in several of the invertebrate phyla and in vertebrates. In insects, the number and complexity of LK-expressing neurons vary, from the simple pattern in the Drosophila larva where the entire CNS has 20 neurons of 3 main types, to cockroaches with about 250 neurons of many different types. Common to all studied insects is the presence or 1–3 pairs of LK-expressing neurosecretory cells in each abdominal neuromere of the ventral nerve cord, that, at least in some insects, regulate secretion in Malpighian tubules. This review summarizes the diverse functional roles of LK signaling in insects, as well as other arthropods and mollusks. These functions include regulation of ion and water homeostasis, feeding, sleep–metabolism interactions, state-dependent memory formation, as well as modulation of gustatory sensitivity and nociception. Other functions are implied by the neuronal distribution of LK, but remain to be investigated.
    [Show full text]