1
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Wright CJ, Stevens L, Mackintosh A, Lawniczak M, Blaxter M. Comparative genomics reveals the dynamics of chromosome evolution in Lepidoptera. Nat Ecol Evol 2024; 8:777-790. [PMID: 38383850 PMCID: PMC11009112 DOI: 10.1038/s41559-024-02329-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/12/2024] [Indexed: 02/23/2024]
Abstract
Chromosomes are a central unit of genome organization. One-tenth of all described species on Earth are butterflies and moths, the Lepidoptera, which generally possess 31 chromosomes. However, some species display dramatic variation in chromosome number. Here we analyse 210 chromosomally complete lepidopteran genomes and show that the chromosomes of extant lepidopterans are derived from 32 ancestral linkage groups, which we term Merian elements. Merian elements have remained largely intact through 250 million years of evolution and diversification. Against this stable background, eight lineages have undergone extensive reorganization either through numerous fissions or a combination of fusion and fission events. Outside these lineages, fusions are rare and fissions are rarer still. Fusions often involve small, repeat-rich Merian elements and the sex-linked element. Our results reveal the constraints on genome architecture in Lepidoptera and provide a deeper understanding of chromosomal rearrangements in eukaryotic genome evolution.
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Affiliation(s)
| | - Lewis Stevens
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK.
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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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Johansen M, Saenko S, Schilthuizen M, Blaxter M, Davison A. Fine mapping of the Cepaea nemoralis shell colour and mid-banded loci using a high-density linkage map. Heredity (Edinb) 2023; 131:327-337. [PMID: 37758900 PMCID: PMC10673960 DOI: 10.1038/s41437-023-00648-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
Molluscs are a highly speciose phylum that exhibits an astonishing array of colours and patterns, yet relatively little progress has been made in identifying the underlying genes that determine phenotypic variation. One prominent example is the land snail Cepaea nemoralis for which classical genetic studies have shown that around nine loci, several physically linked and inherited together as a 'supergene', control the shell colour and banding polymorphism. As a first step towards identifying the genes involved, we used whole-genome resequencing of individuals from a laboratory cross to construct a high-density linkage map, and then trait mapping to identify 95% confidence intervals for the chromosomal region that contains the supergene, specifically the colour locus (C), and the unlinked mid-banded locus (U). The linkage map is made up of 215,593 markers, ordered into 22 linkage groups, with one large group making up ~27% of the genome. The C locus was mapped to a ~1.3 cM region on linkage group 11, and the U locus was mapped to a ~0.7 cM region on linkage group 15. The linkage map will serve as an important resource for further evolutionary and population genomic studies of C. nemoralis and related species, as well as the identification of candidate genes within the supergene and for the mid-banding phenotype.
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Affiliation(s)
- Margrethe Johansen
- School of Life Sciences, University Park, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Suzanne Saenko
- Evolutionary Ecology, Naturalis Biodiversity Center, Leiden, 2333CR, The Netherlands
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden, 2333BE, The Netherlands
| | - Menno Schilthuizen
- Evolutionary Ecology, Naturalis Biodiversity Center, Leiden, 2333CR, The Netherlands
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden, 2333BE, The Netherlands
| | - Mark Blaxter
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Angus Davison
- School of Life Sciences, University Park, University of Nottingham, Nottingham, NG7 2RD, UK
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4
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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du Plessis SJ, Blaxter M, Koepfli KP, Chadwick EA, Hailer F. Genomics Reveals Complex Population History and Unexpected Diversity of Eurasian Otters (Lutra lutra) in Britain Relative to Genetic Methods. Mol Biol Evol 2023; 40:msad207. [PMID: 37713621 PMCID: PMC10630326 DOI: 10.1093/molbev/msad207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/04/2023] [Accepted: 09/06/2023] [Indexed: 09/17/2023] Open
Abstract
Conservation genetic analyses of many endangered species have been based on genotyping of microsatellite loci and sequencing of short fragments of mtDNA. The increase in power and resolution afforded by whole genome approaches may challenge conclusions made on limited numbers of loci and maternally inherited haploid markers. Here, we provide a matched comparison of whole genome sequencing versus microsatellite and control region (CR) genotyping for Eurasian otters (Lutra lutra). Previous work identified four genetically differentiated "stronghold" populations of otter in Britain, derived from regional populations that survived the population crash of the 1950s-1980s. Using whole genome resequencing data from 45 samples from across the British stronghold populations, we confirmed some aspects of population structure derived from previous marker-driven studies. Importantly, we showed that genomic signals of the population crash bottlenecks matched evidence from otter population surveys. Unexpectedly, two strongly divergent mitochondrial lineages were identified that were undetectable using CR fragments, and otters in the east of England were genetically distinct and surprisingly variable. We hypothesize that this previously unsuspected variability may derive from past releases of Eurasian otters from other, non-British source populations in England around the time of the population bottleneck. Our work highlights that even reasonably well-studied species may harbor genetic surprises, if studied using modern high-throughput sequencing methods.
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Affiliation(s)
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA
- Centre for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA
| | | | - Frank Hailer
- School of Biosciences, Cardiff University, Cardiff, UK
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Uliano-Silva M, Ferreira JGRN, Krasheninnikova K, Formenti G, Abueg L, Torrance J, Myers EW, Durbin R, Blaxter M, McCarthy SA. MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads. BMC Bioinformatics 2023; 24:288. [PMID: 37464285 PMCID: PMC10354987 DOI: 10.1186/s12859-023-05385-y] [Citation(s) in RCA: 63] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/13/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND PacBio high fidelity (HiFi) sequencing reads are both long (15-20 kb) and highly accurate (> Q20). Because of these properties, they have revolutionised genome assembly leading to more accurate and contiguous genomes. In eukaryotes the mitochondrial genome is sequenced alongside the nuclear genome often at very high coverage. A dedicated tool for mitochondrial genome assembly using HiFi reads is still missing. RESULTS MitoHiFi was developed within the Darwin Tree of Life Project to assemble mitochondrial genomes from the HiFi reads generated for target species. The input for MitoHiFi is either the raw reads or the assembled contigs, and the tool outputs a mitochondrial genome sequence fasta file along with annotation of protein and RNA genes. Variants arising from heteroplasmy are assembled independently, and nuclear insertions of mitochondrial sequences are identified and not used in organellar genome assembly. MitoHiFi has been used to assemble 374 mitochondrial genomes (368 Metazoa and 6 Fungi species) for the Darwin Tree of Life Project, the Vertebrate Genomes Project and the Aquatic Symbiosis Genome Project. Inspection of 60 mitochondrial genomes assembled with MitoHiFi for species that already have reference sequences in public databases showed the widespread presence of previously unreported repeats. CONCLUSIONS MitoHiFi is able to assemble mitochondrial genomes from a wide phylogenetic range of taxa from Pacbio HiFi data. MitoHiFi is written in python and is freely available on GitHub ( https://github.com/marcelauliano/MitoHiFi ). MitoHiFi is available with its dependencies as a Docker container on GitHub (ghcr.io/marcelauliano/mitohifi:master).
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Affiliation(s)
| | - João Gabriel R. N. Ferreira
- Bio Bureau Biotecnologia, Rio de Janeiro, Brazil
- Instituto de Biofísica Carlos Chagas Filho, UniversidadeFederal Do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | - James Torrance
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA UK
| | - Eugene W. Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Richard Durbin
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA UK
| | - Shane A. McCarthy
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
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7
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Blaxter M, Lawniczak M. The genome sequence of the crab hacker barnacle, Sacculina carcini (Thompson, 1836). Wellcome Open Res 2023. [DOI: 10.12688/wellcomeopenres.18936.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023] Open
Abstract
We present a genome assembly from an individual female Sacculina carcini (crab hacker barnacle; Arthropoda; Crustacea; Thecostraca; Sacculinidae). The genome sequence is 264 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules plus 10 unlocalised. The mitochondrial genome was not identified.
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8
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Challis R, Kumar S, Sotero-Caio C, Brown M, Blaxter M. Genomes on a Tree (GoaT): A versatile, scalable search engine for genomic and sequencing project metadata across the eukaryotic tree of life. Wellcome Open Res 2023; 8:24. [PMID: 36864925 PMCID: PMC9971660 DOI: 10.12688/wellcomeopenres.18658.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2022] [Indexed: 01/19/2023] Open
Abstract
As genomic data transform our understanding of biodiversity, the Earth BioGenome Project (EBP) has set a goal of generating reference quality genome assemblies for all ~1.9 million described eukaryotic taxa. Meeting this goal requires coordination among many individual regional and taxon-focussed projects working under the EBP umbrella. Large-scale sequencing projects require ready access to validated genome-relevant metadata, such as genome sizes and karyotypes, but these data are dispersed across the literature, and directly measured values are lacking for most taxa. To meet these needs, we have developed Genomes on a Tree (GoaT), an Elasticsearch-powered datastore and search index for genome-relevant metadata and sequencing project plans and statuses. GoaT indexes publicly available metadata for all eukaryotic species and interpolates missing values through phylogenetic comparison. GoaT also holds target priority and sequencing status information for many projects affiliated to the EBP to aid project coordination. Metadata and status attributes in GoaT can be queried through a mature API, a web front end, and a command line interface. The web front end additionally provides summary visualisations for data exploration and reporting (see https://goat.genomehubs.org). GoaT currently holds direct or estimated values for over 70 taxon attributes and over 30 assembly attributes across 1.5 million eukaryotic species. The depth and breadth of curated data, frequent updates, and a versatile query interface make GoaT a powerful data aggregator and portal to explore and report underlying data for the eukaryotic tree of life. We illustrate this utility through a series of use cases from planning through to completion of a genome-sequencing project.
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Affiliation(s)
- Richard Challis
- Tree of Life, Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK,
| | - Sujai Kumar
- Tree of Life, Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK
| | | | - Max Brown
- Tree of Life, Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK
| | - Mark Blaxter
- Tree of Life, Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK
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Abstract
We present a genome assembly from an individual Haliclystus octoradiatus (the spotted kaleidoscope jellyfish; Cnidaria; Staurozoa; Stauromedusae; Haliclystidae). The genome sequence is 262 megabases in span. Most of the assembly (98.3%) is scaffolded into nine (9) chromosomal pseudomolecules. The mitochondrial genome was also assembled and is 18.3 kilobases in length.
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Affiliation(s)
- Mark Blaxter
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
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10
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R. N. Ferreira JG, A. Americo J, L. A. S. do Amaral D, Sendim F, R. da Cunha Y, Blaxter M, Uliano-Silva M, de F. Rebelo M. A chromosome-level assembly supports genome-wide investigation of the DMRT gene family in the golden mussel (Limnoperna fortunei). Gigascience 2022; 12:giad072. [PMID: 37776366 PMCID: PMC10541798 DOI: 10.1093/gigascience/giad072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 06/12/2023] [Accepted: 08/21/2023] [Indexed: 10/02/2023] Open
Abstract
BACKGROUND The golden mussel (Limnoperna fortunei) is a highly invasive species that causes environmental and socioeconomic losses in invaded areas. Reference genomes have proven to be a valuable resource for studying the biology of invasive species. While the current golden mussel genome has been useful for identifying new genes, its high fragmentation hinders some applications. FINDINGS In this study, we provide the first chromosome-level reference genome for the golden mussel. The genome was built using PacBio HiFi, 10X, and Hi-C sequencing data. The final assembly contains 99.4% of its total length assembled to the 15 chromosomes of the species and a scaffold N50 of 97.05 Mb. A total of 34,862 protein-coding genes were predicted, of which 84.7% were functionally annotated. A significant (6.48%) proportion of the genome was found to be in a hemizygous state. Using the new genome, we have performed a genome-wide characterization of the Doublesex and Mab-3 related transcription factor gene family, which has been proposed as a target for population control strategies in other species. CONCLUSIONS From the applied research perspective, a higher-quality genome will support genome editing with the aim of developing biotechnology-based solutions to control invasion. From the basic research perspective, the new genome is a high-quality reference for molecular evolutionary studies of Mytilida and other Lophotrochozoa, and it may be used as a reference for future resequencing studies to assess genomic variation among different golden mussel populations, unveiling potential routes of dispersion and helping to establish better control policies.
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Affiliation(s)
- João Gabriel R. N. Ferreira
- Bio Bureau Biotecnologia, Rio de Janeiro 21941-850, Brazil
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil
| | | | | | - Fábio Sendim
- Bio Bureau Biotecnologia, Rio de Janeiro 21941-850, Brazil
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil
| | - Yasmin R. da Cunha
- Bio Bureau Biotecnologia, Rio de Janeiro 21941-850, Brazil
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil
| | | | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Hinxton CB10 1RQ, UK
| | | | - Mauro de F. Rebelo
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-170, Brazil
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11
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Qiu S, Bradley JM, Zhang P, Chaudhuri R, Blaxter M, Butlin RK, Scholes JD. Genome-enabled discovery of candidate virulence loci in Striga hermonthica, a devastating parasite of African cereal crops. New Phytol 2022; 236:622-638. [PMID: 35699626 PMCID: PMC9795911 DOI: 10.1111/nph.18305] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Parasites have evolved proteins, virulence factors (VFs), that facilitate plant colonisation, however VFs mediating parasitic plant-host interactions are poorly understood. Striga hermonthica is an obligate, root-parasitic plant of cereal hosts in sub-Saharan Africa, causing devastating yield losses. Understanding the molecular nature and allelic variation of VFs in S. hermonthica is essential for breeding resistance and delaying the evolution of parasite virulence. We assembled the S. hermonthica genome and identified secreted proteins using in silico prediction. Pooled sequencing of parasites growing on a susceptible and a strongly resistant rice host allowed us to scan for loci where selection imposed by the resistant host had elevated the frequency of alleles contributing to successful colonisation. Thirty-eight putatively secreted VFs had very different allele frequencies with functions including host cell wall modification, protease or protease inhibitor and kinase activities. These candidate loci had significantly higher Tajima's D than the genomic background, consistent with balancing selection. Our results reveal diverse strategies used by S. hermonthica to overcome different layers of host resistance. Understanding the maintenance of variation at virulence loci by balancing selection will be critical to managing the evolution of virulence as part of a sustainable control strategy.
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Affiliation(s)
- Suo Qiu
- School of BiosciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
| | - James M. Bradley
- School of BiosciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
| | - Peijun Zhang
- School of BiosciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
| | - Roy Chaudhuri
- School of BiosciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
| | - Mark Blaxter
- Institute of Evolutionary Biology, School of Biological SciencesThe University of Edinburgh, Ashworth LaboratoriesCharlotte Auerbach RoadEdinburghEH9 3FLUK
- Wellcome Sanger InstituteWellcome Genome Campus, HinxtonCambridgeCB10 1SAUK
| | - Roger K. Butlin
- School of BiosciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
- Department of Marine SciencesUniversity of GothenburgS‐405 30GothenburgSweden
| | - Julie D. Scholes
- School of BiosciencesUniversity of SheffieldWestern BankSheffieldS10 2TNUK
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12
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Lawniczak MK, Davey RP, Rajan J, Pereira-da-Conceicoa LL, Kilias E, Hollingsworth PM, Barnes I, Allen H, Blaxter M, Burgin J, Broad GR, Crowley LM, Gaya E, Holroyd N, Lewis OT, McTaggart S, Mieszkowska N, Minotto A, Shaw F, Richards TA, Sivess LA. Specimen and sample metadata standards for biodiversity genomics: a proposal from the Darwin Tree of Life project. Wellcome Open Res 2022. [DOI: 10.12688/wellcomeopenres.17605.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The vision of the Earth BioGenome Project1 is to complete reference genomes for all of the planet’s ~2M described eukaryotic species in the coming decade. To contribute to this global endeavour, the Darwin Tree of Life Project (DToL2) was launched in 2019 with the aim of generating complete genomes for the ~70k described eukaryotic species that can be found in Britain and Ireland. One of the early tasks of the DToL project was to determine, define, and standardise the important metadata that must accompany every sample contributing to this ambitious project. This ensures high-quality contextual information is available for the associated data, enabling a richer set of information upon which to search and filter datasets as well as enabling interoperability between datasets used for downstream analysis. Here we describe some of the key factors we considered in the process of determining, defining, and documenting the metadata required for DToL project samples. The manifest and Standard Operating Procedure that are referred to throughout this paper are likely to be useful for other projects, and we encourage re-use while maintaining the standards and rules set out here.
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13
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Sloat SA, Noble LM, Paaby AB, Bernstein M, Chang A, Kaur T, Yuen J, Tintori SC, Jackson JL, Martel A, Salome Correa JA, Stevens L, Kiontke K, Blaxter M, Rockman MV. Caenorhabditis nematodes colonize ephemeral resource patches in neotropical forests. Ecol Evol 2022; 12:e9124. [PMID: 35898425 PMCID: PMC9309040 DOI: 10.1002/ece3.9124] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/17/2022] [Accepted: 06/23/2022] [Indexed: 01/09/2023] Open
Abstract
Factors shaping the distribution and abundance of species include life-history traits, population structure, and stochastic colonization-extinction dynamics. Field studies of model species groups help reveal the roles of these factors. Species of Caenorhabditis nematodes are highly divergent at the sequence level but exhibit highly conserved morphology, and many of these species live in sympatry on microbe-rich patches of rotten material. Here, we use field experiments and large-scale opportunistic collections to investigate species composition, abundance, and colonization efficiency of Caenorhabditis species in two of the world's best-studied lowland tropical field sites: Barro Colorado Island in Panamá and La Selva in Sarapiquí, Costa Rica. We observed seven species of Caenorhabditis, four of them known only from these collections. We formally describe two species and place them within the Caenorhabditis phylogeny. While these localities contain species from many parts of the phylogeny, both localities were dominated by globally distributed androdiecious species. We found that Caenorhabditis individuals were able to colonize baits accessible only through phoresy and preferentially colonized baits that were in direct contact with the ground. We estimate the number of colonization events per patch to be low.
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Affiliation(s)
- Solomon A. Sloat
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Luke M. Noble
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Annalise B. Paaby
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
- School of Biological SciencesGeorgia Institute of TechnologyAtlantaGeorgiaUSA
| | - Max Bernstein
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Audrey Chang
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Taniya Kaur
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - John Yuen
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
- Renaissance School of MedicineStony Brook UniversityStony BrookNew YorkUSA
| | - Sophia C. Tintori
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Jacqueline L. Jackson
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Arielle Martel
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Jose A. Salome Correa
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | | | - Karin Kiontke
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger InstituteHinxtonUK
| | - Matthew V. Rockman
- Department of Biology and Center for Genomics and Systems BiologyNew York UniversityNew YorkNew YorkUSA
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14
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Blaxter M, Archibald JM, Childers AK, Coddington JA, Crandall KA, Di Palma F, Durbin R, Edwards SV, Graves JAM, Hackett KJ, Hall N, Jarvis ED, Johnson RN, Karlsson EK, Kress WJ, Kuraku S, Lawniczak MKN, Lindblad-Toh K, Lopez JV, Moran NA, Robinson GE, Ryder OA, Shapiro B, Soltis PS, Warnow T, Zhang G, Lewin HA. Why sequence all eukaryotes? Proc Natl Acad Sci U S A 2022; 119:e2115636118. [PMID: 35042801 PMCID: PMC8795522 DOI: 10.1073/pnas.2115636118] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing maintenance of biodiversity on Earth? The history of life and the code for the working parts of cells and systems are written in the genome. The Earth BioGenome Project has proposed that the genomes of all extant, named eukaryotes-about 2 million species-should be sequenced to high quality to produce a digital library of life on Earth, beginning with strategic phylogenetic, ecological, and high-impact priorities. Here we discuss why we should sequence all eukaryotic species, not just a representative few scattered across the many branches of the tree of life. We suggest that many questions of evolutionary and ecological significance will only be addressable when whole-genome data representing divergences at all of the branchings in the tree of life or all species in natural ecosystems are available. We envisage that a genomic tree of life will foster understanding of the ongoing processes of speciation, adaptation, and organismal dependencies within entire ecosystems. These explorations will resolve long-standing problems in phylogenetics, evolution, ecology, conservation, agriculture, bioindustry, and medicine.
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Affiliation(s)
- Mark Blaxter
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4H7, Canada
| | - Anna K Childers
- Bee Research Laboratory, Agricultural Research Service, US Department of Agriculture (USDA), Beltsville, MD 20705
| | - Jonathan A Coddington
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Keith A Crandall
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, George Washington University, Washington, DC 20052
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC 20013
| | - Federica Di Palma
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Richard Durbin
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Jennifer A M Graves
- School of Life Sciences, La Trobe University, Bundoora, VIC 751 23, Australia
- University of Canberra, Bruce, ACT 2617, Australia
| | - Kevin J Hackett
- Crop Production and Protection, Office of National Programs, Agricultural Research Service, USDA, Beltsville, MD 20705
| | - Neil Hall
- Earlham Institute, Norwich, Norfolk NR4 7UZ, United Kingdom
| | - Erich D Jarvis
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY 10065
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - Rebecca N Johnson
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Elinor K Karlsson
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - W John Kress
- Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012
| | - Shigehiro Kuraku
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | | | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 751 23, Sweden
| | - Jose V Lopez
- Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University, Dania Beach, FL 33004
- Guy Harvey Oceanographic Center, Dania Beach, FL 33004
| | - Nancy A Moran
- Integrative Biology, University of Texas at Austin, Austin, TX 78712
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Oliver A Ryder
- Conservation Genetics, Division of Biology, San Diego Zoo Wildlife Alliance, Escondido, CA 92027
- Department of Evolution, Behavior and Ecology, University of California, San Diego, La Jolla, CA 92039
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611
- Biodiversity Institute, University of Florida, Gainesville, FL 32611
| | - Tandy Warnow
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61301
| | - Guojie Zhang
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
- China National Genebank, Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China
| | - Harris A Lewin
- Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, CA 95616
- Department of Population Health and Reproduction, University of California, Davis, CA 95616
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15
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Abstract
We present a genome assembly from an individual
Lineus longissimus (the bootlace worm; Nemertea; Pilidiophora; Heteronemertea; Lineidae). The genome sequence is 391 megabases in span. The majority of the assembly is scaffolded into 19 chromosomal pseudomolecules.
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Affiliation(s)
| | - Mark Blaxter
- Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
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16
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Mead D, Ogden R, Meredith A, Peniche G, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Doulcan J, Holmes N, Wright V, Loose M, Quail MA, McCarthy SA, Howe K, Chow W, Torrance J, Collins J, Challis R, Durbin R, Blaxter M. The genome sequence of the European golden eagle, Aquila chrysaetos chrysaetos Linnaeus 1758. Wellcome Open Res 2021; 6:112. [PMID: 34671705 PMCID: PMC8499043 DOI: 10.12688/wellcomeopenres.16631.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2021] [Indexed: 11/26/2022] Open
Abstract
We present a genome assembly from an individual female
Aquila chrysaetos chrysaetos (the European golden eagle; Chordata; Aves; Accipitridae). The genome sequence is 1.23 gigabases in span. The majority of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the W and Z sex chromosomes.
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Affiliation(s)
- Dan Mead
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.,Owlstone Medical, Cambridge Science Park, Cambridge, CB4 0GJ, UK
| | - Rob Ogden
- Royal (Dick) School of Veterinary Sciences and Roslin Institute, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Anna Meredith
- Royal (Dick) School of Veterinary Sciences and Roslin Institute, University of Edinburgh, Midlothian, EH25 9RG, UK.,Melbourne Veterinary School, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Gabriela Peniche
- Royal (Dick) School of Veterinary Sciences and Roslin Institute, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Michelle Smith
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Craig Corton
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Karen Oliver
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Jason Skelton
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | | | - Jale Doulcan
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.,Achilles Therapeutics plc, London, W6 8PW, UK
| | - Nadine Holmes
- Deep Seq, University of Nottingham, Nottingham, NG7 2UH, UK
| | | | - Matt Loose
- Deep Seq, University of Nottingham, Nottingham, NG7 2UH, UK
| | | | - Shane A McCarthy
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.,Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Kerstin Howe
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - William Chow
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - James Torrance
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Joanna Collins
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | | | - Richard Durbin
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.,Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Mark Blaxter
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
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17
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Hansen T, Fjelldal PG, Lien S, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Doulcan J, Fedrigo O, Mountcastle J, Jarvis E, McCarthy SA, Chow W, Howe K, Torrance J, Wood J, Sims Y, Haggerty L, Challis R, Threlfall J, Mead D, Durbin R, Blaxter M. The genome sequence of the brown trout, Salmo trutta Linnaeus 1758. Wellcome Open Res 2021; 6:108. [PMID: 34632087 PMCID: PMC8488904 DOI: 10.12688/wellcomeopenres.16838.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2021] [Indexed: 11/20/2022] Open
Abstract
We present a genome assembly from an individual female Salmo trutta (the brown trout; Chordata; Actinopteri; Salmoniformes; Salmonidae). The genome sequence is 2.37 gigabases in span. The majority of the assembly is scaffolded into 40 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl has identified 43,935 protein coding genes.
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Affiliation(s)
- Tom Hansen
- Institute of Marine Research (IMR), Matredal, Norway
| | | | - Sigbjørn Lien
- Norwegian University of Life Sciences, Ås, 1432, Norway
| | - Michelle Smith
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Craig Corton
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Karen Oliver
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jason Skelton
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Emma Betteridge
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jale Doulcan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,Achilles Therapeutics plc, London, W6 8PW, UK
| | | | | | - Erich Jarvis
- The Rockefeller University, New York, New York, 10065, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, 20815, USA
| | - Shane A McCarthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - William Chow
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Kerstin Howe
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - James Torrance
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jonathan Wood
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ying Sims
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Leanne Haggerty
- EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Richard Challis
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jonathan Threlfall
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Daniel Mead
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,Owlstone Medical, Cambridge Science Park, Cambridge, CB4 0GJ, UK
| | - Richard Durbin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Mark Blaxter
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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18
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McKenna V, Archibald JM, Beinart R, Dawson MN, Hentschel U, Keeling PJ, Lopez JV, Martín-Durán JM, Petersen JM, Sigwart JD, Simakov O, Sutherland KR, Sweet M, Talbot N, Thompson AW, Bender S, Harrison PW, Rajan J, Cochrane G, Berriman M, Lawniczak M, Blaxter M. The Aquatic Symbiosis Genomics Project: probing the evolution of symbiosis across the tree of life. Wellcome Open Res 2021. [DOI: 10.12688/wellcomeopenres.17222.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present the Aquatic Symbiosis Genomics Project, a global collaboration to generate high quality genome sequences for a wide range of eukaryotes and their microbial symbionts. Launched under the Symbiosis in Aquatic Systems Initiative of the Gordon and Betty Moore Foundation, the ASG Project brings together researchers from across the globe who hope to use these reference genomes to augment and extend their analyses of the dynamics, mechanisms and environmental importance of symbiosis. Applying large-scale, high-throughput sequencing and assembly technologies, the ASG collaboration will assemble and annotate the genomes of 500 symbiotic organisms – both the “hosts” and the microbial symbionts with which they associate. These data will be released openly to benefit all who work on symbiosis, from conservation geneticists to those interested in the origin of the eukaryotic cell.
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19
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Dunn JC, Hamer KC, Morris AJ, Grice PV, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Dolucan J, Quail MA, McCarthy SA, Uliano-Silva M, Howe K, Torrance J, Chow W, Pelan S, Sims Y, Challis R, Threlfall J, Mead D, Blaxter M. The genome sequence of the European turtle dove, Streptopelia turtur Linnaeus 1758. Wellcome Open Res 2021. [DOI: 10.12688/wellcomeopenres.17060.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
We present a genome assembly from an individual female Streptopelia turtur (the European turtle dove; Chordata; Aves; Columbidae). The genome sequence is 1.18 gigabases in span. The majority of the assembly is scaffolded into 35 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled.
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20
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Gonzalez de la Rosa PM, Thomson M, Trivedi U, Tracey A, Tandonnet S, Blaxter M. A telomere-to-telomere assembly of Oscheius tipulae and the evolution of rhabditid nematode chromosomes. G3 (Bethesda) 2021; 11:6026964. [PMID: 33561231 PMCID: PMC8022731 DOI: 10.1093/g3journal/jkaa020] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/25/2020] [Indexed: 12/20/2022]
Abstract
Eukaryotic chromosomes have phylogenetic persistence. In many taxa, each chromosome has a single functional centromere with essential roles in spindle attachment and segregation. Fusion and fission can generate chromosomes with no or multiple centromeres, leading to genome instability. Groups with holocentric chromosomes (where centromeric function is distributed along each chromosome) might be expected to show karyotypic instability. This is generally not the case, and in Caenorhabditis elegans, it has been proposed that the role of maintenance of a stable karyotype has been transferred to the meiotic pairing centers, which are found at one end of each chromosome. Here, we explore the phylogenetic stability of nematode chromosomes using a new telomere-to-telomere assembly of the rhabditine nematode Oscheius tipulae generated from nanopore long reads. The 60-Mb O. tipulae genome is resolved into six chromosomal molecules. We find the evidence of specific chromatin diminution at all telomeres. Comparing this chromosomal O. tipulae assembly with chromosomal assemblies of diverse rhabditid nematodes, we identify seven ancestral chromosomal elements (Nigon elements) and present a model for the evolution of nematode chromosomes through rearrangement and fusion of these elements. We identify frequent fusion events involving NigonX, the element associated with the rhabditid X chromosome, and thus sex chromosome-associated gene sets differ markedly between species. Despite the karyotypic stability, gene order within chromosomes defined by Nigon elements is not conserved. Our model for nematode chromosome evolution provides a platform for investigation of the tensions between local genome rearrangement and karyotypic evolution in generating extant genome architectures.
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Affiliation(s)
| | - Marian Thomson
- Edinburgh Genomics, School of Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Urmi Trivedi
- Edinburgh Genomics, School of Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Sophie Tandonnet
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo (USP), São Paulo, SP 05508-090, Brazil
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
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21
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Dunn JC, Liedvogel M, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Dolucan J, Quail MA, Uliano-Silva M, McCarthy SA, Howe K, Torrance J, Wood J, Pelan S, Sims Y, Challis R, Threlfall J, Mead D, Blaxter M. The genome sequence of the European robin, Erithacus rubecula Linnaeus 1758. Wellcome Open Res 2021. [DOI: 10.12688/wellcomeopenres.16988.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
We present a genome assembly from an individual female Erithacus rubecula (the European robin; Chordata; Aves; Passeriformes; Turdidae). The genome sequence is 1.09 gigabases in span. The majority of the assembly is scaffolded into 36 chromosomal pseudomolecules, with both W and Z sex chromosomes assembled.
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22
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Mead D, Saccheri I, Yung CJ, Lohse K, Lohse C, Ashmole P, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Quail MA, Dolucan J, McCarthy SA, Howe K, Wood J, Torrance J, Tracey A, Whiteford S, Challis R, Durbin R, Blaxter M. The genome sequence of the ringlet, Aphantopus hyperantus Linnaeus 1758. Wellcome Open Res 2021. [DOI: 10.12688/wellcomeopenres.16983.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
We present a genome assembly based on an individual female Aphantopus hyperantus, also known as Maniola hyperantus (the ringlet butterfly; Arthropoda; Insecta; Lepidoptera, Nymphalidae), scaffolded using data from a second, unrelated specimen. The genome sequence is 411 megabases in span. The majority of the assembly is scaffolded into 29 chromosomal pseudomolecules, including the Z sex chromosome.
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23
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Carpenter AI, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Doulcan J, Quail MA, McCarthy SA, Uliano Da Silva M, Howe K, Torrance J, Wood J, Pelan S, Sims Y, Tricomi FF, Challis R, Threlfall J, Mead D, Blaxter M. The genome sequence of the European water vole, Arvicola amphibius Linnaeus 1758. Wellcome Open Res 2021; 6:162. [PMID: 35600244 PMCID: PMC9114827 DOI: 10.12688/wellcomeopenres.16753.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2021] [Indexed: 11/20/2022] Open
Abstract
We present a genome assembly from an individual male Arvicola amphibius (the European water vole; Chordata; Mammalia; Rodentia; Cricetidae). The genome sequence is 2.30 gigabases in span. The majority of the assembly is scaffolded into 18 chromosomal pseudomolecules, including the X sex chromosome. Gene annotation of this assembly on Ensembl has identified 21,394 protein coding genes.
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Affiliation(s)
| | - Michelle Smith
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Craig Corton
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Karen Oliver
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jason Skelton
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Emma Betteridge
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jale Doulcan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Achilles Therapeutics Plc, London, W6 8PW, UK
| | - Michael A. Quail
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Shane A. McCarthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | | | - Kerstin Howe
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - James Torrance
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jonathan Wood
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Sarah Pelan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ying Sims
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | | | - Richard Challis
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jonathan Threlfall
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Daniel Mead
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Owlstone Medical, Cambridge Science Park, Cambridge, CB4 0GJ, UK
| | - Mark Blaxter
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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24
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Yarra T, Ramesh K, Blaxter M, Hüning A, Melzner F, Clark MS. Transcriptomic analysis of shell repair and biomineralization in the blue mussel, Mytilus edulis. BMC Genomics 2021; 22:437. [PMID: 34112105 PMCID: PMC8194122 DOI: 10.1186/s12864-021-07751-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 05/27/2021] [Indexed: 12/13/2022] Open
Abstract
Background Biomineralization by molluscs involves regulated deposition of calcium carbonate crystals within a protein framework to produce complex biocomposite structures. Effective biomineralization is a key trait for aquaculture, and animal resilience under future climate change. While many enzymes and structural proteins have been identified from the shell and in mantle tissue, understanding biomieralization is impeded by a lack of fundamental knowledge of the genes and pathways involved. In adult bivalves, shells are secreted by the mantle tissue during growth, maintenance and repair, with the repair process, in particular, amenable to experimental dissection at the transcriptomic level in individual animals. Results Gene expression dynamics were explored in the adult blue mussel, Mytilus edulis, during experimentally induced shell repair, using the two valves of each animal as a matched treatment-control pair. Gene expression was assessed using high-resolution RNA-Seq against a de novo assembled database of functionally annotated transcripts. A large number of differentially expressed transcripts were identified in the repair process. Analysis focused on genes encoding proteins and domains identified in shell biology, using a new database of proteins and domains previously implicated in biomineralization in mussels and other molluscs. The genes implicated in repair included many otherwise novel transcripts that encoded proteins with domains found in other shell matrix proteins, as well as genes previously associated with primary shell formation in larvae. Genes with roles in intracellular signalling and maintenance of membrane resting potential were among the loci implicated in the repair process. While haemocytes have been proposed to be actively involved in repair, no evidence was found for this in the M. edulis data. Conclusions The shell repair experimental model and a newly developed shell protein domain database efficiently identified transcripts involved in M. edulis shell production. In particular, the matched pair analysis allowed factoring out of much of the inherent high level of variability between individual mussels. This snapshot of the damage repair process identified a large number of genes putatively involved in biomineralization from initial signalling, through calcium mobilization to shell construction, providing many novel transcripts for future in-depth functional analyses.
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Affiliation(s)
- Tejaswi Yarra
- Ashworth Laboratories, University of Edinburgh, Institute of Evolutionary Biology, Charlotte Auerbach Road, EH9 3FL, Edinburgh, UK.,British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, CB3 0ET, Cambridge, UK
| | - Kirti Ramesh
- GEOMAR Helmholtz Centre for Ocean Research, 24105, Kiel, Germany
| | - Mark Blaxter
- Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, Saffron Walden, UK
| | - Anne Hüning
- GEOMAR Helmholtz Centre for Ocean Research, 24105, Kiel, Germany
| | - Frank Melzner
- GEOMAR Helmholtz Centre for Ocean Research, 24105, Kiel, Germany
| | - Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, CB3 0ET, Cambridge, UK.
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25
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Abstract
The Tree of Life Gateway uses Genome Note publications to announce the completion of genomes assembled by the Tree of Life programme, based at the Wellcome Sanger Institute and involving numerous partner organisations and institutes. Tree of Life participates in the Darwin Tree of Life Project, which aims to sequence the genomes of all 70,000+ eukaryotic species in the Atlantic archipelago of Britain and Ireland, the Aquatic Symbiosis Genomics Project, which will sequence 1000 species involved in 500 symbioses between eukaryotic hosts and their microbial 'cobionts', and other initiatives, such as the Vertebrate Genome Project. These Genome Notes report the origins of ethically sourced samples used for sequencing, give the methods used to generate the sequence and use statistics and interactive figures to demonstrate the quality of the genome sequences. In addition to describing the production of these sequences, each Genome Note gives citeable credit to those who participated in producing the genome assembly and announces the availability of the data for reuse by all. It is through the use and reuse of this openly and publicly released data that we hope effective and lasting solutions to the ongoing biodiversity crisis can be found.
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Affiliation(s)
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Hinxton, Cambridge, UK
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26
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Abstract
Mollusc shells are a result of the deposition of crystalline and amorphous calcite catalysed by enzymes and shell matrix proteins. Developing a detailed understanding of bivalve mollusc biomineralization pathways is complicated not only by the multiplicity of shell forms and microstructures in this class, but also by the evolution of associated proteins by domain co-option and domain shuffling. In spite of this, a minimal biomineralization toolbox comprising proteins and protein domains critical for shell production across species has been identified. Using a matched pair design to reduce experimental noise from inter-individual variation, combined with damage-repair experiments and a database of biomineralization shell matrix proteins (SMP) derived from published works, proteins were identified that are likely to be involved in shell calcification. Eighteen new, shared proteins likely to be involved in the processes related to the calcification of shells were identified by analysis of genes expressed during repair in Crassostrea gigas, Mytilus edulis and Pecten maximus. Genes involved in ion transport were also identified as potentially involved in calcification either via the maintenance of cell acid-base balance or transport of critical ions to the extrapallial space, the site of shell assembly. These data expand the number of candidate biomineralization proteins in bivalve molluscs for future functional studies and define a minimal functional protein domain set required to produce solid microstructures from soluble calcium carbonate. This is important for understanding molluscan shell evolution, the likely impacts of environmental change on biomineralization processes, materials science, and biomimicry research.
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Affiliation(s)
- Tejaswi Yarra
- University of Edinburgh, Institute of Evolutionary Biology, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK.,British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Mark Blaxter
- Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
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27
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Howe K, Dwinell M, Shimoyama M, Corton C, Betteridge E, Dove A, Quail MA, Smith M, Saba L, Williams RW, Chen H, Kwitek AE, McCarthy SA, Uliano-Silva M, Chow W, Tracey A, Torrance J, Sims Y, Challis R, Threlfall J, Blaxter M. The genome sequence of the Norway rat, Rattus norvegicus Berkenhout 1769. Wellcome Open Res 2021; 6:118. [PMID: 34660910 PMCID: PMC8495504 DOI: 10.12688/wellcomeopenres.16854.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2021] [Indexed: 11/20/2022] Open
Abstract
We present a genome assembly from an individual male Rattus norvegicus (the Norway rat; Chordata; Mammalia; Rodentia; Muridae). The genome sequence is 2.44 gigabases in span. The majority of the assembly is scaffolded into 20 chromosomal pseudomolecules, with both X and Y sex chromosomes assembled. This genome assembly, mRatBN7.2, represents the new reference genome for R. norvegicus and has been adopted by the Genome Reference Consortium.
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Affiliation(s)
- Kerstin Howe
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Melinda Dwinell
- Medical College of Wisconsin, Milwaukee, Wisconsin, 53226, USA
| | - Mary Shimoyama
- Medical College of Wisconsin, Milwaukee, Wisconsin, 53226, USA
| | - Craig Corton
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Emma Betteridge
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Alexander Dove
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Michael A. Quail
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Michelle Smith
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Laura Saba
- Skaggs School of Pharmacy and Pharmaceutical Sciences,, University of Colorado Anschutz Medical Center, Aurora, Colorado, 80045, USA
| | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, 38103, USA
| | - Hao Chen
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, Tennessee, 38103, USA
| | - Anne E. Kwitek
- Medical College of Wisconsin, Milwaukee, Wisconsin, 53226, USA
| | - Shane A. McCarthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Marcela Uliano-Silva
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - William Chow
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Alan Tracey
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - James Torrance
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ying Sims
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Richard Challis
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jonathan Threlfall
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Mark Blaxter
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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28
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Vine C, Teeling EC, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Doulcan J, Quail MA, McCarthy SA, Howe K, Torrance J, Wood J, Pelan S, Sims Y, Challis R, Threlfall J, Mead D, Blaxter M. The genome sequence of the common pipistrelle, Pipistrellus pipistrellus Schreber 1774. Wellcome Open Res 2021. [DOI: 10.12688/wellcomeopenres.16895.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present a genome assembly from an individual female Pipistrellus pipistrellus (the common pipistrelle; Chordata; Mammalia; Chiroptera; Vespertilionidae). The genome sequence is 1.76 gigabases in span. The majority of the assembly is scaffolded into 21 chromosomal pseudomolecules, with the X sex chromosome assembled.
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29
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Caurcel C, Laetsch DR, Challis R, Kumar S, Gharbi K, Blaxter M. MolluscDB: a genome and transcriptome database for molluscs. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200157. [PMID: 33813885 PMCID: PMC8059625 DOI: 10.1098/rstb.2020.0157] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
As sequencing becomes more accessible and affordable, the analysis of genomic and transcriptomic data has become a cornerstone of many research initiatives. Communities with a focus on particular taxa or ecosystems need solutions capable of aggregating genomic resources and serving them in a standardized and analysis-friendly manner. Taxon-focussed resources can be more flexible in addressing the needs of a research community than can universal or general databases. Here, we present MolluscDB, a genome and transcriptome database for molluscs. MolluscDB offers a rich ecosystem of tools, including an Ensembl browser, a BLAST server for homology searches and an HTTP server from which any dataset present in the database can be downloaded. To demonstrate the utility of the database and verify the quality of its data, we imported data from assembled genomes and transcriptomes of 22 species, estimated the phylogeny of Mollusca using single-copy orthologues, explored patterns of gene family size change and interrogated the data for biomineralization-associated enzymes and shell matrix proteins. MolluscDB provides an easy-to-use and openly accessible data resource for the research community. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
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Affiliation(s)
- Carlos Caurcel
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Richard Challis
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK.,Tree of Life Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sujai Kumar
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK.,Tree of Life Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Karim Gharbi
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK.,Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Mark Blaxter
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK.,Tree of Life Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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30
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Abstract
Gene flow is predicted to impede parallel adaptation via de novo mutation, because it can introduce pre-existing adaptive alleles from population to population. We test this using Hawaiian crickets (Teleogryllus oceanicus) in which 'flatwing' males that lack sound-producing wing structures recently arose and spread under selection from an acoustically-orienting parasitoid. Morphometric and genetic comparisons identify distinct flatwing phenotypes in populations on three islands, localized to different loci. Nevertheless, we detect strong, recent and ongoing gene flow among the populations. Using genome scans and gene expression analysis we find that parallel evolution of flatwing on different islands is associated with shared genomic hotspots of adaptation that contain the gene doublesex, but the form of selection differs among islands and corresponds to known flatwing demographics in the wild. We thus show how parallel adaptation can occur on contemporary timescales despite gene flow, indicating that it could be less constrained than previously appreciated.
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Affiliation(s)
- Xiao Zhang
- School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK.
| | - Jack G Rayner
- School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Nathan W Bailey
- School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK.
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31
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Mead D, Fingland K, Cripps R, Portela Miguez R, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Doulcan J, Quail MA, McCarthy SA, Howe K, Sims Y, Torrance J, Tracey A, Challis R, Durbin R, Blaxter M. The genome sequence of the eastern grey squirrel, Sciurus carolinensis Gmelin, 1788. Wellcome Open Res 2020; 5:27. [PMID: 33215047 PMCID: PMC7653645 DOI: 10.12688/wellcomeopenres.15721.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2020] [Indexed: 12/02/2022] Open
Abstract
We present a genome assembly from an individual male
Sciurus carolinensis (the eastern grey squirrel; Vertebrata; Mammalia; Eutheria; Rodentia; Sciuridae). The genome sequence is 2.82 gigabases in span. The majority of the assembly (92.3%) is scaffolded into 21 chromosomal-level scaffolds, with both X and Y sex chromosomes assembled.
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Affiliation(s)
- Dan Mead
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Kathryn Fingland
- Nottingham Trent University, School of Animal, Rural and Environmental Sciences, Nottingham, NG25 0QF, UK
| | - Rachel Cripps
- Red Squirrel Officer, The Wildlife Trust for Lancashire, Manchester and North Merseyside, The Barn, Berkeley Drive, Bamber Bridge, Preston, PR5 6BY, UK
| | | | - Michelle Smith
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Craig Corton
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Karen Oliver
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Jason Skelton
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Emma Betteridge
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Jale Doulcan
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Michael A Quail
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Shane A McCarthy
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Ying Sims
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - James Torrance
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Richard Challis
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Richard Durbin
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute,Wellcome Genome Campus, Hinxton, CB10 1SA, UK
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32
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Stevens L, Rooke S, Falzon LC, Machuka EM, Momanyi K, Murungi MK, Njoroge SM, Odinga CO, Ogendo A, Ogola J, Fèvre EM, Blaxter M. The Genome of Caenorhabditis bovis. Curr Biol 2020; 30:1023-1031.e4. [PMID: 32109387 DOI: 10.1016/j.cub.2020.01.074] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/10/2019] [Accepted: 01/23/2020] [Indexed: 11/26/2022]
Abstract
The free-living nematode Caenorhabditis elegans is a key laboratory model for metazoan biology. C. elegans has also become a model for parasitic nematodes despite being only distantly related to most parasitic species. All of the ∼65 Caenorhabditis species currently in culture are free-living, with most having been isolated from decaying plant or fungal matter. Caenorhabditis bovis is a particularly unusual species that has been isolated several times from the inflamed ears of Zebu cattle in Eastern Africa, where it is associated with the disease bovine parasitic otitis. C. bovis is therefore of particular interest to researchers interested in the evolution of nematode parasitism. However, as C. bovis is not in laboratory culture, it remains little studied. Here, by sampling livestock markets and slaughterhouses in Western Kenya, we successfully reisolated C. bovis from the ear of adult female Zebu. We sequenced the genome of C. bovis using the Oxford Nanopore MinION platform in a nearby field laboratory and used the data to generate a chromosome-scale draft genome sequence. We exploited this draft genome sequence to reconstruct the phylogenetic relationships of C. bovis to other Caenorhabditis species and reveal the changes in genome size and content that have occurred during its evolution. We also identified expansions in several gene families that have been implicated in parasitism in other nematode species. The high-quality draft genome and our analyses thereof represent a significant advancement in our understanding of this unusual Caenorhabditis species.
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Affiliation(s)
- Lewis Stevens
- Institute of Evolutionary Biology, Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK.
| | - Stefan Rooke
- Usher Institute, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Laura C Falzon
- Institute of Infection and Global Health, University of Liverpool, 8 West Derby Street, Liverpool L69 7BE, UK; International Livestock Research Institute, Old Naivasha Road, PO Box 30709 00100, Nairobi, Kenya
| | - Eunice M Machuka
- Biosciences, Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, Old Naivasha Road, PO Box 30709 00100, Nairobi, Kenya
| | - Kelvin Momanyi
- International Livestock Research Institute, Old Naivasha Road, PO Box 30709 00100, Nairobi, Kenya
| | - Maurice K Murungi
- International Livestock Research Institute, Old Naivasha Road, PO Box 30709 00100, Nairobi, Kenya
| | - Samuel M Njoroge
- International Livestock Research Institute, Old Naivasha Road, PO Box 30709 00100, Nairobi, Kenya; Centre for Microbiology Research, Kenya Medical Research Institute, KNH Grounds, PO Box 54840 00200, Nairobi, Kenya
| | - Christian O Odinga
- International Livestock Research Institute, Old Naivasha Road, PO Box 30709 00100, Nairobi, Kenya
| | - Allan Ogendo
- Veterinary Department, Busia County Government, PO Box Private Bag 50400, Busia, Kenya
| | - Joseph Ogola
- Veterinary Department, Bungoma County Government, PO Box 2489 50200, Bungoma, Kenya
| | - Eric M Fèvre
- Institute of Infection and Global Health, University of Liverpool, 8 West Derby Street, Liverpool L69 7BE, UK; International Livestock Research Institute, Old Naivasha Road, PO Box 30709 00100, Nairobi, Kenya
| | - Mark Blaxter
- Institute of Evolutionary Biology, Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
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33
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Mead D, Hailer F, Chadwick E, Portela Miguez R, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Doulcan JD, Dudchenko O, Omer A, Weisz D, Lieberman Aiden E, McCarthy S, Howe K, Sims Y, Torrance J, Tracey A, Challis R, Durbin R, Blaxter M. The genome sequence of the Eurasian river otter, Lutra lutra Linnaeus 1758. Wellcome Open Res 2020; 5:33. [PMID: 32258427 PMCID: PMC7097881 DOI: 10.12688/wellcomeopenres.15722.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2020] [Indexed: 01/10/2023] Open
Abstract
We present a genome assembly from an individual male Lutra lutra (the Eurasian river otter; Vertebrata; Mammalia; Eutheria; Carnivora; Mustelidae). The genome sequence is 2.44 gigabases in span. The majority of the assembly is scaffolded into 20 chromosomal pseudomolecules, with both X and Y sex chromosomes assembled.
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Affiliation(s)
- Dan Mead
- Wellcome Genome Campus, Wellcome Sanger Institute,, Hinxton, CB10 1SA, UK
| | - Frank Hailer
- Cardiff Otter Project, Cardiff University School of Biosciences, Cardiff, CF10 3AX, UK
| | - Elisabeth Chadwick
- Cardiff Otter Project, Cardiff University School of Biosciences, Cardiff, CF10 3AX, UK
| | | | - Michelle Smith
- Wellcome Genome Campus, Wellcome Sanger Institute,, Hinxton, CB10 1SA, UK
| | - Craig Corton
- Wellcome Genome Campus, Wellcome Sanger Institute,, Hinxton, CB10 1SA, UK
| | - Karen Oliver
- Wellcome Genome Campus, Wellcome Sanger Institute,, Hinxton, CB10 1SA, UK
| | - Jason Skelton
- Wellcome Genome Campus, Wellcome Sanger Institute,, Hinxton, CB10 1SA, UK
| | - Emma Betteridge
- Wellcome Genome Campus, Wellcome Sanger Institute,, Hinxton, CB10 1SA, UK
| | | | - Olga Dudchenko
- Baylor College of Medicine, Houston, Texas, TX 77030 USA, USA
| | - Arina Omer
- Baylor College of Medicine, Houston, Texas, TX 77030 USA, USA
| | - David Weisz
- Baylor College of Medicine, Houston, Texas, TX 77030 USA, USA
| | | | - Shane McCarthy
- Wellcome Genome Campus, Wellcome Sanger Institute,, Hinxton, CB10 1SA, UK
| | - Kerstin Howe
- Wellcome Genome Campus, Wellcome Sanger Institute,, Hinxton, CB10 1SA, UK
| | - Ying Sims
- Wellcome Genome Campus, Wellcome Sanger Institute,, Hinxton, CB10 1SA, UK
| | - James Torrance
- Wellcome Genome Campus, Wellcome Sanger Institute,, Hinxton, CB10 1SA, UK
| | - Alan Tracey
- Wellcome Genome Campus, Wellcome Sanger Institute,, Hinxton, CB10 1SA, UK
| | - Richard Challis
- Wellcome Genome Campus, Wellcome Sanger Institute,, Hinxton, CB10 1SA, UK
| | - Richard Durbin
- Wellcome Genome Campus, Wellcome Sanger Institute,, Hinxton, CB10 1SA, UK
| | - Mark Blaxter
- Wellcome Genome Campus, Wellcome Sanger Institute,, Hinxton, CB10 1SA, UK
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34
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Mead D, Fingland K, Cripps R, Portela Miguez R, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Dolucan J, Dudchenko O, Omer AD, Weisz D, Lieberman Aiden E, Fedrigo O, Mountcastle J, Jarvis E, McCarthy SA, Sims Y, Torrance J, Tracey A, Howe K, Challis R, Durbin R, Blaxter M. The genome sequence of the Eurasian red squirrel, Sciurus vulgaris Linnaeus 1758. Wellcome Open Res 2020; 5:18. [PMID: 32587897 PMCID: PMC7309416 DOI: 10.12688/wellcomeopenres.15679.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2020] [Indexed: 01/27/2023] Open
Abstract
We present a genome assembly from an individual male Sciurus vulgaris (the Eurasian red squirrel; Vertebrata; Mammalia; Eutheria; Rodentia; Sciuridae). The genome sequence is 2.88 gigabases in span. The majority of the assembly is scaffolded into 21 chromosomal-level scaffolds, with both X and Y sex chromosomes assembled.
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Affiliation(s)
- Daniel Mead
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Kathryn Fingland
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Nottingham, NG25 0QF, UK
| | - Rachel Cripps
- The Wildlife Trust for Lancashire, Manchester and North Merseyside, Preston, PR5 6BY, UK
| | | | - Michelle Smith
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Craig Corton
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Karen Oliver
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Jason Skelton
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Emma Betteridge
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Jale Dolucan
- Baylor College of Medicine, Houston, TX, 77030, USA
| | | | | | - David Weisz
- Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Olivier Fedrigo
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, 10065, USA
| | - Jacquelyn Mountcastle
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, 10065, USA
| | - Erich Jarvis
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, 10065, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Shane A. McCarthy
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Ying Sims
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - James Torrance
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Richard Challis
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Richard Durbin
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
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35
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Pascoal S, Risse JE, Zhang X, Blaxter M, Cezard T, Challis RJ, Gharbi K, Hunt J, Kumar S, Langan E, Liu X, Rayner JG, Ritchie MG, Snoek BL, Trivedi U, Bailey NW. Field cricket genome reveals the footprint of recent, abrupt adaptation in the wild. Evol Lett 2019; 4:19-33. [PMID: 32055408 PMCID: PMC7006468 DOI: 10.1002/evl3.148] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/21/2019] [Accepted: 11/13/2019] [Indexed: 12/31/2022] Open
Abstract
Evolutionary adaptation is generally thought to occur through incremental mutational steps, but large mutational leaps can occur during its early stages. These are challenging to study in nature due to the difficulty of observing new genetic variants as they arise and spread, but characterizing their genomic dynamics is important for understanding factors favoring rapid adaptation. Here, we report genomic consequences of recent, adaptive song loss in a Hawaiian population of field crickets (Teleogryllus oceanicus). A discrete genetic variant, flatwing, appeared and spread approximately 15 years ago. Flatwing erases sound‐producing veins on male wings. These silent flatwing males are protected from a lethal, eavesdropping parasitoid fly. We sequenced, assembled and annotated the cricket genome, produced a linkage map, and identified a flatwing quantitative trait locus covering a large region of the X chromosome. Gene expression profiling showed that flatwing is associated with extensive genome‐wide effects on embryonic gene expression. We found that flatwing male crickets express feminized chemical pheromones. This male feminizing effect, on a different sexual signaling modality, is genetically associated with the flatwing genotype. Our findings suggest that the early stages of evolutionary adaptation to extreme pressures can be accompanied by greater genomic and phenotypic disruption than previously appreciated, and highlight how abrupt adaptation might involve suites of traits that arise through pleiotropy or genomic hitchhiking.
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Affiliation(s)
- Sonia Pascoal
- Department of Zoology University of Cambridge Cambridge CB2 3EJ United Kingdom
| | - Judith E Risse
- Division of Bioinformatics, Department of Plant Sciences Wageningen University & Research Wageningen 6708 PB The Netherlands.,Animal Ecology Netherlands Institute of Ecology Wageningen 6700 AB The Netherlands
| | - Xiao Zhang
- School of Biology University of St Andrews St Andrews Fife KY16 9TH United Kingdom
| | - Mark Blaxter
- Edinburgh Genomics University of Edinburgh Edinburgh EH9 3JT United Kingdom.,Institute of Evolutionary Biology University of Edinburgh Edinburgh EH9 3JT United Kingdom
| | - Timothee Cezard
- Edinburgh Genomics University of Edinburgh Edinburgh EH9 3JT United Kingdom
| | - Richard J Challis
- Edinburgh Genomics University of Edinburgh Edinburgh EH9 3JT United Kingdom
| | - Karim Gharbi
- Edinburgh Genomics University of Edinburgh Edinburgh EH9 3JT United Kingdom.,Earlham Institute Norwich Research Park Norwich NR4 7UZ United Kingdom
| | - John Hunt
- School of Science and Health and the Hawkesbury Institute for the Environment Western Sydney University Penrith NSW 2751 Australia.,Centre for Ecology and Conservation University of Exeter Penryn TR10 9FE United Kingdom
| | - Sujai Kumar
- Edinburgh Genomics University of Edinburgh Edinburgh EH9 3JT United Kingdom
| | - Emma Langan
- Edinburgh Genomics University of Edinburgh Edinburgh EH9 3JT United Kingdom.,School of Environmental Sciences University of East Anglia Norwich NR4 7UZ United Kingdom
| | - Xuan Liu
- Centre for Genomic Research University of Liverpool Liverpool L69 7ZB United Kingdom
| | - Jack G Rayner
- School of Biology University of St Andrews St Andrews Fife KY16 9TH United Kingdom
| | - Michael G Ritchie
- School of Biology University of St Andrews St Andrews Fife KY16 9TH United Kingdom
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics Utrecht University Utrecht 3584 CH The Netherlands.,Terrestrial Ecology Netherlands Institute of Ecology Wageningen 6700 AB The Netherlands
| | - Urmi Trivedi
- Edinburgh Genomics University of Edinburgh Edinburgh EH9 3JT United Kingdom
| | - Nathan W Bailey
- School of Biology University of St Andrews St Andrews Fife KY16 9TH United Kingdom
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36
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Schiffer PH, Danchin EGJ, Burnell AM, Creevey CJ, Wong S, Dix I, O'Mahony G, Culleton BA, Rancurel C, Stier G, Martínez-Salazar EA, Marconi A, Trivedi U, Kroiher M, Thorne MAS, Schierenberg E, Wiehe T, Blaxter M. Signatures of the Evolution of Parthenogenesis and Cryptobiosis in the Genomes of Panagrolaimid Nematodes. iScience 2019; 21:587-602. [PMID: 31759330 PMCID: PMC6889759 DOI: 10.1016/j.isci.2019.10.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 07/17/2019] [Accepted: 10/21/2019] [Indexed: 12/12/2022] Open
Abstract
Most animal species reproduce sexually and fully parthenogenetic lineages are usually short lived in evolution. Still, parthenogenesis may be advantageous as it avoids the cost of sex and permits colonization by single individuals. Panagrolaimid nematodes have colonized environments ranging from arid deserts to Arctic and Antarctic biomes. Many are obligatory meiotic parthenogens, and most have cryptobiotic abilities, being able to survive repeated cycles of complete desiccation and freezing. To identify systems that may contribute to these striking abilities, we sequenced and compared the genomes and transcriptomes of parthenogenetic and outcrossing panagrolaimid species, including cryptobionts and non-cryptobionts. The parthenogens are triploids, most likely originating through hybridization. Adaptation to cryptobiosis shaped the genomes of panagrolaimid nematodes and is associated with the expansion of gene families and signatures of selection on genes involved in cryptobiosis. All panagrolaimids have acquired genes through horizontal gene transfer, some of which are likely to contribute to cryptobiosis.
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Affiliation(s)
- Philipp H Schiffer
- CLOE, Department for Biosciences, University College London, London, UK; Zoologisches Institut, Universität zu Köln, 50674 Köln, Germany; Institut für Genetik, Universität zu Köln, 50674 Köln, Germany.
| | | | - Ann M Burnell
- Maynooth University Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland
| | | | - Simon Wong
- Irish Centre for High-End Computing, Tower Building, Trinity Technology & Enterprise Campus, Grand Canal Quay, Dublin D02 HP83, Ireland
| | - Ilona Dix
- Maynooth University Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland
| | - Georgina O'Mahony
- Maynooth University Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland
| | - Bridget A Culleton
- Maynooth University Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland; Megazyme, Bray Business Park, Bray, Co. Wicklow A98 YV29, Ireland
| | | | - Gary Stier
- Zoologisches Institut, Universität zu Köln, 50674 Köln, Germany
| | - Elizabeth A Martínez-Salazar
- Unidad Académica de Ciencias Biológicas, Laboratorio de Colecciones Biológicas y Sistemática Molecular, Universidad Autónoma de Zacatecas, Zacatecas, México
| | - Aleksandra Marconi
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Urmi Trivedi
- Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Michael Kroiher
- Zoologisches Institut, Universität zu Köln, 50674 Köln, Germany
| | - Michael A S Thorne
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | | | - Thomas Wiehe
- Institut für Genetik, Universität zu Köln, 50674 Köln, Germany
| | - Mark Blaxter
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3FL, UK; Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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37
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Hearn J, Blaxter M, Schönrogge K, Nieves-Aldrey JL, Pujade-Villar J, Huguet E, Drezen JM, Shorthouse JD, Stone GN. Genomic dissection of an extended phenotype: Oak galling by a cynipid gall wasp. PLoS Genet 2019; 15:e1008398. [PMID: 31682601 PMCID: PMC6855507 DOI: 10.1371/journal.pgen.1008398] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/14/2019] [Accepted: 10/23/2019] [Indexed: 12/13/2022] Open
Abstract
Galls are plant tissues whose development is induced by another organism for the inducer's benefit. 30,000 arthropod species induce galls, and in most cases the inducing effectors and target plant systems are unknown. Cynipid gall wasps are a speciose monophyletic radiation that induce structurally complex galls on oaks and other plants. We used a model system comprising the gall wasp Biorhiza pallida and the oak Quercus robur to characterise inducer and host plant gene expression at defined stages through the development of galled and ungalled plant tissues, and tested alternative hypotheses for the origin and type of galling effectors and plant metabolic pathways involved. Oak gene expression patterns diverged markedly during development of galled and normal buds. Young galls showed elevated expression of oak genes similar to legume root nodule Nod factor-induced early nodulin (ENOD) genes and developmental parallels with oak buds. In contrast, mature galls showed substantially different patterns of gene expression to mature leaves. While most oak transcripts could be functionally annotated, many gall wasp transcripts of interest were novel. We found no evidence in the gall wasp for involvement of third-party symbionts in gall induction, for effector delivery using virus-like-particles, or for gallwasp expression of genes coding for plant hormones. Many differentially and highly expressed genes in young larvae encoded secretory peptides, which we hypothesise are effector proteins exported to plant tissues. Specifically, we propose that host arabinogalactan proteins and gall wasp chitinases interact in young galls to generate a somatic embryogenesis-like process in oak tissues surrounding the gall wasp larvae. Gall wasp larvae also expressed genes encoding multiple plant cell wall degrading enzymes (PCWDEs). These have functional orthologues in other gall inducing cynipids but not in figitid parasitoid sister groups, suggesting that they may be evolutionary innovations associated with cynipid gall induction. Plant galls are induced by organisms that manipulate host plant development to produce novel structures. The organisms involved range from mutualistic (such as nitrogen fixing bacteria) to parasitic. In the case of parasites, the gall benefits only the gall-inducing partner. A wide range of organisms can induce galls, but the processes involved are understood only for some bacterial and fungal galls. Cynipid gall wasps induce diverse and structurally complex galls, particularly on oaks (Quercus). We used transcriptome and genome sequencing for one gall wasp and its host oak to identify genes active in gall development. On the plant side, when compared to normally developing bud tissues, young gall tissues showed elevated expression of loci similar to those found in nitrogen-fixing root nodules of leguminous plants. On the wasp side, we found no evidence for involvement of viruses or microorganisms carried by the insects in gall induction or delivery of inducing stimuli. We found that gall wasps express many genes whose products may be secreted to the host, including enzymes that degrade plant cell walls. Genome comparisons between galling and non-galling relatives showed cell wall-degrading enzymes are restricted to gall inducers, and hence potentially key components of a gall inducing lifestyle.
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Affiliation(s)
- Jack Hearn
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Institute of Evolutionary Biology, University of Edinburgh, King’s Buildings, Edinburgh, United Kingdom
- * E-mail: (JH); (GNS)
| | - Mark Blaxter
- Institute of Evolutionary Biology, University of Edinburgh, King’s Buildings, Edinburgh, United Kingdom
| | | | - José-Luis Nieves-Aldrey
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (CSIC), Madrid, Spain
| | | | - Elisabeth Huguet
- UMR 7261 CNRS, Institut de Recherche sur la Biologie de l’Insecte, Faculté des Sciences et Techniques, Université de Tours, France
| | - Jean-Michel Drezen
- UMR 7261 CNRS, Institut de Recherche sur la Biologie de l’Insecte, Faculté des Sciences et Techniques, Université de Tours, France
| | | | - Graham N. Stone
- Institute of Evolutionary Biology, University of Edinburgh, King’s Buildings, Edinburgh, United Kingdom
- * E-mail: (JH); (GNS)
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38
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Edelman NB, Frandsen PB, Miyagi M, Clavijo B, Davey J, Dikow RB, García-Accinelli G, Van Belleghem SM, Patterson N, Neafsey DE, Challis R, Kumar S, Moreira GRP, Salazar C, Chouteau M, Counterman BA, Papa R, Blaxter M, Reed RD, Dasmahapatra KK, Kronforst M, Joron M, Jiggins CD, McMillan WO, Di Palma F, Blumberg AJ, Wakeley J, Jaffe D, Mallet J. Genomic architecture and introgression shape a butterfly radiation. Science 2019; 366:594-599. [PMID: 31672890 PMCID: PMC7197882 DOI: 10.1126/science.aaw2090] [Citation(s) in RCA: 229] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 09/16/2019] [Indexed: 12/26/2022]
Abstract
We used 20 de novo genome assemblies to probe the speciation history and architecture of gene flow in rapidly radiating Heliconius butterflies. Our tests to distinguish incomplete lineage sorting from introgression indicate that gene flow has obscured several ancient phylogenetic relationships in this group over large swathes of the genome. Introgressed loci are underrepresented in low-recombination and gene-rich regions, consistent with the purging of foreign alleles more tightly linked to incompatibility loci. Here, we identify a hitherto unknown inversion that traps a color pattern switch locus. We infer that this inversion was transferred between lineages by introgression and is convergent with a similar rearrangement in another part of the genus. These multiple de novo genome sequences enable improved understanding of the importance of introgression and selective processes in adaptive radiation.
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Affiliation(s)
- Nathaniel B Edelman
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20560, USA
| | - Miriam Miyagi
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - John Davey
- Bioscience Technology Facility, Department of Biology, University of York, York YO10 5DD, UK
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Rebecca B Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20560, USA
| | | | - Steven M Van Belleghem
- Department of Biology, University of Puerto Rico, Río Piedras Campus, San Juan, PR 00931-3360, Puerto Rico
| | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
| | - Daniel E Neafsey
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Harvard TH Chan School of Public Health, Boston, MA 02115, USA
| | - Richard Challis
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Sujai Kumar
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Gilson R P Moreira
- Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, 91501-970 Brasil
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Carrera 24, No. 63C-69, Bogotá D.C. 111221, Colombia
| | - Mathieu Chouteau
- Laboratoire Ecologie, Evolution, Interactions des Systèmes Amazoniens (LEEISA), USR 3456, Université De Guyane, CNRS Guyane, 275 Route de Montabo, 97334 Cayenne, French Guiana
| | - Brian A Counterman
- Department of Biological Sciences, Mississippi State University, Starkville, MS 39762, USA
| | - Riccardo Papa
- Department of Biology, University of Puerto Rico, Río Piedras Campus, San Juan, PR 00931-3360, Puerto Rico
- Molecular Sciences and Research Center, University of Puerto Rico, San Juan, PR 00931-3360, Puerto Rico
| | - Mark Blaxter
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Kanchon K Dasmahapatra
- Bioscience Technology Facility, Department of Biology, University of York, York YO10 5DD, UK
| | - Marcus Kronforst
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - Mathieu Joron
- CEFE, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, EPHE, IRD, 34090 Montpellier, France
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Apartado 0843-03092 Panamá, Panama
| | | | - Andrew J Blumberg
- Department of Mathematics, University of Texas, Austin, TX 78712, USA
| | - John Wakeley
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - David Jaffe
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- 10x Genomics, Pleasanton, CA 94566, USA
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
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39
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Chow FWN, Koutsovoulos G, Ovando-Vázquez C, Neophytou K, Bermúdez-Barrientos JR, Laetsch DR, Robertson E, Kumar S, Claycomb JM, Blaxter M, Abreu-Goodger C, Buck AH. Secretion of an Argonaute protein by a parasitic nematode and the evolution of its siRNA guides. Nucleic Acids Res 2019; 47:3594-3606. [PMID: 30820541 PMCID: PMC6468290 DOI: 10.1093/nar/gkz142] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 02/16/2019] [Accepted: 02/25/2019] [Indexed: 12/18/2022] Open
Abstract
Extracellular RNA has been proposed to mediate communication between cells and organisms however relatively little is understood regarding how specific sequences are selected for export. Here, we describe a specific Argonaute protein (exWAGO) that is secreted in extracellular vesicles (EVs) released by the gastrointestinal nematode Heligmosomoides bakeri, at multiple copies per EV. Phylogenetic and gene expression analyses demonstrate exWAGO orthologues are highly conserved and abundantly expressed in related parasites but highly diverged in free-living genus Caenorhabditis. We show that the most abundant small RNAs released from the nematode parasite are not microRNAs as previously thought, but rather secondary small interfering RNAs (siRNAs) that are produced by RNA-dependent RNA Polymerases. The siRNAs that are released in EVs have distinct evolutionary properties compared to those resident in free-living or parasitic nematodes. Immunoprecipitation of exWAGO demonstrates that it specifically associates with siRNAs from transposons and newly evolved repetitive elements that are packaged in EVs and released into the host environment. Together this work demonstrates molecular and evolutionary selectivity in the small RNA sequences that are released in EVs into the host environment and identifies a novel Argonaute protein as the mediator of this.
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Affiliation(s)
- Franklin Wang-Ngai Chow
- Institute of Immunology and Infection Research, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Georgios Koutsovoulos
- Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Cesaré Ovando-Vázquez
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato 36824, México
| | - Kyriaki Neophytou
- Institute of Immunology and Infection Research, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Jose R Bermúdez-Barrientos
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato 36824, México
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Elaine Robertson
- Institute of Immunology and Infection Research, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Sujai Kumar
- Institute of Immunology and Infection Research, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Mark Blaxter
- Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JT, UK.,Centre for Immunity, Infection and Evolution, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Cei Abreu-Goodger
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato 36824, México
| | - Amy H Buck
- Institute of Immunology and Infection Research, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JT, UK.,Centre for Immunity, Infection and Evolution, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JT, UK
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40
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Wan F, Yin C, Tang R, Chen M, Wu Q, Huang C, Qian W, Rota-Stabelli O, Yang N, Wang S, Wang G, Zhang G, Guo J, Gu LA, Chen L, Xing L, Xi Y, Liu F, Lin K, Guo M, Liu W, He K, Tian R, Jacquin-Joly E, Franck P, Siegwart M, Ometto L, Anfora G, Blaxter M, Meslin C, Nguyen P, Dalíková M, Marec F, Olivares J, Maugin S, Shen J, Liu J, Guo J, Luo J, Liu B, Fan W, Feng L, Zhao X, Peng X, Wang K, Liu L, Zhan H, Liu W, Shi G, Jiang C, Jin J, Xian X, Lu S, Ye M, Li M, Yang M, Xiong R, Walters JR, Li F. A chromosome-level genome assembly of Cydia pomonella provides insights into chemical ecology and insecticide resistance. Nat Commun 2019; 10:4237. [PMID: 31530873 PMCID: PMC6748993 DOI: 10.1038/s41467-019-12175-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 08/20/2019] [Indexed: 01/27/2023] Open
Abstract
The codling moth Cydia pomonella, a major invasive pest of pome fruit, has spread around the globe in the last half century. We generated a chromosome-level scaffold assembly including the Z chromosome and a portion of the W chromosome. This assembly reveals the duplication of an olfactory receptor gene (OR3), which we demonstrate enhances the ability of C. pomonella to exploit kairomones and pheromones in locating both host plants and mates. Genome-wide association studies contrasting insecticide-resistant and susceptible strains identify hundreds of single nucleotide polymorphisms (SNPs) potentially associated with insecticide resistance, including three SNPs found in the promoter of CYP6B2. RNAi knockdown of CYP6B2 increases C. pomonella sensitivity to two insecticides, deltamethrin and azinphos methyl. The high-quality genome assembly of C. pomonella informs the genetic basis of its invasiveness, suggesting the codling moth has distinctive capabilities and adaptive potential that may explain its worldwide expansion. The codling moth, Cydia pomonella, is one of the major pests of pome fruit (apples and pears) and walnuts. Here, the authors sequence and analyze its genome, providing insights on olfactory and detoxification processes that may underlie its worldwide expansion.
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Affiliation(s)
- Fanghao Wan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. .,Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
| | - Chuanlin Yin
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Rui Tang
- MARA-CABI Joint Laboratory for Bio-safety, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Maohua Chen
- Northwest A&F University, State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture, Yangling, 712100, China
| | - Qiang Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Cong Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Plant Protection, Hunan Agricultural University, Changsha, 410128, China
| | - Wanqiang Qian
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Omar Rota-Stabelli
- Department of Sustainable Agro-ecosystems and Bioresources, IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010, San Michele all'Adige (TN), Italy
| | - Nianwan Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Shuping Wang
- Technical Centre for Animal Plant and Food Inspection and Quarantine, Shanghai Custom, Shanghai, 200135, China
| | - Guirong Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Guifen Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jianyang Guo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Liuqi Aloy Gu
- Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66046, USA
| | - Longfei Chen
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Longsheng Xing
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yu Xi
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Feiling Liu
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Kejian Lin
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Mengbo Guo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wei Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Kang He
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Ruizheng Tian
- Northwest A&F University, State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture, Yangling, 712100, China
| | | | - Pierre Franck
- INRA, Plantes et Systèmes de culture Horticole, 228 route de l'Aérodrome, 84914, Avignon Cedex 09, France
| | - Myriam Siegwart
- INRA, Plantes et Systèmes de culture Horticole, 228 route de l'Aérodrome, 84914, Avignon Cedex 09, France
| | - Lino Ometto
- Department of Sustainable Agro-ecosystems and Bioresources, IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010, San Michele all'Adige (TN), Italy.,Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy
| | - Gianfranco Anfora
- Department of Sustainable Agro-ecosystems and Bioresources, IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010, San Michele all'Adige (TN), Italy.,Centre Agriculture Food Environment (C3A), University of Trento, 38010, San Michele all'Adige (TN), Italy
| | - Mark Blaxter
- Edinburgh Genomics, and Institute of Evolutionary Biology, School of Biological Sciences, The King's Buildings, The University of Edinburgh, Edinburgh, EH9 3JT, UK
| | - Camille Meslin
- INRA, Institute of Ecology and Environmental Sciences of Paris, 78000, Versailles, France
| | - Petr Nguyen
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 37005, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, Branišovská 1760, 37005, České Budějovice, Czech Republic
| | - Martina Dalíková
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 37005, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, Branišovská 1760, 37005, České Budějovice, Czech Republic
| | - František Marec
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 37005, České Budějovice, Czech Republic
| | - Jérôme Olivares
- INRA, Plantes et Systèmes de culture Horticole, 228 route de l'Aérodrome, 84914, Avignon Cedex 09, France
| | - Sandrine Maugin
- INRA, Plantes et Systèmes de culture Horticole, 228 route de l'Aérodrome, 84914, Avignon Cedex 09, France
| | - Jianru Shen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jinding Liu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinmeng Guo
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiapeng Luo
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Bo Liu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Wei Fan
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Likai Feng
- Institute of Plant Protection, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Xianxin Zhao
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xiong Peng
- Northwest A&F University, State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture, Yangling, 712100, China
| | - Kang Wang
- Northwest A&F University, State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture, Yangling, 712100, China
| | - Lang Liu
- Northwest A&F University, State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau of Ministry of Agriculture, Yangling, 712100, China
| | - Haixia Zhan
- MARA-CABI Joint Laboratory for Bio-safety, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wanxue Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Guoliang Shi
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chunyan Jiang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jisu Jin
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Plant Protection, Hunan Agricultural University, Changsha, 410128, China
| | - Xiaoqing Xian
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Sha Lu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Mingli Ye
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou, 310015, China
| | - Meizhen Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Minglu Yang
- Xinjiang Production & Construction Corps Key Laboratory of Integrated Pest Management on Agriculture in South Xinjiang, Tarim University, Alar, 843300, China
| | - Renci Xiong
- Xinjiang Production & Construction Corps Key Laboratory of Integrated Pest Management on Agriculture in South Xinjiang, Tarim University, Alar, 843300, China
| | - James R Walters
- Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66046, USA.
| | - Fei Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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41
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Grosmaire M, Launay C, Siegwald M, Brugière T, Estrada-Virrueta L, Berger D, Burny C, Modolo L, Blaxter M, Meister P, Félix MA, Gouyon PH, Delattre M. Males as somatic investment in a parthenogenetic nematode. Science 2019; 363:1210-1213. [PMID: 30872523 DOI: 10.1126/science.aau0099] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 02/13/2019] [Indexed: 12/20/2022]
Abstract
We report the reproductive strategy of the nematode Mesorhabditis belari This species produces only 9% males, whose sperm is necessary to fertilize and activate the eggs. However, most of the fertilized eggs develop without using the sperm DNA and produce female individuals. Only in 9% of eggs is the male DNA utilized, producing sons. We found that mixing of parental genomes only gives rise to males because the Y-bearing sperm of males are much more competent than the X-bearing sperm for penetrating the eggs. In this previously unrecognized strategy, asexual females produce few sexual males whose genes never reenter the female pool. Here, production of males is of interest only if sons are more likely to mate with their sisters. Using game theory, we show that in this context, the production of 9% males by M. belari females is an evolutionary stable strategy.
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Affiliation(s)
- Manon Grosmaire
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, ENS, UCBL, CNRS, INSERM, UMR 5239, U 1210, F-69364 Lyon, France
| | - Caroline Launay
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, ENS, UCBL, CNRS, INSERM, UMR 5239, U 1210, F-69364 Lyon, France
| | - Marion Siegwald
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, SU, EPHE, UA, CP 39, 57 rue Cuvier, 75005 Paris, France
| | - Thibault Brugière
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, ENS, UCBL, CNRS, INSERM, UMR 5239, U 1210, F-69364 Lyon, France
| | - Lilia Estrada-Virrueta
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, ENS, UCBL, CNRS, INSERM, UMR 5239, U 1210, F-69364 Lyon, France
| | - Duncan Berger
- The Ashworth Laboratories, Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Claire Burny
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, ENS, UCBL, CNRS, INSERM, UMR 5239, U 1210, F-69364 Lyon, France.,Present address: Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna A-1210, Austria
| | - Laurent Modolo
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, ENS, UCBL, CNRS, INSERM, UMR 5239, U 1210, F-69364 Lyon, France
| | - Mark Blaxter
- The Ashworth Laboratories, Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Peter Meister
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
| | - Marie-Anne Félix
- Département de Biologie, Ecole Normale Supérieure, IBENS, CNRS, Inserm, PSL Research University, 75005 Paris, France
| | - Pierre-Henri Gouyon
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, SU, EPHE, UA, CP 39, 57 rue Cuvier, 75005 Paris, France
| | - Marie Delattre
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, ENS, UCBL, CNRS, INSERM, UMR 5239, U 1210, F-69364 Lyon, France.
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42
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Stevens L, Félix M, Beltran T, Braendle C, Caurcel C, Fausett S, Fitch D, Frézal L, Gosse C, Kaur T, Kiontke K, Newton MD, Noble LM, Richaud A, Rockman MV, Sudhaus W, Blaxter M. Comparative genomics of 10 new Caenorhabditis species. Evol Lett 2019; 3:217-236. [PMID: 31007946 PMCID: PMC6457397 DOI: 10.1002/evl3.110] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 02/08/2019] [Accepted: 02/25/2019] [Indexed: 01/29/2023] Open
Abstract
The nematode Caenorhabditis elegans has been central to the understanding of metazoan biology. However, C. elegans is but one species among millions and the significance of this important model organism will only be fully revealed if it is placed in a rich evolutionary context. Global sampling efforts have led to the discovery of over 50 putative species from the genus Caenorhabditis, many of which await formal species description. Here, we present species descriptions for 10 new Caenorhabditis species. We also present draft genome sequences for nine of these new species, along with a transcriptome assembly for one. We exploit these whole-genome data to reconstruct the Caenorhabditis phylogeny and use this phylogenetic tree to dissect the evolution of morphology in the genus. We reveal extensive variation in genome size and investigate the molecular processes that underlie this variation. We show unexpected complexity in the evolutionary history of key developmental pathway genes. These new species and the associated genomic resources will be essential in our attempts to understand the evolutionary origins of the C. elegans model.
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Affiliation(s)
- Lewis Stevens
- Institute of Evolutionary Biology, Ashworth Laboratories, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3JTUnited Kingdom
| | - Marie‐Anne Félix
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, École Normale SupérieureParis Sciences et Lettres75005ParisFrance
| | - Toni Beltran
- MRC London Institute of Medical SciencesLondonW12 0NNUnited Kingdom
| | - Christian Braendle
- Université Côte d'Azur, Centre National de la Recherche Scientifique, InsermInstitute of Biology Valrose06108NiceFrance
| | - Carlos Caurcel
- Institute of Evolutionary Biology, Ashworth Laboratories, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3JTUnited Kingdom
| | - Sarah Fausett
- Université Côte d'Azur, Centre National de la Recherche Scientifique, InsermInstitute of Biology Valrose06108NiceFrance
| | - David Fitch
- Department of BiologyNew York UniversityNew YorkNew York10003
| | - Lise Frézal
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, École Normale SupérieureParis Sciences et Lettres75005ParisFrance
| | - Charlie Gosse
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, École Normale SupérieureParis Sciences et Lettres75005ParisFrance
| | - Taniya Kaur
- Center for Genomics and Systems Biology, Department of BiologyNew York UniversityNew YorkNew York10003
| | - Karin Kiontke
- Department of BiologyNew York UniversityNew YorkNew York10003
| | - Matthew D. Newton
- MRC London Institute of Medical SciencesLondonW12 0NNUnited Kingdom
- Molecular Virology, Department of MedicineImperial College LondonDu Cane RoadLondonW12 0NNUnited Kingdom
| | - Luke M. Noble
- Center for Genomics and Systems Biology, Department of BiologyNew York UniversityNew YorkNew York10003
| | - Aurélien Richaud
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, École Normale SupérieureParis Sciences et Lettres75005ParisFrance
| | - Matthew V. Rockman
- Center for Genomics and Systems Biology, Department of BiologyNew York UniversityNew YorkNew York10003
| | - Walter Sudhaus
- Institut für Biologie/ZoologieFreie Universität BerlinBerlinD‐14195Germany
| | - Mark Blaxter
- Institute of Evolutionary Biology, Ashworth Laboratories, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3JTUnited Kingdom
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43
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Hearn J, Pearson M, Blaxter M, Wilson PJ, Little TJ. Genome-wide methylation is modified by caloric restriction in Daphnia magna. BMC Genomics 2019; 20:197. [PMID: 30849937 PMCID: PMC6408862 DOI: 10.1186/s12864-019-5578-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 03/01/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The degradation of epigenetic control with age is associated with progressive diseases of ageing, including cancers, immunodeficiency and diabetes. Reduced caloric intake slows the effects of ageing and age-related disease in vertebrates and invertebrates, a process potentially mediated by the impact of caloric restriction on epigenetic factors such as DNA methylation. We used whole genome bisulphite sequencing to study how DNA methylation patterns change with diet in a small invertebrate, the crustacean Daphnia magna. Daphnia show the classic response of longer life under caloric restriction (CR), and they reproduce clonally, which permits the study of epigenetic changes in the absence of genetic variation. RESULTS Global cytosine followed by guanine (CpG) methylation was 0.7-0.9%, and there was no difference in overall methylation levels between normal and calorie restricted replicates. However, 333 differentially methylated regions (DMRs) were evident between the normally fed and CR replicates post-filtering. Of these 65% were hypomethylated in the CR group, and 35% were hypermethylated in the CR group. CONCLUSIONS Our results demonstrate an effect of CR on the genome-wide methylation profile. This adds to a growing body of research in Daphnia magna that demonstrate an epigenomic response to environmental stimuli. Specifically, gene Ontology (GO) term enrichment of genes associated with hyper and hypo-methylated DMRs showed significant enrichment for methylation and acyl-CoA dehydrogenase activity, which are linked to current understanding of their roles in CR in invertebrate model organisms.
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Affiliation(s)
- Jack Hearn
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Marianne Pearson
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Mark Blaxter
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Philip J. Wilson
- School of Energy, Geoscience, Infrastructure & Environment, Heriot-Watt University, Edinburgh, UK
| | - Tom J. Little
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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44
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Sjokvist E, Lemcke R, Kamble M, Turner F, Blaxter M, Havis NHD, Lyngkjær MF, Radutoiu S. Dissection of Ramularia Leaf Spot Disease by Integrated Analysis of Barley and Ramularia collo-cygni Transcriptome Responses. Mol Plant Microbe Interact 2019; 32:176-193. [PMID: 30681911 DOI: 10.1094/mpmi-05-18-0113-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Ramularia leaf spot disease (RLS), caused by the ascomycete fungus Ramularia collo-cygni, has emerged as a major economic disease of barley. No substantial resistance has been identified, so far, among barley genotypes and, based on the epidemiology of the disease, a quantitative genetic determinacy of RLS has been suggested. The relative contributions of barley and R. collo-cygni genetics to disease infection and epidemiology are practically unknown. Here, we present an integrated genome-wide analysis of host and pathogen transcriptome landscapes identified in a sensitive barley cultivar following infection by an aggressive R. collo-cygni isolate. We compared transcriptional responses in the infected and noninfected leaf samples in order to identify which molecular events are associated with RLS symptom development. We found a large proportion of R. collo-cygni genes to be expressed in planta and that many were also closely associated with the infection stage. The transition from surface to apoplastic colonization was associated with downregulation of cell wall-degrading genes and upregulation of nutrient uptake and resistance to oxidative stresses. Interestingly, the production of secondary metabolites was dynamically regulated within the fungus, indicating that R. collo-cygni produces a diverse panel of toxic compounds according to the infection stage. A defense response against R. collo-cygni was identified in barley at the early, asymptomatic infection and colonization stages. We found activation of ethylene signaling, jasmonic acid signaling, and phenylpropanoid and flavonoid pathways to be highly induced, indicative of a classical response to necrotrophic pathogens. Disease development was found to be associated with gene expression patterns similar to those found at the onset of leaf senescence, when nutrients, possibly, are used by the infecting fungus. These analyses, combining both barley and R. collo-cygni transcript profiles, demonstrate the activation of complex transcriptional programs in both organisms.
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Affiliation(s)
- Elisabet Sjokvist
- 1 Scotlands Rural College, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JG, Scotland, U.K
- 2 Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3JT, U.K
| | - Rene Lemcke
- 3 Department of Plant and Environmental Sciences, Copenhagen University, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Manoj Kamble
- 4 Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds vej 10, Aarhus, Denmark; and
| | - Frances Turner
- 5 Edinburgh Genomics, School of Biological Sciences, The University of Edinburgh; Scotland, U.K
| | - Mark Blaxter
- 2 Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3JT, U.K
| | - Neil H D Havis
- 1 Scotlands Rural College, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JG, Scotland, U.K
| | - Michael F Lyngkjær
- 3 Department of Plant and Environmental Sciences, Copenhagen University, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Simona Radutoiu
- 4 Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds vej 10, Aarhus, Denmark; and
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45
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Beltran T, Barroso C, Birkle TY, Stevens L, Schwartz HT, Sternberg PW, Fradin H, Gunsalus K, Piano F, Sharma G, Cerrato C, Ahringer J, Martínez-Pérez E, Blaxter M, Sarkies P. Comparative Epigenomics Reveals that RNA Polymerase II Pausing and Chromatin Domain Organization Control Nematode piRNA Biogenesis. Dev Cell 2019; 48:793-810.e6. [PMID: 30713076 PMCID: PMC6436959 DOI: 10.1016/j.devcel.2018.12.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 12/06/2018] [Accepted: 12/27/2018] [Indexed: 12/30/2022]
Abstract
Piwi-interacting RNAs (piRNAs) are important for genome regulation across metazoans, but their biogenesis evolves rapidly. In Caenorhabditis elegans, piRNA loci are clustered within two 3-Mb regions on chromosome IV. Each piRNA locus possesses an upstream motif that recruits RNA polymerase II to produce an ∼28 nt primary transcript. We used comparative epigenomics across nematodes to gain insight into the origin, evolution, and mechanism of nematode piRNA biogenesis. We show that the piRNA upstream motif is derived from core promoter elements controlling snRNA transcription. We describe two alternative modes of piRNA organization in nematodes: in C. elegans and closely related nematodes, piRNAs are clustered within repressive H3K27me3 chromatin, while in other species, typified by Pristionchus pacificus, piRNAs are found within introns of active genes. Additionally, we discover that piRNA production depends on sequence signals associated with RNA polymerase II pausing. We show that pausing signals synergize with chromatin to control piRNA transcription. Nematode piRNA transcription evolved from small nuclear RNA biogenesis Clustered piRNAs are produced from regulated (H3K27me3) chromatin domains Dispersed piRNAs are produced from active (H3K36me3) chromatin domains RNA polymerase II pausing determines the short (∼28 nt) length of piRNA precursors
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Affiliation(s)
- Toni Beltran
- MRC London Institute of Medical Sciences, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, London W12 0NN, UK
| | - Consuelo Barroso
- MRC London Institute of Medical Sciences, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, London W12 0NN, UK
| | - Timothy Y Birkle
- MRC London Institute of Medical Sciences, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, London W12 0NN, UK
| | - Lewis Stevens
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3TF, UK
| | - Hillel T Schwartz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hélène Fradin
- Department of Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Kristin Gunsalus
- Department of Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Fabio Piano
- Department of Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Garima Sharma
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Chiara Cerrato
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Julie Ahringer
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Enrique Martínez-Pérez
- MRC London Institute of Medical Sciences, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, London W12 0NN, UK
| | - Mark Blaxter
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3TF, UK.
| | - Peter Sarkies
- MRC London Institute of Medical Sciences, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, London W12 0NN, UK.
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46
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McLean F, Berger D, Laetsch DR, Schwartz HT, Blaxter M. Improving the annotation of the Heterorhabditis bacteriophora genome. Gigascience 2018; 7:4958981. [PMID: 29617768 PMCID: PMC5906903 DOI: 10.1093/gigascience/giy034] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 03/23/2018] [Indexed: 12/03/2022] Open
Abstract
Background Genome assembly and annotation remain exacting tasks. As the tools available for these tasks improve, it is useful to return to data produced with earlier techniques to assess their credibility and correctness. The entomopathogenic nematode Heterorhabditis bacteriophora is widely used to control insect pests in horticulture. The genome sequence for this species was reported to encode an unusually high proportion of unique proteins and a paucity of secreted proteins compared to other related nematodes. Findings We revisited the H. bacteriophora genome assembly and gene predictions to determine whether these unusual characteristics were biological or methodological in origin. We mapped an independent resequencing dataset to the genome and used the blobtools pipeline to identify potential contaminants. While present (0.2% of the genome span, 0.4% of predicted proteins), assembly contamination was not significant. Conclusions Re-prediction of the gene set using BRAKER1 and published transcriptome data generated a predicted proteome that was very different from the published one. The new gene set had a much reduced complement of unique proteins, better completeness values that were in line with other related species’ genomes, and an increased number of proteins predicted to be secreted. It is thus likely that methodological issues drove the apparent uniqueness of the initial H. bacteriophora genome annotation and that similar contamination and misannotation issues affect other published genome assemblies.
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Affiliation(s)
- Florence McLean
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Duncan Berger
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Hillel T Schwartz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Mark Blaxter
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
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47
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Fleming JF, Kristensen RM, Sørensen MV, Park TYS, Arakawa K, Blaxter M, Rebecchi L, Guidetti R, Williams TA, Roberts NW, Vinther J, Pisani D. Molecular palaeontology illuminates the evolution of ecdysozoan vision. Proc Biol Sci 2018; 285:20182180. [PMID: 30518575 PMCID: PMC6283943 DOI: 10.1098/rspb.2018.2180] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 11/13/2018] [Indexed: 12/25/2022] Open
Abstract
Colour vision is known to have arisen only twice-once in Vertebrata and once within the Ecdysozoa, in Arthropoda. However, the evolutionary history of ecdysozoan vision is unclear. At the molecular level, visual pigments, composed of a chromophore and a protein belonging to the opsin family, have different spectral sensitivities and these mediate colour vision. At the morphological level, ecdysozoan vision is conveyed by eyes of variable levels of complexity; from the simple ocelli observed in the velvet worms (phylum Onychophora) to the marvellously complex eyes of insects, spiders, and crustaceans. Here, we explore the evolution of ecdysozoan vision at both the molecular and morphological level; combining analysis of a large-scale opsin dataset that includes previously unknown ecdysozoan opsins with morphological analyses of key Cambrian fossils with preserved eye structures. We found that while several non-arthropod ecdysozoan lineages have multiple opsins, arthropod multi-opsin vision evolved through a series of gene duplications that were fixed in a period of 35-71 million years (Ma) along the stem arthropod lineage. Our integrative study of the fossil and molecular record of vision indicates that fossils with more complex eyes were likely to have possessed a larger complement of opsin genes.
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Affiliation(s)
- James F Fleming
- School of Earth Sciences, University of Bristol, Queen's Road, Bristol, UK
| | | | | | - Tae-Yoon S Park
- Division of Polar Earth-System Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Mark Blaxter
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Lorena Rebecchi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Campi 213/D, Modena, Italy
| | - Roberto Guidetti
- Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Campi 213/D, Modena, Italy
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Tyndall Avenue, Bristol, UK
| | - Nicholas W Roberts
- School of Biological Sciences, University of Bristol, Tyndall Avenue, Bristol, UK
| | - Jakob Vinther
- School of Earth Sciences, University of Bristol, Queen's Road, Bristol, UK
| | - Davide Pisani
- School of Earth Sciences, University of Bristol, Queen's Road, Bristol, UK
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48
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Regan T, Barnett MW, Laetsch DR, Bush SJ, Wragg D, Budge GE, Highet F, Dainat B, de Miranda JR, Watson M, Blaxter M, Freeman TC. Characterisation of the British honey bee metagenome. Nat Commun 2018; 9:4995. [PMID: 30478343 PMCID: PMC6255801 DOI: 10.1038/s41467-018-07426-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 10/29/2018] [Indexed: 12/30/2022] Open
Abstract
The European honey bee (Apis mellifera) plays a major role in pollination and food production. Honey bee health is a complex product of the environment, host genetics and associated microbes (commensal, opportunistic and pathogenic). Improved understanding of these factors will help manage modern challenges to bee health. Here we used DNA sequencing to characterise the genomes and metagenomes of 19 honey bee colonies from across Britain. Low heterozygosity was observed in many Scottish colonies which had high similarity to the native dark bee. Colonies exhibited high diversity in composition and relative abundance of individual microbiome taxa. Most non-bee sequences were derived from known honey bee commensal bacteria or pathogens. However, DNA was also detected from additional fungal, protozoan and metazoan species. To classify cobionts lacking genomic information, we developed a novel network analysis approach for clustering orphan DNA contigs. Our analyses shed light on microbial communities associated with honey bees and demonstrate the power of high-throughput, directed metagenomics for identifying novel biological threats in agroecosystems.
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Affiliation(s)
- Tim Regan
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, Edinburgh, UK.
| | - Mark W Barnett
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, Edinburgh, UK
| | - Dominik R Laetsch
- The Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, EH9 3JG, UK
| | - Stephen J Bush
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, Edinburgh, UK
| | - David Wragg
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, Edinburgh, UK
| | - Giles E Budge
- Fera, The National Agrifood Innovation Campus, Sand Hutton, YO41 1LZ, York, UK
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Fiona Highet
- Science and Advice for Scottish Agriculture, 1 Roddinglaw Road, Edinburgh, EH12 9FJ, UK
| | - Benjamin Dainat
- Agroscope, Swiss Bee Research Centre, Schwarzenburgstrasse 161, CH-3003, Bern, Switzerland
| | - Joachim R de Miranda
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Mick Watson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, Edinburgh, UK
| | - Mark Blaxter
- The Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, EH9 3JG, UK.
| | - Tom C Freeman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, Edinburgh, UK.
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49
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Llorens C, Arcos SC, Robertson L, Ramos R, Futami R, Soriano B, Ciordia S, Careche M, González-Muñoz M, Jiménez-Ruiz Y, Carballeda-Sangiao N, Moneo I, Albar JP, Blaxter M, Navas A. Functional insights into the infective larval stage of Anisakis simplex s.s., Anisakis pegreffii and their hybrids based on gene expression patterns. BMC Genomics 2018; 19:592. [PMID: 30086708 PMCID: PMC6080401 DOI: 10.1186/s12864-018-4970-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 07/30/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Anisakis simplex sensu stricto and Anisakis pegreffii are sibling species of nematodes parasitic on marine mammals. Zoonotic human infection with third stage infective larvae causes anisakiasis, a debilitating and potentially fatal disease. These 2 species show evidence of hybridisation in geographical areas where they are sympatric. How the species and their hybrids differ is still poorly understood. RESULTS Third stage larvae of Anisakis simplex s.s., Anisakis pegreffii and hybrids were sampled from Merluccius merluccius (Teleosti) hosts captured in waters of the FAO 27 geographical area. Specimens of each species and hybrids were distinguished with a diagnostic genetic marker (ITS). RNA was extracted from pools of 10 individuals of each taxon. Transcriptomes were generated using Illumina RNA-Seq, and assembled de novo. A joint assembly (here called merged transcriptome) of all 3 samples was also generated. The inferred transcript sets were functionally annotated and compared globally and also on subsets of secreted proteins and putative allergen families. While intermediary metabolism appeared to be typical for nematodes in the 3 evaluated taxa, their transcriptomes present strong levels of differential expression and enrichment, mainly of transcripts related to metabolic pathways and gene ontologies associated to energy metabolism and other pathways, with significant presence of excreted/secreted proteins, most of them allergens. The allergome of the 2 species and their hybrids has also been thoroughly studied; at least 74 different allergen families were identified in the transcriptomes. CONCLUSIONS A. simplex s.s., A. pegreffi and their hybrids differ in gene expression patterns in the L3 stage. Strong parent-of-origin effects were observed: A. pegreffi alleles dominate in the expression patterns of hybrids albeit the latter, and A. pegreffii also display significant differences indicating that hybrids are intermediate biological entities among their parental species, and thus of outstanding interest in the study of speciation in nematodes. Analyses of differential expression based on genes coding for secreted proteins suggests that co-infections presents different repertoires of released protein to the host environment. Both species and their hybrids, share more allergen genes than previously thought and are likely to induce overlapping disease responses.
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Affiliation(s)
- C. Llorens
- Biotechvana, Scientific Park, University of Valencia, Calle Catedrático José Beltrán 2, 46980 Paterna, Valencia Spain
| | - S. C. Arcos
- Departamento Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Calle José Gutiérrez Abascal, 2, 28006 Madrid, Spain
| | - L. Robertson
- Departamento Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Calle José Gutiérrez Abascal, 2, 28006 Madrid, Spain
| | - R. Ramos
- Unidad de Genómica, Campus de Cantoblanco, Scientific Park of Madrid, Calle Faraday, 7, Campus de Cantoblanco, 28049 Madrid, Spain
| | - R. Futami
- Biotechvana, Scientific Park, University of Valencia, Calle Catedrático José Beltrán 2, 46980 Paterna, Valencia Spain
| | - B. Soriano
- Biotechvana, Scientific Park, University of Valencia, Calle Catedrático José Beltrán 2, 46980 Paterna, Valencia Spain
| | - S. Ciordia
- Unidad de Proteomica Centro Nacional de Biotecnología, CSIC, Calle Darwin, 3, 28049 Madrid, Spain
| | - M. Careche
- Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), Calle José Antonio Novais, 10, 28040 Madrid, Spain
| | - M. González-Muñoz
- Servicio de Immunología, Hospital Universitario La Paz, Paseo de la Castellana, 261, 28046 Madrid, Spain
| | - Y. Jiménez-Ruiz
- Departamento Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Calle José Gutiérrez Abascal, 2, 28006 Madrid, Spain
| | - N. Carballeda-Sangiao
- Servicio de Immunología, Hospital Universitario La Paz, Paseo de la Castellana, 261, 28046 Madrid, Spain
| | - I. Moneo
- Servicio de Immunología, Hospital Universitario La Paz, Paseo de la Castellana, 261, 28046 Madrid, Spain
| | - J. P. Albar
- Unidad de Proteomica Centro Nacional de Biotecnología, CSIC, Calle Darwin, 3, 28049 Madrid, Spain
| | - M. Blaxter
- Edinburgh Genomics, and Institute of Evolutionary Biology, School of Biological Sciences, The King’s Buildings, The University of Edinburgh, Edinburgh, EH9 3JT UK
| | - A. Navas
- Departamento Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Calle José Gutiérrez Abascal, 2, 28006 Madrid, Spain
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50
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McMullan M, Rafiqi M, Kaithakottil G, Clavijo BJ, Bilham L, Orton E, Percival-Alwyn L, Ward BJ, Edwards A, Saunders DGO, Garcia Accinelli G, Wright J, Verweij W, Koutsovoulos G, Yoshida K, Hosoya T, Williamson L, Jennings P, Ioos R, Husson C, Hietala AM, Vivian-Smith A, Solheim H, MaClean D, Fosker C, Hall N, Brown JKM, Swarbreck D, Blaxter M, Downie JA, Clark MD. The ash dieback invasion of Europe was founded by two genetically divergent individuals. Nat Ecol Evol 2018; 2:1000-1008. [PMID: 29686237 PMCID: PMC5969572 DOI: 10.1038/s41559-018-0548-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 03/27/2018] [Indexed: 11/22/2022]
Abstract
Accelerating international trade and climate change make pathogen spread an increasing concern. Hymenoscyphus fraxineus, the causal agent of ash dieback, is a fungal pathogen that has been moving across continents and hosts from Asian to European ash. Most European common ash trees (Fraxinus excelsior) are highly susceptible to H. fraxineus, although a minority (~5%) have partial resistance to dieback. Here, we assemble and annotate a H. fraxineus draft genome which approaches chromosome scale. Pathogen genetic diversity across Europe and in Japan, reveals a strong bottleneck in Europe, though a signal of adaptive diversity remains in key host interaction genes. We find that the European population was founded by two divergent haploid individuals. Divergence between these haplotypes represents the ancestral polymorphism within a large source population. Subsequent introduction from this source would greatly increase adaptive potential of the pathogen. Thus, further introgression of H. fraxineus into Europe represents a potential threat and Europe-wide biological security measures are needed to manage this disease.
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Affiliation(s)
- Mark McMullan
- The Earlham Institute, Norwich Research Park, Norwich, UK.
| | | | | | | | | | | | | | - Ben J Ward
- The Earlham Institute, Norwich Research Park, Norwich, UK
| | - Anne Edwards
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | | | - Walter Verweij
- The Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - Kentaro Yoshida
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK.,Graduate school of Agricultural Science, Kobe University, Kobe, Hyogo, Japan
| | - Tsuyoshi Hosoya
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
| | | | | | - Renaud Ioos
- ANSES Laboratoire de la Santé des Végétaux, Malzéville, France
| | | | - Ari M Hietala
- Norwegian Institute of Bioeconomy Research, Ås, Norway
| | | | | | - Dan MaClean
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | | | - Neil Hall
- The Earlham Institute, Norwich Research Park, Norwich, UK
| | | | | | - Mark Blaxter
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, UK.,Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Matthew D Clark
- The Earlham Institute, Norwich Research Park, Norwich, UK. .,Department of Life Sciences, Natural History Museum, London, UK.
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