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dc.contributor.authorTigano, Anna
dc.contributor.authorJacobs, Arne
dc.contributor.authorWilder, Aryn P.
dc.contributor.authorNand, Ankita
dc.contributor.authorZhan, Ye
dc.contributor.authorDekker, Job
dc.contributor.authorTherkildsen, Nina Overgaard
dc.date2022-08-11T08:10:00.000
dc.date.accessioned2022-08-23T16:52:04Z
dc.date.available2022-08-23T16:52:04Z
dc.date.issued2021-06-08
dc.date.submitted2021-10-27
dc.identifier.citation<p>Tigano A, Jacobs A, Wilder AP, Nand A, Zhan Y, Dekker J, Therkildsen NO. Chromosome-Level Assembly of the Atlantic Silverside Genome Reveals Extreme Levels of Sequence Diversity and Structural Genetic Variation. Genome Biol Evol. 2021 Jun 8;13(6):evab098. doi: 10.1093/gbe/evab098. Erratum in: Genome Biol Evol. 2021 Jul 6;13(7): PMID: 33964136; PMCID: PMC8214408. <a href="https://doi.org/10.1093/gbe/evab098">Link to article on publisher's site</a></p>
dc.identifier.issn1759-6653 (Linking)
dc.identifier.doi10.1093/gbe/evab098
dc.identifier.pmid33964136
dc.identifier.urihttp://hdl.handle.net/20.500.14038/41981
dc.description<p>This article is based on a previously available preprint in <a href="https://doi.org/10.1101/2020.10.27.357293" target="_blank" title="view preprint">bioRxiv</a>.</p>
dc.description.abstractThe levels and distribution of standing genetic variation in a genome can provide a wealth of insights about the adaptive potential, demographic history, and genome structure of a population or species. As structural variants are increasingly associated with traits important for adaptation and speciation, investigating both sequence and structural variation is essential for wholly tapping this potential. Using a combination of shotgun sequencing, 10x Genomics linked reads and proximity-ligation data (Chicago and Hi-C), we produced and annotated a chromosome-level genome assembly for the Atlantic silverside (Menidia menidia)-an established ecological model for studying the phenotypic effects of natural and artificial selection-and examined patterns of genomic variation across two individuals sampled from different populations with divergent local adaptations. Levels of diversity varied substantially across each chromosome, consistently being highly elevated near the ends (presumably near telomeric regions) and dipping to near zero around putative centromeres. Overall, our estimate of the genome-wide average heterozygosity in the Atlantic silverside is among the highest reported for a fish, or any vertebrate (1.32-1.76% depending on inference method and sample). Furthermore, we also found extreme levels of structural variation, affecting approximately 23% of the total genome sequence, including multiple large inversions ( > 1 Mb and up to 12.6 Mb) associated with previously identified haploblocks showing strong differentiation between locally adapted populations. These extreme levels of standing genetic variation are likely associated with large effective population sizes and may help explain the remarkable adaptive divergence among populations of the Atlantic silverside.
dc.language.isoen_US
dc.relation<p><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=33964136&dopt=Abstract">Link to Article in PubMed</a></p>
dc.rightsCopyright The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectHi-C
dc.subjectfish
dc.subjectgenome assembly
dc.subjectheterozygosity
dc.subjectinversions
dc.subjectnucleotide diversity
dc.subjectEcology and Evolutionary Biology
dc.subjectGenomics
dc.subjectStructural Biology
dc.titleChromosome-Level Assembly of the Atlantic Silverside Genome Reveals Extreme Levels of Sequence Diversity and Structural Genetic Variation
dc.typeJournal Article
dc.source.journaltitleGenome biology and evolution
dc.source.volume13
dc.source.issue6
dc.identifier.legacyfulltexthttps://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=5817&amp;context=oapubs&amp;unstamped=1
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/oapubs/4784
dc.identifier.contextkey25625670
refterms.dateFOA2022-08-23T16:52:05Z
html.description.abstract<p>The levels and distribution of standing genetic variation in a genome can provide a wealth of insights about the adaptive potential, demographic history, and genome structure of a population or species. As structural variants are increasingly associated with traits important for adaptation and speciation, investigating both sequence and structural variation is essential for wholly tapping this potential. Using a combination of shotgun sequencing, 10x Genomics linked reads and proximity-ligation data (Chicago and Hi-C), we produced and annotated a chromosome-level genome assembly for the Atlantic silverside (Menidia menidia)-an established ecological model for studying the phenotypic effects of natural and artificial selection-and examined patterns of genomic variation across two individuals sampled from different populations with divergent local adaptations. Levels of diversity varied substantially across each chromosome, consistently being highly elevated near the ends (presumably near telomeric regions) and dipping to near zero around putative centromeres. Overall, our estimate of the genome-wide average heterozygosity in the Atlantic silverside is among the highest reported for a fish, or any vertebrate (1.32-1.76% depending on inference method and sample). Furthermore, we also found extreme levels of structural variation, affecting approximately 23% of the total genome sequence, including multiple large inversions ( > 1 Mb and up to 12.6 Mb) associated with previously identified haploblocks showing strong differentiation between locally adapted populations. These extreme levels of standing genetic variation are likely associated with large effective population sizes and may help explain the remarkable adaptive divergence among populations of the Atlantic silverside.</p>
dc.identifier.submissionpathoapubs/4784
dc.contributor.departmentProgram in Systems Biology
dc.source.pagesevab098


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Copyright The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Except where otherwise noted, this item's license is described as Copyright The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.