Chromosome-Level Assembly of the Atlantic Silverside Genome Reveals Extreme Levels of Sequence Diversity and Structural Genetic Variation
Authors
Tigano, AnnaJacobs, Arne
Wilder, Aryn P.
Nand, Ankita
Zhan, Ye
Dekker, Job
Therkildsen, Nina Overgaard
UMass Chan Affiliations
Program in Systems BiologyDocument Type
Journal ArticlePublication Date
2021-06-08Keywords
Hi-Cfish
genome assembly
heterozygosity
inversions
nucleotide diversity
Ecology and Evolutionary Biology
Genomics
Structural Biology
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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.Source
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. Link to article on publisher's site
DOI
10.1093/gbe/evab098Permanent Link to this Item
http://hdl.handle.net/20.500.14038/41981PubMed ID
33964136Notes
This article is based on a previously available preprint in bioRxiv.
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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.Distribution License
http://creativecommons.org/licenses/by/4.0/ae974a485f413a2113503eed53cd6c53
10.1093/gbe/evab098
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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.