1
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Sivell O, Sivell D, Geiser M. The genome sequence of the Cow Parsley Leaf Beetle, Chrysolina oricalcia (O.F. Müller, 1776). Wellcome Open Res 2024; 8:400. [PMID: 39193091 PMCID: PMC11347920 DOI: 10.12688/wellcomeopenres.19985.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2024] [Indexed: 08/29/2024] Open
Abstract
We present a genome assembly from an individual Cow Parsley Leaf Beetle Chrysolina oricalcia (the Cow Parsley Leaf Beetle; Arthropoda; Insecta; Coleoptera; Chrysomelidae). The genome sequence is 1,423.4 megabases in span. Most of the assembly is scaffolded into 22 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.93 kilobases in length. Gene annotation of this assembly on Ensembl identified 35,990 protein coding genes.
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2
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Mayeur H, Leyhr J, Mulley J, Leurs N, Michel L, Sharma K, Lagadec R, Aury JM, Osborne OG, Mulhair P, Poulain J, Mangenot S, Mead D, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Dolucan J, Dudchenko O, Omer AD, Weisz D, Aiden EL, McCarthy S, Sims Y, Torrance J, Tracey A, Howe K, Baril T, Hayward A, Martinand-Mari C, Sanchez S, Haitina T, Martin K, Korsching SI, Mazan S, Debiais-Thibaud M. The sensory shark: high-quality morphological, genomic and transcriptomic data for the small-spotted catshark Scyliorhinus canicula reveal the molecular bases of sensory organ evolution in jawed vertebrates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.23.595469. [PMID: 39005470 PMCID: PMC11244906 DOI: 10.1101/2024.05.23.595469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Cartilaginous fishes (chimaeras and elasmobranchs -sharks, skates and rays) hold a key phylogenetic position to explore the origin and diversifications of jawed vertebrates. Here, we report and integrate reference genomic, transcriptomic and morphological data in the small-spotted catshark Scyliorhinus canicula to shed light on the evolution of sensory organs. We first characterise general aspects of the catshark genome, confirming the high conservation of genome organisation across cartilaginous fishes, and investigate population genomic signatures. Taking advantage of a dense sampling of transcriptomic data, we also identify gene signatures for all major organs, including chondrichthyan specializations, and evaluate expression diversifications between paralogs within major gene families involved in sensory functions. Finally, we combine these data with 3D synchrotron imaging and in situ gene expression analyses to explore chondrichthyan-specific traits and more general evolutionary trends of sensory systems. This approach brings to light, among others, novel markers of the ampullae of Lorenzini electro-sensory cells, a duplication hotspot for crystallin genes conserved in jawed vertebrates, and a new metazoan clade of the Transient-receptor potential (TRP) family. These resources and results, obtained in an experimentally tractable chondrichthyan model, open new avenues to integrate multiomics analyses for the study of elasmobranchs and jawed vertebrates.
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3
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Rueda-M N, Pardo-Diaz C, Montejo-Kovacevich G, McMillan WO, Kozak KM, Arias CF, Ready J, McCarthy S, Durbin R, Jiggins CD, Meier JI, Salazar C. Genomic evidence reveals three W-autosome fusions in Heliconius butterflies. PLoS Genet 2024; 20:e1011318. [PMID: 39024186 PMCID: PMC11257349 DOI: 10.1371/journal.pgen.1011318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/24/2024] [Indexed: 07/20/2024] Open
Abstract
Sex chromosomes are evolutionarily labile in many animals and sometimes fuse with autosomes, creating so-called neo-sex chromosomes. Fusions between sex chromosomes and autosomes have been proposed to reduce sexual conflict and to promote adaptation and reproductive isolation among species. Recently, advances in genomics have fuelled the discovery of such fusions across the tree of life. Here, we discovered multiple fusions leading to neo-sex chromosomes in the sapho subclade of the classical adaptive radiation of Heliconius butterflies. Heliconius butterflies generally have 21 chromosomes with very high synteny. However, the five Heliconius species in the sapho subclade show large variation in chromosome number ranging from 21 to 60. We find that the W chromosome is fused with chromosome 4 in all of them. Two sister species pairs show subsequent fusions between the W and chromosomes 9 or 14, respectively. These fusions between autosomes and sex chromosomes make Heliconius butterflies an ideal system for studying the role of neo-sex chromosomes in adaptive radiations and the degeneration of sex chromosomes over time. Our findings emphasize the capability of short-read resequencing to detect genomic signatures of fusion events between sex chromosomes and autosomes even when sex chromosomes are not explicitly assembled.
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Affiliation(s)
- Nicol Rueda-M
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Carolina Pardo-Diaz
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | | | | | - Krzysztof M. Kozak
- Smithsonian Tropical Research Institute, Panama City, Panama
- Museum of Vertebrate Zoology, Berkeley, California, United States of America
| | - Carlos F. Arias
- Smithsonian Tropical Research Institute, Panama City, Panama
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, Washington DC, United States of America
| | - Jonathan Ready
- Institute for Biological Sciences, Federal University of Pará - UFPA, Belém, Brazil
- Centre for Advanced Studies of Biodiversity - CEABIO, Belém, Brazil
| | - Shane McCarthy
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Richard Durbin
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Chris D. Jiggins
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Joana I. Meier
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
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4
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Kieninger M, Stevens L, Collins JC, Blaxter M. The genome sequence of the nematode Caenorhabditis drosophilae (Rhabditida, Rhabditidae) (Kiontke, 1997). Wellcome Open Res 2024; 9:292. [PMID: 39114493 PMCID: PMC11303941 DOI: 10.12688/wellcomeopenres.22416.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2024] [Indexed: 08/10/2024] Open
Abstract
We present a genome assembly of the free-living nematode Caenorhabditis drosophilae (Nematoda; Chromadorea; Rhabditida; Rhabditidae). The genome sequence is 51.3 megabases in span. Most of the assembly is scaffolded into six chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 15.15 kilobases in length.
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Affiliation(s)
| | - Lewis Stevens
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | | | | | | | | | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
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5
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Skipp S, Wallace I. The genome sequence of the Grey Sedge caddis fly, Odontocerum albicorne (Scopoli, 1769). Wellcome Open Res 2024; 8:445. [PMID: 38784714 PMCID: PMC11112305 DOI: 10.12688/wellcomeopenres.20124.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2024] [Indexed: 05/25/2024] Open
Abstract
We present a genome assembly from an individual male Odontocerum albicorne (the Grey Sedge caddis fly; Arthropoda; Insecta; Trichoptera; Odontoceridae). The genome sequence is 1,287.3 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.57 kilobases in length.
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Affiliation(s)
- Sue Skipp
- Environment Agency, Rochester, England, UK
| | - Ian Wallace
- British Caddis Recording Scheme, Wirral, England, UK
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6
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Boyes D, Broad GR, Holland PWH. The genome sequence of the Oak Nycteoline moth, Nycteola revayana (Scopoli, 1772). Wellcome Open Res 2024; 9:258. [PMID: 39267994 PMCID: PMC11391193 DOI: 10.12688/wellcomeopenres.21567.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2024] [Indexed: 09/15/2024] Open
Abstract
We present a genome assembly from an individual male Nycteola revayana (the Oak Nycteoline moth; Arthropoda; Insecta; Lepidoptera; Nolidae). The genome sequence is 621.0 megabases in span. Most of the assembly is scaffolded into 26 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.25 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,235 protein-coding genes.
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Affiliation(s)
- Douglas Boyes
- UK Centre for Ecology & Hydrology, Wallingford, England, UK
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7
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Millar A, Vernes SC, Teeling EC, Mai M. The genome sequence of the Brown Long-eared bat, Plecotus auritus (Linnaeus 1758). Wellcome Open Res 2024; 9:246. [PMID: 39045151 PMCID: PMC11263909 DOI: 10.12688/wellcomeopenres.21501.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2024] [Indexed: 07/25/2024] Open
Abstract
We present a genome assembly from a female Plecotus auritus (Brown Long-eared bat; Chordata; Mammalia; Chiroptera; Vespertilionidae). The genome sequence is 2163.2 megabases in span. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.91 kilobases in length.
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Affiliation(s)
- Amanda Millar
- Independent researcher, Bat Hospital, Hurstpierpoint, England, UK
| | - Sonja C. Vernes
- School of Biology, University of St Andrews, St Andrews, Scotland, UK
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, Gelderland, The Netherlands
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Leinster, Ireland
- Wellcome Sanger Institute, Hinxton, England, UK
| | - Meike Mai
- School of Biology, University of St Andrews, St Andrews, Scotland, UK
| | - Natural History Museum Genome Acquisition Lab
- Independent researcher, Bat Hospital, Hurstpierpoint, England, UK
- School of Biology, University of St Andrews, St Andrews, Scotland, UK
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, Gelderland, The Netherlands
- School of Biology and Environmental Science, University College Dublin, Dublin, Leinster, Ireland
- Wellcome Sanger Institute, Hinxton, England, UK
| | - Darwin Tree of Life Barcoding collective
- Independent researcher, Bat Hospital, Hurstpierpoint, England, UK
- School of Biology, University of St Andrews, St Andrews, Scotland, UK
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, Gelderland, The Netherlands
- School of Biology and Environmental Science, University College Dublin, Dublin, Leinster, Ireland
- Wellcome Sanger Institute, Hinxton, England, UK
| | - Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team
- Independent researcher, Bat Hospital, Hurstpierpoint, England, UK
- School of Biology, University of St Andrews, St Andrews, Scotland, UK
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, Gelderland, The Netherlands
- School of Biology and Environmental Science, University College Dublin, Dublin, Leinster, Ireland
- Wellcome Sanger Institute, Hinxton, England, UK
| | - Wellcome Sanger Institute Scientific Operations: Sequencing Operations
- Independent researcher, Bat Hospital, Hurstpierpoint, England, UK
- School of Biology, University of St Andrews, St Andrews, Scotland, UK
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, Gelderland, The Netherlands
- School of Biology and Environmental Science, University College Dublin, Dublin, Leinster, Ireland
- Wellcome Sanger Institute, Hinxton, England, UK
| | - Wellcome Sanger Institute Tree of Life Core Informatics team
- Independent researcher, Bat Hospital, Hurstpierpoint, England, UK
- School of Biology, University of St Andrews, St Andrews, Scotland, UK
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, Gelderland, The Netherlands
- School of Biology and Environmental Science, University College Dublin, Dublin, Leinster, Ireland
- Wellcome Sanger Institute, Hinxton, England, UK
| | - Tree of Life Core Informatics collective
- Independent researcher, Bat Hospital, Hurstpierpoint, England, UK
- School of Biology, University of St Andrews, St Andrews, Scotland, UK
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, Gelderland, The Netherlands
- School of Biology and Environmental Science, University College Dublin, Dublin, Leinster, Ireland
- Wellcome Sanger Institute, Hinxton, England, UK
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8
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Schvarcz CR, Stancheva R, Turk-Kubo KA, Wilson ST, Zehr JP, Edwards KF, Steward GF, Archibald JM, Oatley G, Sinclair E, Santos C, Paulini M, Aunin E, Gettle N, Niu H, McKenna V, O’Brien R. The genome sequences of the marine diatom Epithemia pelagica strain UHM3201 (Schvarcz, Stancheva & Steward, 2022) and its nitrogen-fixing, endosymbiotic cyanobacterium. Wellcome Open Res 2024; 9:232. [PMID: 38867757 PMCID: PMC11167328 DOI: 10.12688/wellcomeopenres.21534.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2024] [Indexed: 06/14/2024] Open
Abstract
We present the genome assembly of the pennate diatom Epithemia pelagica strain UHM3201 (Ochrophyta; Bacillariophyceae; Rhopalodiales; Rhopalodiaceae) and that of its cyanobacterial endosymbiont (Chroococcales: Aphanothecaceae). The genome sequence of the diatom is 60.3 megabases in span, and the cyanobacterial genome has a length of 2.48 megabases. Most of the diatom nuclear genome assembly is scaffolded into 15 chromosomal pseudomolecules. The organelle genomes have also been assembled, with the mitochondrial genome 40.08 kilobases and the plastid genome 130.75 kilobases in length. A number of other prokaryote MAGs were also assembled.
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Affiliation(s)
- Christopher R. Schvarcz
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, Hawaii, USA
| | - Rosalina Stancheva
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
| | - Kendra A. Turk-Kubo
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, USA
| | - Samuel T. Wilson
- School of Natural & Environmental Sciences, Newcastle University, Newcastle upon Tyne, England, UK
| | - Jonathan P. Zehr
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, USA
| | - Kyle F. Edwards
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, Hawaii, USA
| | - Grieg F. Steward
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, Hawaii, USA
| | - John M. Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Graeme Oatley
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | | | - Camilla Santos
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Michael Paulini
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Eerik Aunin
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Noah Gettle
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Haoyu Niu
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | | | - Rebecca O’Brien
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory Team
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, Hawaii, USA
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, USA
- School of Natural & Environmental Sciences, Newcastle University, Newcastle upon Tyne, England, UK
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Wellcome Sanger Institute Scientific Operations: Sequencing Operations
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, Hawaii, USA
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, USA
- School of Natural & Environmental Sciences, Newcastle University, Newcastle upon Tyne, England, UK
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Wellcome Sanger Institute Tree of Life Core Informatics Team
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, Hawaii, USA
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, USA
- School of Natural & Environmental Sciences, Newcastle University, Newcastle upon Tyne, England, UK
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - EBI Aquatic Symbiosis Genomics Data Portal Team
- Department of Oceanography, Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawai'i at Manoa, Honolulu, Hawaii, USA
- Department of Environmental Science and Policy, George Mason University, Fairfax, Virginia, USA
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, USA
- School of Natural & Environmental Sciences, Newcastle University, Newcastle upon Tyne, England, UK
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
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9
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Boyes D, Crowley LM, McCulloch J, Boyes C. The genome sequence of the Elm Groundling moth, Carpatolechia fugitivella (Zeller, 1839). Wellcome Open Res 2024; 9:211. [PMID: 39139614 PMCID: PMC11320048 DOI: 10.12688/wellcomeopenres.21267.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2024] [Indexed: 08/15/2024] Open
Abstract
We present a genome assembly from an individual male Carpatolechia fugitivella (the Elm Groundling; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence is 493.1 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.26 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,721 protein coding genes.
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Affiliation(s)
- Douglas Boyes
- UK Centre for Ecology & Hydrology, Wallingford, England, UK
| | | | | | - Clare Boyes
- Independent researcher, Welshpool, Wales, UK
| | | | | | - Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team
- UK Centre for Ecology & Hydrology, Wallingford, England, UK
- University of Oxford, Oxford, England, UK
- Independent researcher, Welshpool, Wales, UK
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10
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Butlin R, Mérot C. The genome sequence of a kelp fly, Coelopa pilipes Haliday, 1838. Wellcome Open Res 2024; 9:197. [PMID: 39114490 PMCID: PMC11303939 DOI: 10.12688/wellcomeopenres.21222.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2024] [Indexed: 08/10/2024] Open
Abstract
We present a genome assembly from an individual male Coelopa pilipes (kelp fly; Arthropoda; Insecta; Diptera; Coelopidae). The genome sequence is 263.0 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.86 kilobases in length.
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Affiliation(s)
- Roger Butlin
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Sheffield, England, UK
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | - Claire Mérot
- UMR 6553 Ecobio, OSUR, CNRS, Université de Rennes, Rennes, France
| | - Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Sheffield, England, UK
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
- UMR 6553 Ecobio, OSUR, CNRS, Université de Rennes, Rennes, France
| | - Wellcome Sanger Institute Scientific Operations: Sequencing Operations
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Sheffield, England, UK
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
- UMR 6553 Ecobio, OSUR, CNRS, Université de Rennes, Rennes, France
| | - Wellcome Sanger Institute Tree of Life Core Informatics team
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Sheffield, England, UK
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
- UMR 6553 Ecobio, OSUR, CNRS, Université de Rennes, Rennes, France
| | - Tree of Life Core Informatics collective
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Sheffield, England, UK
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
- UMR 6553 Ecobio, OSUR, CNRS, Université de Rennes, Rennes, France
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11
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Rüber L, Britz R, Conway K, Bista I, McCarthy S, Wood J, Smith M, Oliver K, Howe K, Durbin R. The genome sequence of the Dracula fish, Danionella dracula (Britz, Conway & Rüber, 2009). Wellcome Open Res 2024; 9:194. [PMID: 39224769 PMCID: PMC11367074 DOI: 10.12688/wellcomeopenres.21117.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2024] [Indexed: 09/04/2024] Open
Abstract
We present a genome assembly from an individual Danionella dracula (the Dracula fish; Chordata; Actinopterygii; Cypriniformes; Danionidae; Danioninae). The genome sequence is 665.21 megabases in span. This is a scaffold-level assembly, with a scaffold N50 of 10.29 Mb.
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Affiliation(s)
- Lukas Rüber
- Naturhistorisches Museum Bern & Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Ralf Britz
- Senckenberg Naturhistorische Sammlungen Museum fur Tierkunde Dresden, Dresden, Saxony, Germany
| | - Kevin Conway
- Texas A&M University, College Station, Texas, USA
| | - Iliana Bista
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt, Germany
- Senckenberg Research Institute, Frankfurt, Germany
| | - Shane McCarthy
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Jonathan Wood
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Michelle Smith
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Karen Oliver
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Richard Durbin
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
- University of Cambridge, Cambridge, England, UK
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12
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Jentoft S, Tørresen OK, Tooming-Klunderud A, Skage M, Kollias S, Jakobsen KS. The genome sequence of the Atlantic cod, Gadus morhua (Linnaeus, 1758). Wellcome Open Res 2024; 9:189. [PMID: 39224768 PMCID: PMC11367075 DOI: 10.12688/wellcomeopenres.21122.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2024] [Indexed: 09/04/2024] Open
Abstract
We present a genome assembly from an individual male Gadus morhua (the Atlantic cod; Chordata; Actinopteri; Gadiformes; Gadidae). The genome sequence is 669.9 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl identified 23,515 protein coding genes.
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Affiliation(s)
- Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Ole K. Tørresen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Ave Tooming-Klunderud
- Norwegian Sequencing Centre, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Morten Skage
- Norwegian Sequencing Centre, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Spyridon Kollias
- Norwegian Sequencing Centre, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kjetill S. Jakobsen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | | | | | | | - Tree of Life Core Informatics collective
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
- Norwegian Sequencing Centre, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Darwin Tree of Life Consortium
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
- Norwegian Sequencing Centre, Department of Biosciences, University of Oslo, Oslo, Norway
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13
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Habtewold T, Wagah M, Tambwe MM, Moore S, Windbichler N, Christophides G, Johnson H, Heaton H, Collins J, Krasheninnikova K, Pelan SE, Pointon DLB, Sims Y, Torrance JW, Tracey A, Uliano Da Silva M, Wood JMD, von Wyschetzki K, McCarthy SA, Neafsey DE, Makunin A, Lawniczak MK, Lawniczak M. A chromosomal reference genome sequence for the malaria mosquito, Anopheles gambiae, Giles, 1902, Ifakara strain. Wellcome Open Res 2024; 8:74. [PMID: 37424773 PMCID: PMC10326452 DOI: 10.12688/wellcomeopenres.18854.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2024] [Indexed: 04/01/2024] Open
Abstract
We present a genome assembly from an individual female Anopheles gambiae (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae), Ifakara strain. The genome sequence is 264 megabases in span. Most of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.
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Affiliation(s)
- Tibebu Habtewold
- Department of Life Sciences, Imperial College London, London, UK
| | - Martin Wagah
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK
| | - Mgeni Mohamed Tambwe
- Vector Control Product Testing Unit, Ifakara Health institute, Bagamoyo, Tanzania
| | - Sarah Moore
- Vector Control Product Testing Unit, Ifakara Health institute, Bagamoyo, Tanzania
- Vector Biology Unit, Swiss Tropical and Public Health Institute, Bagamoyo, Tanzania
| | | | | | - Harriet Johnson
- Scientific Operations, Wellcome Sanger Institute, Hinxton, UK
| | | | | | | | | | | | - Ying Sims
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK
| | | | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK
| | | | | | | | - Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective
- Department of Life Sciences, Imperial College London, London, UK
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK
- Vector Control Product Testing Unit, Ifakara Health institute, Bagamoyo, Tanzania
- Vector Biology Unit, Swiss Tropical and Public Health Institute, Bagamoyo, Tanzania
- Scientific Operations, Wellcome Sanger Institute, Hinxton, UK
- CSSE, Auburn University, Auburn, Alabama, USA
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | - Daniel E. Neafsey
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Alex Makunin
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK
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14
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Adkins P, Mrowicki R, Harley J, Mieszkowska N, Ferreira JGRN. The genome sequence of the grey top shell, Steromphala cineraria (Linnaeus, 1758). Wellcome Open Res 2024; 7:44. [PMID: 38715953 PMCID: PMC11074690 DOI: 10.12688/wellcomeopenres.17677.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2024] [Indexed: 05/12/2024] Open
Abstract
We present a genome assembly from an individual Steromphala cineraria (the grey topshell; Mollusca; Gastropoda; Trochida; Trochidae). The genome sequence is 1,270 megabases in span. Most of the assembly (99.23%) is scaffolded into 18 chromosomal pseudomolecules.
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Affiliation(s)
| | - Robert Mrowicki
- Marine Biological Association, Plymouth, Devon, UK
- Natural History Museum, London, UK
| | | | | | - João G. R. N. Ferreira
- Bio Bureau Biotechnology, Rio de Janeiro, Brazil
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Marine Biological Association Genome Acquisition Lab
- Marine Biological Association, Plymouth, Devon, UK
- Natural History Museum, London, UK
- Bio Bureau Biotechnology, Rio de Janeiro, Brazil
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Darwin Tree of Life Barcoding collective
- Marine Biological Association, Plymouth, Devon, UK
- Natural History Museum, London, UK
- Bio Bureau Biotechnology, Rio de Janeiro, Brazil
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Wellcome Sanger Institute Tree of Life programme
- Marine Biological Association, Plymouth, Devon, UK
- Natural History Museum, London, UK
- Bio Bureau Biotechnology, Rio de Janeiro, Brazil
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective
- Marine Biological Association, Plymouth, Devon, UK
- Natural History Museum, London, UK
- Bio Bureau Biotechnology, Rio de Janeiro, Brazil
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Tree of Life Core Informatics collective
- Marine Biological Association, Plymouth, Devon, UK
- Natural History Museum, London, UK
- Bio Bureau Biotechnology, Rio de Janeiro, Brazil
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
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15
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Crowley LM. The genome sequence of the devil's coach horse beetle, Ocypus olens (Müller, 1764). Wellcome Open Res 2024; 6:293. [PMID: 35572471 PMCID: PMC9069170 DOI: 10.12688/wellcomeopenres.17342.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2024] [Indexed: 03/26/2024] Open
Abstract
We present a genome assembly from an individual female Ocypus olens (the devil's coach horse; Arthropoda; Insecta; Coleoptera; Staphylinidae). The genome sequence is 1,084 megabases in span. The majority (98.81%) of the assembly is scaffolded into 20 chromosomal pseudomolecules, with the X sex chromosome assembled.
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16
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Christenhusz MJM, Leitch AR, Leitch IJ, Fay MF. The genome sequence of rosebay willowherb Chamaenerion angustifolium (L.) Scop., 1771 (syn. Epilobium angustifolium L., 1753) (Onagraceae). Wellcome Open Res 2024; 9:163. [PMID: 38903872 PMCID: PMC11187524 DOI: 10.12688/wellcomeopenres.21163.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2024] [Indexed: 06/22/2024] Open
Abstract
We present a genome assembly from an individual Chamaenerion angustifolium (fireweed; Tracheophyta; Magnoliopsida; Myrtales; Onagraceae). The genome sequence is 655.9 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 495.18 kilobases and 160.41 kilobases in length, respectively.
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Affiliation(s)
| | | | | | | | | | - Plant Genome Sizing collective
- Royal Botanic Gardens Kew, Richmond, England, UK
- Curtin University, Perth, Western Australia, Australia
- Queen Mary University of London, London, England, UK
| | | | - Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team
- Royal Botanic Gardens Kew, Richmond, England, UK
- Curtin University, Perth, Western Australia, Australia
- Queen Mary University of London, London, England, UK
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17
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Li R, Li J, Lopez JV, Oatley G, Clayton-Lucey IA, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R. The genome sequence of the giant clam, Tridacna gigas (Linnaeus, 1758). Wellcome Open Res 2024; 9:145. [PMID: 38800516 PMCID: PMC11116938 DOI: 10.12688/wellcomeopenres.21136.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2024] [Indexed: 05/29/2024] Open
Abstract
We present a chromosomal-level genome assembly from an individual Tridacna gigas (the giant clam; Mollusca; Bivalvia; Veneroida; Cardiidae). The genome sequence is 1,175.9 megabases in span. Most of the assembly is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 25.34 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,177 protein coding genes.
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Affiliation(s)
- Ruiqi Li
- Ecology & Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Jingchun Li
- Ecology & Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, USA
- Museum of Natural History, University of Colorado Boulder, Boulder, Colorado, USA
| | - Jose Victor Lopez
- Department of Biological Sciences, Nova Southeastern University, Dania Beach, Florida, USA
| | - Graeme Oatley
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | | | | | - Eerik Aunin
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Noah Gettle
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Camilla Santos
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Michael Paulini
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Haoyu Niu
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | | | - Rebecca O’Brien
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory Team
- Ecology & Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, USA
- Museum of Natural History, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Biological Sciences, Nova Southeastern University, Dania Beach, Florida, USA
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Wellcome Sanger Institute Scientific Operations: Sequencing Operations
- Ecology & Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, USA
- Museum of Natural History, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Biological Sciences, Nova Southeastern University, Dania Beach, Florida, USA
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Wellcome Sanger Institute Tree of Life Core Informatics Team
- Ecology & Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, USA
- Museum of Natural History, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Biological Sciences, Nova Southeastern University, Dania Beach, Florida, USA
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - EBI Aquatic Symbiosis Genomics Data Portal Team
- Ecology & Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, USA
- Museum of Natural History, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Biological Sciences, Nova Southeastern University, Dania Beach, Florida, USA
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
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18
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Brittain R, Adkins P, Mrowicki RJ, Harley J, Modepali V. The genome sequence of the thickback sole, Microchirus variegatus (Donovan, 1808). Wellcome Open Res 2024; 9:152. [PMID: 38938521 PMCID: PMC11208857 DOI: 10.12688/wellcomeopenres.21139.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2024] [Indexed: 06/29/2024] Open
Abstract
We present a genome assembly from an individual female Microchirus variegatus (the thickback sole; Chordata; Actinopteri; Pleuronectiformes; Soleidae). The genome sequence is 724.7 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.42 kilobases in length.
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Affiliation(s)
| | - Patrick Adkins
- The Marine Biological Association, Plymouth, England, UK
| | | | - Joanna Harley
- The Marine Biological Association, Plymouth, England, UK
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19
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Li R, Li J, Lemer S, Lopez JV, Oatley G, Clayton-Lucey IA, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R. The genome sequence of a heart cockle, Fragum fragum (Linnaeus, 1758). Wellcome Open Res 2024; 9:129. [PMID: 38989474 PMCID: PMC11234083 DOI: 10.12688/wellcomeopenres.21134.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2024] [Indexed: 07/12/2024] Open
Abstract
We present a genome assembly from an individual specimen of Fragum fragum (a heart cockle; Mollusca; Bivalvia; Veneroida; Cardiidae). The genome sequence is 1,153.1 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 22.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,262 protein coding genes.
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Affiliation(s)
- Ruiqi Li
- Ecology & Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Jingchun Li
- Ecology & Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, USA
- Museum of Natural History, University of Colorado Boulder, Boulder, Colorado, USA
| | - Sarah Lemer
- University of Guam Marine Lab, Mangilao, Guam
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Hamburg, Germany
| | - Jose Victor Lopez
- Department of Biological Sciences, Nova Southeastern University, Dania Beach, Florida, USA
| | - Graeme Oatley
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | | | | | - Eerik Aunin
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Noah Gettle
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Camilla Santos
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Michael Paulini
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Haoyu Niu
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | | | - Rebecca O’Brien
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory Team
- Ecology & Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, USA
- Museum of Natural History, University of Colorado Boulder, Boulder, Colorado, USA
- University of Guam Marine Lab, Mangilao, Guam
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Hamburg, Germany
- Department of Biological Sciences, Nova Southeastern University, Dania Beach, Florida, USA
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Wellcome Sanger Institute Scientific Operations: Sequencing Operations
- Ecology & Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, USA
- Museum of Natural History, University of Colorado Boulder, Boulder, Colorado, USA
- University of Guam Marine Lab, Mangilao, Guam
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Hamburg, Germany
- Department of Biological Sciences, Nova Southeastern University, Dania Beach, Florida, USA
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Wellcome Sanger Institute Tree of Life Core Informatics Team
- Ecology & Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, USA
- Museum of Natural History, University of Colorado Boulder, Boulder, Colorado, USA
- University of Guam Marine Lab, Mangilao, Guam
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Hamburg, Germany
- Department of Biological Sciences, Nova Southeastern University, Dania Beach, Florida, USA
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - EBI Aquatic Symbiosis Genomics Data Portal Team
- Ecology & Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, USA
- Museum of Natural History, University of Colorado Boulder, Boulder, Colorado, USA
- University of Guam Marine Lab, Mangilao, Guam
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Hamburg, Germany
- Department of Biological Sciences, Nova Southeastern University, Dania Beach, Florida, USA
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
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20
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Christenhusz MJM. The genome sequence of field madder, Sherardia arvensis L., 1753 (Rubiaceae). Wellcome Open Res 2024; 9:126. [PMID: 39139616 PMCID: PMC11320180 DOI: 10.12688/wellcomeopenres.21027.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2024] [Indexed: 08/15/2024] Open
Abstract
We present a genome assembly from an individual Sherardia arvensis (field madder; Tracheophyta; Magnoliopsida; Gentianales; Rubiaceae). The genome sequence is 440.9 megabases in span. Most of the assembly is scaffolded into 11 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 203.98 kilobases and 152.73 kilobases in length, respectively.
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21
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Christenhusz MJM, Hollingsworth PM. The genome sequence of common knotgrass, Polygonum aviculare L. (Polygonaceae). Wellcome Open Res 2024; 9:112. [PMID: 39101050 PMCID: PMC11294812 DOI: 10.12688/wellcomeopenres.21001.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2024] [Indexed: 08/06/2024] Open
Abstract
We present a genome assembly from an individual Polygonum aviculare (common knotgrass; Eudicot; Magnoliopsida; Caryophyllales; Polygonaceae). The genome sequence is 351.6 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 333.39 kilobases and 163.28 kilobases in length, respectively.
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Affiliation(s)
| | | | | | - Plant Genome Sizing collective
- Royal Botanic Gardens Kew, Richmond, England, UK
- Curtin University, Perth, Western Australia, Australia
- Royal Botanic Garden Edinburgh, Edinburgh, Scotland, UK
| | | | - Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team
- Royal Botanic Gardens Kew, Richmond, England, UK
- Curtin University, Perth, Western Australia, Australia
- Royal Botanic Garden Edinburgh, Edinburgh, Scotland, UK
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22
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Goodwin ZA, Bell D, Hart ML, Hollingsworth PM. The genome sequence of great wood-rush, Luzula sylvatica (Huds) Gaudin. Wellcome Open Res 2024; 9:124. [PMID: 39246514 PMCID: PMC11380069 DOI: 10.12688/wellcomeopenres.20997.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2024] [Indexed: 09/10/2024] Open
Abstract
We present a genome assembly from an individual specimen of Luzula sylvatica (great wood-rush; Tracheophyta; Magnoliopsida; Poales; Juncaceae). The genome sequence is 444.5 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 633.36 kilobases and 201.32 kilobases in length, respectively.
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Affiliation(s)
- Zoë A Goodwin
- Royal Botanic Garden Edinburgh, Edinburgh, Scotland, UK
| | - David Bell
- Royal Botanic Garden Edinburgh, Edinburgh, Scotland, UK
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23
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Henriques S. The genome sequence of the Black Lace-weaver spider, Amaurobius ferox (Walckenaer, 1830). Wellcome Open Res 2024; 9:105. [PMID: 39015616 PMCID: PMC11249506 DOI: 10.12688/wellcomeopenres.21080.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2024] [Indexed: 07/18/2024] Open
Abstract
We present a genome assembly from an individual female Amaurobius ferox (the Black Lace-weaver; Arthropoda; Arachnida; Araneae; Amaurobiidae). The genome sequence is 3,564.8 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules, including the X 1, X 2 and X 3 sex chromosomes. The mitochondrial genome has also been assembled and is 14.24 kilobases in length.
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24
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Bukhman YV, Morin PA, Meyer S, Chu LF, Jacobsen JK, Antosiewicz-Bourget J, Mamott D, Gonzales M, Argus C, Bolin J, Berres ME, Fedrigo O, Steill J, Swanson SA, Jiang P, Rhie A, Formenti G, Phillippy AM, Harris RS, Wood JMD, Howe K, Kirilenko BM, Munegowda C, Hiller M, Jain A, Kihara D, Johnston JS, Ionkov A, Raja K, Toh H, Lang A, Wolf M, Jarvis ED, Thomson JA, Chaisson MJP, Stewart R. A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography. Mol Biol Evol 2024; 41:msae036. [PMID: 38376487 PMCID: PMC10919930 DOI: 10.1093/molbev/msae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 02/21/2024] Open
Abstract
The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance to cancer. To further this and other blue whale-related research, we report a reference-quality, long-read-based genome assembly of this fascinating species. We assembled the genome from PacBio long reads and utilized Illumina/10×, optical maps, and Hi-C data for scaffolding, polishing, and manual curation. We also provided long read RNA-seq data to facilitate the annotation of the assembly by NCBI and Ensembl. Additionally, we annotated both haplotypes using TOGA and measured the genome size by flow cytometry. We then compared the blue whale genome with other cetaceans and artiodactyls, including vaquita (Phocoena sinus), the world's smallest cetacean, to investigate blue whale's unique biological traits. We found a dramatic amplification of several genes in the blue whale genome resulting from a recent burst in segmental duplications, though the possible connection between this amplification and giant body size requires further study. We also discovered sites in the insulin-like growth factor-1 gene correlated with body size in cetaceans. Finally, using our assembly to examine the heterozygosity and historical demography of Pacific and Atlantic blue whale populations, we found that the genomes of both populations are highly heterozygous and that their genetic isolation dates to the last interglacial period. Taken together, these results indicate how a high-quality, annotated blue whale genome will serve as an important resource for biology, evolution, and conservation research.
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Affiliation(s)
- Yury V Bukhman
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration (NOAA), La Jolla, CA 92037, USA
| | - Susanne Meyer
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Li-Fang Chu
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Canada
| | | | | | - Daniel Mamott
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Maylie Gonzales
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Cara Argus
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Jennifer Bolin
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Mark E Berres
- University of Wisconsin Biotechnology Center, Bioinformatics Resource Center, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Olivier Fedrigo
- Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA
| | - John Steill
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Scott A Swanson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Peng Jiang
- Center for Gene Regulation in Health and Disease (GRHD), Cleveland State University, Cleveland, OH, USA
- Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH, USA
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Arang Rhie
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Giulio Formenti
- Laboratory of Neurogenetics of Language, The Rockefeller University/HHMI, New York, NY 10065, USA
| | - Adam M Phillippy
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Robert S Harris
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | | | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Bogdan M Kirilenko
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Chetan Munegowda
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Aashish Jain
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Alexander Ionkov
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Kalpana Raja
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Huishi Toh
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Aimee Lang
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration (NOAA), La Jolla, CA 92037, USA
| | - Magnus Wolf
- Institute for Evolution and Biodiversity (IEB), University of Muenster, 48149, Muenster, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
| | - Erich D Jarvis
- Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University/HHMI, New York, NY 10065, USA
| | - James A Thomson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53726, USA
| | - Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA
| | - Ron Stewart
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
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25
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Crowley LM, Falk S. The genome sequence of the wood-carving leafcutter bee, Megachile ligniseca (Kirby, 1802). Wellcome Open Res 2024; 9:103. [PMID: 38903870 PMCID: PMC11187525 DOI: 10.12688/wellcomeopenres.21002.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2024] [Indexed: 06/22/2024] Open
Abstract
We present a genome assembly from an individual female Megachile ligniseca (the wood-carving leafcutter bee; Arthropoda; Insecta; Hymenoptera; Megachilidae). The genome sequence is 290.0 megabases in span. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 23.71 kilobases in length. Gene annotation of this assembly on Ensembl 11,722 protein coding genes.
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Affiliation(s)
| | - Steven Falk
- Independent researcher, Kenilworth, England, UK
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26
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Christenhusz MJM, Pannell JR, Twyford AD. The genome sequence of the Annual Mercury, Mercurialis annua L., 1753 (Euphorbiaceae). Wellcome Open Res 2024; 9:102. [PMID: 38854694 PMCID: PMC11157195 DOI: 10.12688/wellcomeopenres.21004.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2024] [Indexed: 06/11/2024] Open
Abstract
We present a genome assembly from a diploid female Mercurialis annua (the Annual Mercury; Tracheophyta; Magnoliopsida; Malpighiales; Euphorbiaceae). The genome sequence is 453.2 megabases in span. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules, including the X chromosome. The organelle genomes have also been assembled, and the mitochondrial genome is 435.28 kilobases in length, while the plastid genome is 169.65 kilobases in length.
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Affiliation(s)
| | - John R. Pannell
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Alex D. Twyford
- The University of Edinburgh, Edinburgh, Scotland, UK
- Royal Botanic Garden Edinburgh, Edinburgh, Scotland, UK
| | - Royal Botanic Gardens Kew Genome Acquisition Lab
- Royal Botanic Gardens Kew, Richmond, England, UK
- Curtin University, Perth, Western Australia, Australia
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- The University of Edinburgh, Edinburgh, Scotland, UK
- Royal Botanic Garden Edinburgh, Edinburgh, Scotland, UK
| | - Plant Genome Sizing collective
- Royal Botanic Gardens Kew, Richmond, England, UK
- Curtin University, Perth, Western Australia, Australia
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- The University of Edinburgh, Edinburgh, Scotland, UK
- Royal Botanic Garden Edinburgh, Edinburgh, Scotland, UK
| | - Darwin Tree of Life Barcoding collective
- Royal Botanic Gardens Kew, Richmond, England, UK
- Curtin University, Perth, Western Australia, Australia
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- The University of Edinburgh, Edinburgh, Scotland, UK
- Royal Botanic Garden Edinburgh, Edinburgh, Scotland, UK
| | - Wellcome Sanger Institute Tree of Life programme
- Royal Botanic Gardens Kew, Richmond, England, UK
- Curtin University, Perth, Western Australia, Australia
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- The University of Edinburgh, Edinburgh, Scotland, UK
- Royal Botanic Garden Edinburgh, Edinburgh, Scotland, UK
| | - Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective
- Royal Botanic Gardens Kew, Richmond, England, UK
- Curtin University, Perth, Western Australia, Australia
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- The University of Edinburgh, Edinburgh, Scotland, UK
- Royal Botanic Garden Edinburgh, Edinburgh, Scotland, UK
| | - Tree of Life Core Informatics collective
- Royal Botanic Gardens Kew, Richmond, England, UK
- Curtin University, Perth, Western Australia, Australia
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- The University of Edinburgh, Edinburgh, Scotland, UK
- Royal Botanic Garden Edinburgh, Edinburgh, Scotland, UK
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27
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Falk S, Crowley LM. The genome sequence of the Mournful Wasp, Pemphredon lugubris (Fabricius, 1793). Wellcome Open Res 2024; 9:93. [PMID: 39221445 PMCID: PMC11364974 DOI: 10.12688/wellcomeopenres.20948.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2024] [Indexed: 09/04/2024] Open
Abstract
We present a genome assembly from an individual male Pemphredon lugubris (the Mournful Wasp; Arthropoda; Insecta; Hymenoptera; Crabronidae). The genome sequence is 328.1 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.88 kilobases in length. Gene annotation of this assembly on Ensembl identified 10,335 protein coding genes.
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Affiliation(s)
- Steven Falk
- Independent researcher, Kenilworth, England, UK
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28
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Falk S, Grzywacz A. The genome sequence of a muscid fly, Hydrotaea cyrtoneurina (Zetterstedt, 1845). Wellcome Open Res 2024; 9:60. [PMID: 38725453 PMCID: PMC11079579 DOI: 10.12688/wellcomeopenres.20638.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2023] [Indexed: 05/12/2024] Open
Abstract
We present a genome assembly from an individual female Hydrotaea cyrtoneurina (muscid fly; Arthropoda; Insecta; Diptera; Muscidae). The genome sequence is 575.2 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.6 kilobases in length.
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Affiliation(s)
- Steven Falk
- Independent researcher, Wallingford, England, UK
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29
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Telfer MG, Phillips D. The genome sequence of a metallic wood-boring beetle, Agrilus cyanescens (Ratzeburg, 1837). Wellcome Open Res 2024; 9:46. [PMID: 38779150 PMCID: PMC11109541 DOI: 10.12688/wellcomeopenres.20877.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2024] [Indexed: 05/25/2024] Open
Abstract
We present a genome assembly from an individual female Agrilus cyanescens (metallic wood-boring beetle; Arthropoda; Insecta; Coleoptera; Buprestidae). The genome sequence is 292.3 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 15.91 kilobases in length.
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30
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Crowley LM. The genome sequence of the Lobe-spurred Furrow Bee, Lasioglossum pauxillum (Schenck, 1853). Wellcome Open Res 2024; 9:86. [PMID: 39176035 PMCID: PMC11339594 DOI: 10.12688/wellcomeopenres.20950.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2024] [Indexed: 08/24/2024] Open
Abstract
We present a genome assembly from an individual female Lasioglossum pauxillum (the Lobe-spurred Furrow Bee; Arthropoda; Insecta; Hymenoptera; Halictidae). The genome sequence is 432.0 megabases in span. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 27.71 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,353 protein coding genes.
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31
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Sivell D. The genome sequence of a barkfly, Mesopsocus fuscifrons Meinander, 1966. Wellcome Open Res 2024; 9:72. [PMID: 39114494 PMCID: PMC11303940 DOI: 10.12688/wellcomeopenres.20641.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2023] [Indexed: 08/10/2024] Open
Abstract
We present a genome assembly from an individual female Mesopsocus fuscifrons (barkfly; Arthropoda; Insecta; Psocodea; Mesopsocidae). The genome sequence is 184.3 megabases in span. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 20.13 kilobases in length.
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32
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Hawkins SJ, Mieszkowska N, Mrowicki R. The genome sequence of the black-footed limpet, Patella depressa (Pennant, 1777). Wellcome Open Res 2024; 9:47. [PMID: 38779153 PMCID: PMC11109591 DOI: 10.12688/wellcomeopenres.20687.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2023] [Indexed: 05/25/2024] Open
Abstract
We present a genome assembly from an individual Patella depressa (the black-footed limpet; Mollusca; Gastropoda; Patellogastropoda; Patellidae). The genome sequence is 683.7 megabases in span. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl identified 20,502 protein coding genes.
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Affiliation(s)
| | | | - Rob Mrowicki
- The Marine Biological Association, Plymouth, England, UK
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33
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Crowley LM, Baker E, Holland PWH. The genome sequence of the Emperor moth, Saturnia pavonia (Linnaeus, 1758). Wellcome Open Res 2024; 9:48. [PMID: 38764484 PMCID: PMC11101921 DOI: 10.12688/wellcomeopenres.20652.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2023] [Indexed: 05/21/2024] Open
Abstract
We present a genome assembly from an individual male Saturnia pavonia (the Emperor moth; Arthropoda; Insecta; Lepidoptera; Saturniidae). The genome sequence is 489.9 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.29 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,903 protein coding genes.
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34
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Bukhman YV, Meyer S, Chu LF, Abueg L, Antosiewicz-Bourget J, Balacco J, Brecht M, Dinatale E, Fedrigo O, Formenti G, Fungtammasan A, Giri SJ, Hiller M, Howe K, Kihara D, Mamott D, Mountcastle J, Pelan S, Rabbani K, Sims Y, Tracey A, Wood JMD, Jarvis ED, Thomson JA, Chaisson MJP, Stewart R. Chromosome level genome assembly of the Etruscan shrew Suncus etruscus. Sci Data 2024; 11:176. [PMID: 38326333 PMCID: PMC10850158 DOI: 10.1038/s41597-024-03011-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 01/26/2024] [Indexed: 02/09/2024] Open
Abstract
Suncus etruscus is one of the world's smallest mammals, with an average body mass of about 2 grams. The Etruscan shrew's small body is accompanied by a very high energy demand and numerous metabolic adaptations. Here we report a chromosome-level genome assembly using PacBio long read sequencing, 10X Genomics linked short reads, optical mapping, and Hi-C linked reads. The assembly is partially phased, with the 2.472 Gbp primary pseudohaplotype and 1.515 Gbp alternate. We manually curated the primary assembly and identified 22 chromosomes, including X and Y sex chromosomes. The NCBI genome annotation pipeline identified 39,091 genes, 19,819 of them protein-coding. We also identified segmental duplications, inferred GO term annotations, and computed orthologs of human and mouse genes. This reference-quality genome will be an important resource for research on mammalian development, metabolism, and body size control.
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Affiliation(s)
- Yury V Bukhman
- Regenerative Biology, Morgridge Institute for Research, 330 N. Orchard St., Madison, WI, 53715, USA.
| | - Susanne Meyer
- Neuroscience Research Institute, University of California - Santa Barbara, 494 UCEN Rd, Isla Vista, CA, 93117, USA
| | - Li-Fang Chu
- Department of Comparative Biology and Experimental Medicine, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada
| | - Linelle Abueg
- Vertebrate Genome Lab, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | | | - Jennifer Balacco
- Vertebrate Genome Lab, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Michael Brecht
- BCCN/Humboldt University Berlin, Philippstr, 13 House 6, 10115, Berlin, Germany
| | - Erica Dinatale
- Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Olivier Fedrigo
- Vertebrate Genome Lab, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Giulio Formenti
- Laboratory of Neurogenetics of Language, The Rockefeller University/HHMI, 1230 York Avenue, New York, NY, 10065, USA
| | | | - Swagarika Jaharlal Giri
- Department of Computer Science, Purdue University, 249 S. Martin Jischke Dr, West Lafayette, IN, 47907, USA
| | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt, Germany
- Senckenberg Research Institute, Senckenberganlage 25, 60325, Frankfurt, Germany
- Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, 249 S. Martin Jischke Dr, West Lafayette, IN, 47907, USA
- Department of Biological Sciences, Purdue University, 249 S. Martin Jischke Dr., West Lafayette, IN, 47907, USA
| | - Daniel Mamott
- Regenerative Biology, Morgridge Institute for Research, 330 N. Orchard St., Madison, WI, 53715, USA
| | - Jacquelyn Mountcastle
- Vertebrate Genome Lab, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Sarah Pelan
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Keon Rabbani
- Department of Quantitative and Computational Biology, University of Southern California, 1050 Childs Way RRI 408, Los Angeles, CA, 90089, USA
| | - Ying Sims
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | | | - Erich D Jarvis
- Vertebrate Genome Lab, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University/HHMI, 1230 York Avenue, New York, NY, 10065, USA
| | - James A Thomson
- Regenerative Biology, Morgridge Institute for Research, 330 N. Orchard St., Madison, WI, 53715, USA
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53726, USA
| | - Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, 1050 Childs Way RRI 408, Los Angeles, CA, 90089, USA
| | - Ron Stewart
- Regenerative Biology, Morgridge Institute for Research, 330 N. Orchard St., Madison, WI, 53715, USA
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35
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Christenhusz MJM, Fay MF. The genome sequence of the English holly, Ilex aquifolium L. (Aquifoliaceae). Wellcome Open Res 2024; 9:1. [PMID: 38779152 PMCID: PMC11109700 DOI: 10.12688/wellcomeopenres.20748.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2023] [Indexed: 05/25/2024] Open
Abstract
We present a genome assembly from an individual Ilex aquifolium (the English holly; Eudicot; Magnoliopsida; Aquifoliales; Aquifoliaceae). The genome sequence is 800.0 megabases in span. Most of the assembly is scaffolded into 20 chromosomal pseudomolecules. The assembled mitochondrial and plastid genomes have lengths of 538.43 kilobases and 157.52 kilobases in length, respectively.
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36
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Boyes D, Blaxter ML. The genome sequence of the Tipped Oak Case-bearer, Coleophora flavipennella (Duponchel 1843). Wellcome Open Res 2024; 9:3. [PMID: 38686023 PMCID: PMC11056683 DOI: 10.12688/wellcomeopenres.19917.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2023] [Indexed: 05/02/2024] Open
Abstract
We present a genome assembly from an individual female Coleophora flavipennella (the Tipped Oak Case-bearer; Arthropoda; Insecta; Lepidoptera; Coleophoridae). The genome sequence is 989.3 megabases in span. Most of the assembly is scaffolded into 57 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.77 kilobases in length.
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Affiliation(s)
- Douglas Boyes
- UK Centre for Ecology & Hydrology, Wallingford, England, UK
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37
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Stevens L, Kieninger M, Chan B, Wood JMD, Gonzalez de la Rosa P, Allen J, Blaxter M. The genome of Litomosoides sigmodontis illuminates the origins of Y chromosomes in filarial nematodes. PLoS Genet 2024; 20:e1011116. [PMID: 38227589 PMCID: PMC10817185 DOI: 10.1371/journal.pgen.1011116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/26/2024] [Accepted: 12/26/2023] [Indexed: 01/18/2024] Open
Abstract
Heteromorphic sex chromosomes are usually thought to have originated from a pair of autosomes that acquired a sex-determining locus and subsequently stopped recombining, leading to degeneration of the sex-limited chromosome. The majority of nematode species lack heteromorphic sex chromosomes and determine sex using an X-chromosome counting mechanism, with males being hemizygous for one or more X chromosomes (XX/X0). Some filarial nematode species, including important parasites of humans, have heteromorphic XX/XY karyotypes. It has been assumed that sex is determined by a Y-linked locus in these species. However, karyotypic analyses suggested that filarial Y chromosomes are derived from the unfused homologue of an autosome involved in an X-autosome fusion event. Here, we generated a chromosome-level reference genome for Litomosoides sigmodontis, a filarial nematode with the ancestral filarial karyotype and sex determination mechanism (XX/X0). By mapping the assembled chromosomes to the rhabditid nematode ancestral linkage (or Nigon) elements, we infer that the ancestral filarial X chromosome was the product of a fusion between NigonX (the ancestrally X-linked element) and NigonD (ancestrally autosomal). In the two filarial lineages with XY systems, there have been two independent X-autosome chromosome fusion events involving different autosomal Nigon elements. In both lineages, the region shared by the neo-X and neo-Y chromosomes is within the ancestrally autosomal portion of the X, confirming that the filarial Y chromosomes are derived from the unfused homologue of the autosome. Sex determination in XY filarial nematodes therefore likely continues to operate via the ancestral X-chromosome counting mechanism, rather than via a Y-linked sex-determining locus.
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Affiliation(s)
- Lewis Stevens
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
| | | | - Brian Chan
- Lydia Becker Institute of Immunology and Inflammation, Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, University of Manchester, Manchester, United Kingdom
| | | | | | - Judith Allen
- Lydia Becker Institute of Immunology and Inflammation, Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine & Health, University of Manchester, Manchester, United Kingdom
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge, United Kingdom
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38
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Crowley LM, Woodcock KJ. The genome sequence of the white-footed hoverfly, Platycheirus albimanus (Fabricius, 1781). Wellcome Open Res 2023; 8:572. [PMID: 38836070 PMCID: PMC11148528 DOI: 10.12688/wellcomeopenres.20494.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2023] [Indexed: 06/06/2024] Open
Abstract
We present a genome assembly from an individual female Platycheirus albimanus (the white-footed hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 677.8 megabases in span. Most of the assembly is scaffolded into 4 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 18.17 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,568 protein coding genes.
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Affiliation(s)
- Liam M Crowley
- Department of Biology, University of Oxford, Oxford, England, UK
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39
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Adkins P, Mrowicki R. The genome sequence of the European flat oyster, Ostrea edulis (Linnaeus, 1758). Wellcome Open Res 2023; 8:556. [PMID: 38558925 PMCID: PMC10979132 DOI: 10.12688/wellcomeopenres.19916.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2023] [Indexed: 04/04/2024] Open
Abstract
We present a genome assembly from an individual Ostrea edulis (the European flat oyster; Mollusca; Bivalvia; Ostreida; Ostreidae). The genome sequence is 894.8 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.35 kilobases in length.
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Affiliation(s)
- Patrick Adkins
- The Marine Biological Association, Plymouth, England, UK
| | - Rob Mrowicki
- The Marine Biological Association, Plymouth, England, UK
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40
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Crowley LM. The genome sequence of a digger wasp, Ectemnius lituratus (Panzer,1805). Wellcome Open Res 2023; 8:552. [PMID: 39188773 PMCID: PMC11345589 DOI: 10.12688/wellcomeopenres.20337.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2023] [Indexed: 08/28/2024] Open
Abstract
We present a genome assembly from an individual female Ectemnius lituratus (a digger wasp; Arthropoda; Insecta; Hymenoptera; Crabronidae). The genome sequence is 235.1 megabases in span. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 29.67 kilobases in length. Gene annotation of this assembly on Ensembl identified 9,724 protein coding genes.
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Affiliation(s)
- Liam M. Crowley
- Department of Biology, University of Oxford, Oxford, England, UK
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41
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Stevens L, Martínez-Ugalde I, King E, Wagah M, Absolon D, Bancroft R, Gonzalez de la Rosa P, Hall JL, Kieninger M, Kloch A, Pelan S, Robertson E, Pedersen AB, Abreu-Goodger C, Buck AH, Blaxter M. Ancient diversity in host-parasite interaction genes in a model parasitic nematode. Nat Commun 2023; 14:7776. [PMID: 38012132 PMCID: PMC10682056 DOI: 10.1038/s41467-023-43556-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023] Open
Abstract
Host-parasite interactions exert strong selection pressures on the genomes of both host and parasite. These interactions can lead to negative frequency-dependent selection, a form of balancing selection that is hypothesised to explain the high levels of polymorphism seen in many host immune and parasite antigen loci. Here, we sequence the genomes of several individuals of Heligmosomoides bakeri, a model parasite of house mice, and Heligmosomoides polygyrus, a closely related parasite of wood mice. Although H. bakeri is commonly referred to as H. polygyrus in the literature, their genomes show levels of divergence that are consistent with at least a million years of independent evolution. The genomes of both species contain hyper-divergent haplotypes that are enriched for proteins that interact with the host immune response. Many of these haplotypes originated prior to the divergence between H. bakeri and H. polygyrus, suggesting that they have been maintained by long-term balancing selection. Together, our results suggest that the selection pressures exerted by the host immune response have played a key role in shaping patterns of genetic diversity in the genomes of parasitic nematodes.
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Affiliation(s)
- Lewis Stevens
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK.
| | - Isaac Martínez-Ugalde
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Erna King
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK
| | - Martin Wagah
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK
| | | | - Rowan Bancroft
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Jessica L Hall
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | | | - Sarah Pelan
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK
| | - Elaine Robertson
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Amy B Pedersen
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Cei Abreu-Goodger
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Amy H Buck
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK.
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42
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Bishop J, Wood C, Mrowicki R, Harley J. The genome sequence of the light-bulb sea squirt, Clavelina lepadiformis (Müller, 1776). Wellcome Open Res 2023; 8:543. [PMID: 38404634 PMCID: PMC10884593 DOI: 10.12688/wellcomeopenres.20417.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2023] [Indexed: 02/27/2024] Open
Abstract
We present a genome assembly from an individual Clavelina lepadiformis (the light-bulb sea squirt; Chordata; Ascidiacea; Aplousobranchia; Clavelinidae). The genome sequence is 210.1 megabases in span. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 14.48 kilobases in length.
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Affiliation(s)
- John Bishop
- The Marine Biological Association, Plymouth, England, UK
| | - Christine Wood
- The Marine Biological Association, Plymouth, England, UK
| | - Rob Mrowicki
- The Marine Biological Association, Plymouth, England, UK
| | - Joanna Harley
- The Marine Biological Association, Plymouth, England, UK
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43
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Barclay MVL, Geiser M, Vassiliades D, Bayfield Farrell W, Cristóvão J. The genome sequence of a ground beetle, Pterostichus niger (Schaller, 1783). Wellcome Open Res 2023; 8:544. [PMID: 38434746 PMCID: PMC10907878 DOI: 10.12688/wellcomeopenres.20418.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2023] [Indexed: 03/05/2024] Open
Abstract
We present a genome assembly from an individual male Pterostichus niger (a ground beetle; Arthropoda; Insecta; Coleoptera; Carabidae). The genome sequence is 674.1 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.16 kilobases in length.
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Affiliation(s)
| | - Michael Geiser
- The Marine Biological Association, Plymouth, England, UK
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44
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Rice ES, Alberdi A, Alfieri J, Athrey G, Balacco JR, Bardou P, Blackmon H, Charles M, Cheng HH, Fedrigo O, Fiddaman SR, Formenti G, Frantz LAF, Gilbert MTP, Hearn CJ, Jarvis ED, Klopp C, Marcos S, Mason AS, Velez-Irizarry D, Xu L, Warren WC. A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants. BMC Biol 2023; 21:267. [PMID: 37993882 PMCID: PMC10664547 DOI: 10.1186/s12915-023-01758-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/02/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND The red junglefowl, the wild outgroup of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, many of which have accumulated molecular changes due to drift and selection. While reference-based resequencing is well-suited to cataloging simple variants such as single-nucleotide changes and short insertions and deletions, it is mostly inadequate to discover more complex structural variation in the genome. METHODS We present a pangenome for the domestic chicken consisting of thirty assemblies of chickens from different breeds and research lines. RESULTS We demonstrate how this pangenome can be used to catalog structural variants present in modern breeds and untangle complex nested variation. We show that alignment of short reads from 100 diverse wild and domestic chickens to this pangenome reduces reference bias by 38%, which affects downstream genotyping results. This approach also allows for the accurate genotyping of a large and complex pair of structural variants at the K feathering locus using short reads, which would not be possible using a linear reference. CONCLUSIONS We expect that this new paradigm of genomic reference will allow better pinpointing of exact mutations responsible for specific phenotypes, which will in turn be necessary for breeding chickens that meet new sustainability criteria and are resilient to quickly evolving pathogen threats.
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Affiliation(s)
- Edward S Rice
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen (UCPH), Copenhagen, Denmark
| | - James Alfieri
- Department of Ecology & Evolutionary Biology, Texas A&M University, College Station, TX, USA
| | - Giridhar Athrey
- Department of Poultry Science, Texas A&M University, College Station, TX, USA
| | - Jennifer R Balacco
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Philippe Bardou
- Sigenae, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, 31326, France
| | - Heath Blackmon
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Mathieu Charles
- University Paris-Saclay, INRAE, AgroParisTech, GABI, Sigenae, Jouy-en-Josas, France
| | - Hans H Cheng
- Avian Disease and Oncology Laboratory, USDA, ARS, USNPRC, East Lansing, MI, USA
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | | | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Laurent A F Frantz
- Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4DQ, UK
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen (UCPH), Copenhagen, Denmark
| | - Cari J Hearn
- Avian Disease and Oncology Laboratory, USDA, ARS, USNPRC, East Lansing, MI, USA
| | - Erich D Jarvis
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
- The Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Christophe Klopp
- Sigenae, Genotoul Bioinfo, MIAT UR875, INRAE, Castanet Tolosan, France
| | - Sofia Marcos
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen (UCPH), Copenhagen, Denmark
- Applied Genomics and Bioinformatics, University of the Basque Country (UPV/EHU), Leioa, Bilbao, Spain
| | | | | | - Luohao Xu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Wesley C Warren
- Department of Animal Sciences, University of Missouri, Columbia, MO, USA.
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45
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Green DH, Rad-Menéndez C, Campbell C, Kilias ES. The genome sequence of Pycnococcus provasolii (CCAP190/2) (Guillard, 1991). Wellcome Open Res 2023; 8:520. [PMID: 38808318 PMCID: PMC11130579 DOI: 10.12688/wellcomeopenres.20345.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2023] [Indexed: 05/30/2024] Open
Abstract
We present a genome assembly from cultured Pycnococcus provasolii (a marine green alga; Chlorophyta; None; Pseudoscourfieldiales; Pycnococcaceae). The genome sequence is 32.2 megabases in span. Most of the assembly is scaffolded into 44 chromosomal pseudomolecules (99.67%). The mitochondrial and plastid genomes have also been assembled, and the length of the mitochondrial scaffold is 24.3 kilobases and of the plastid genome has been assembled and is 80.2 kilobases in length.
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Affiliation(s)
- David H. Green
- Culture Collection of Algae and Protozoa, The Scottish Association for Marine Science, Oban, Scotland, UK
| | - Cecilia Rad-Menéndez
- Culture Collection of Algae and Protozoa, The Scottish Association for Marine Science, Oban, Scotland, UK
| | - Christine Campbell
- Culture Collection of Algae and Protozoa, The Scottish Association for Marine Science, Oban, Scotland, UK
| | | | | | | | | | - Darwin Tree of Life Barcoding collective
- Culture Collection of Algae and Protozoa, The Scottish Association for Marine Science, Oban, Scotland, UK
- Department of Biology, University of Oxford, Oxford, England, UK
| | | | | | - Tree of Life Core Informatics collective
- Culture Collection of Algae and Protozoa, The Scottish Association for Marine Science, Oban, Scotland, UK
- Department of Biology, University of Oxford, Oxford, England, UK
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46
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Boyes D, Eljounaidi K. The genome sequence of the Rose-flounced Tabby, Endotricha flammealis (Denis & Schiffermüller, 1775). Wellcome Open Res 2023; 8:516. [PMID: 39086664 PMCID: PMC11289590 DOI: 10.12688/wellcomeopenres.19923.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2023] [Indexed: 08/02/2024] Open
Abstract
We present a genome assembly from an individual female Endotricha flammealis (the Rose-flounced Tabby; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence is 473.9 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.23 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,578 protein coding genes.
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Affiliation(s)
- Douglas Boyes
- UK Centre for Ecology & Hydrology, Wallingford, England, UK
| | - Kaouthar Eljounaidi
- Centre for Novel Agricultural Products (CNAP), University of York, York, England, UK
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47
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Green DH, Rad-Menéndez C. The genome sequence of the Heterolobosean amoeboflagellate, Tetramitus jugosus CCAP 1588/3C. Wellcome Open Res 2023; 8:513. [PMID: 38774489 PMCID: PMC11106597 DOI: 10.12688/wellcomeopenres.20189.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2023] [Indexed: 05/24/2024] Open
Abstract
We present a genome assembly from cultivated Tetramitus jugosus (Heterolobosea; Schizopyrenida; Vahlkampfiidae). The genome sequence is 26.3 megabases in span. Most of the assembly (99.3%) is scaffolded into 52 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 49.46 kilobases in length.
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Affiliation(s)
- David H. Green
- Culture Collection of Algae and Protozoa, The Scottish Association for Marine Science, Oban, Scotland, UK
| | - Cecilia Rad-Menéndez
- Culture Collection of Algae and Protozoa, The Scottish Association for Marine Science, Oban, Scotland, UK
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48
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Boyes D. The genome sequence of the Six-belted Clearwing, Bembecia ichneumoniformis (Denis & Schiffermüller, 1775). Wellcome Open Res 2023; 8:515. [PMID: 38813550 PMCID: PMC11134158 DOI: 10.12688/wellcomeopenres.20279.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2023] [Indexed: 05/31/2024] Open
Abstract
We present a genome assembly from an individual male Bembecia ichneumoniformis (the Six-belted Clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 511.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.32 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,114 protein coding genes.
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Affiliation(s)
- Douglas Boyes
- UK Centre for Ecology & Hydrology, Wallingford, England, UK
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49
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Nsango SN, Agbor JP, Ayala D, Johnson HF, Heaton H, Wagah MG, Collins JC, Krasheninnikova K, Pelan SE, Pointon DLB, Sims Y, Torrance JW, Tracey A, Uliano Da Silva M, Wood JMD, von Wyschetzki K, McCarthy SA, Neafsey DE, Makunin A, Lawniczak M. A chromosomal reference genome sequence for the malaria mosquito, Anopheles moucheti, Evans, 1925. Wellcome Open Res 2023; 8:507. [PMID: 38046191 PMCID: PMC10690039 DOI: 10.12688/wellcomeopenres.20259.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2023] [Indexed: 12/05/2023] Open
Abstract
We present a genome assembly from an individual male Anopheles moucheti (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae), from a wild population in Cameroon. The genome sequence is 271 megabases in span. The majority of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.5 kilobases in length.
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Affiliation(s)
- Sandrine N. Nsango
- Faculte de Medecine et des Sciences Pharmaceutiques, Universite de Douala, Douala, Littoral, Cameroon
| | - Jean-Pierre Agbor
- Faculte de Medecine et des Sciences Pharmaceutiques, Universite de Douala, Douala, Littoral, Cameroon
| | - Diego Ayala
- MIVEGEC, IRD, Montpellier, France
- ESV-GAB, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | | | | | - Martin G. Wagah
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | | | | | - Sarah E. Pelan
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | | | - Ying Sims
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | | | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | | | | | | | - DNA Pipelines collective
- Faculte de Medecine et des Sciences Pharmaceutiques, Universite de Douala, Douala, Littoral, Cameroon
- MIVEGEC, IRD, Montpellier, France
- ESV-GAB, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
- CSSE, Auburn University, Auburn, Alabama, USA
- Department of Genetics, University of Cambridge, Cambridge, England, UK
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, USA
| | - Shane A. McCarthy
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
- Department of Genetics, University of Cambridge, Cambridge, England, UK
| | - Daniel E. Neafsey
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, USA
| | - Alex Makunin
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
| | - Mara Lawniczak
- Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
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50
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Boyes D, Eagles M. The genome sequence of the Flame Shoulder, Ochropleura plecta (Linnaeus, 1761). Wellcome Open Res 2023; 8:506. [PMID: 38404636 PMCID: PMC10884592 DOI: 10.12688/wellcomeopenres.20187.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2023] [Indexed: 02/27/2024] Open
Abstract
We present a genome assembly from an individual female Ochropleura plecta (the Flame Shoulder; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 643.9 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.34 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,016 protein coding genes.
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Affiliation(s)
- Douglas Boyes
- UK Centre for Ecology & Hydrology, Wallingford, England, UK
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