ArticleGenome biology and evolution2021
Chromosome-Level Assembly of the Atlantic Silverside Genome Reveals Extreme Levels of Sequence Diversity and Structural Genetic Variation.
Article in Genome biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 41 citations in OpenAlex.
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- The promise and challenges of characterizing genome-wide structural variants: A case study in a critically endangered parrot.Molecular ecology resources · 2025Article
- Genomic evidence for fisheries-induced evolution in Eastern Baltic cod.Science advances · 2025Article
- Genetic Differentiation is Constrained to Chromosomal Inversions and Putative Centromeres in Locally Adapted Populations With Higher Gene Flow.Molecular biology and evolution · 2025Article
- Population stratification in Northern shrimp (Pandalus borealis) off Iceland evident from RADseq analysis.BMC ecology and evolution · 2025Article
- A Complete Assembly and Annotation of the American Shad Genome Yields Insights into the Origins of Diadromy.Genome biology and evolution · 2025Article
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- Phenotypic and Genomic Signatures of Latitudinal Local Adaptation Along With Prevailing Ocean Current in a Coastal Goby.Molecular ecology · 2025Article
- Complex Genomic Landscape of Inversion Polymorphism in Europe's Most Destructive Forest Pest.Genome biology and evolution · 2024Article
- Near chromosome-level and highly repetitive genome assembly of the snake pipefishGigaByte (Hong Kong, China) · 2024Article
- Detecting parallel polygenic adaptation to novel evolutionary pressure in wild populations: a case study in Atlantic cod (Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2023Article
- Lacustrine speciation associated with chromosomal inversion in a lineage of riverine fishes.Evolution; international journal of organic evolution · 2023Article
- Seascape Genomics and Phylogeography of the Sailfish (Istiophorus platypterus).Genome biology and evolution · 2023Article
- Sequencing Bait: Nuclear and Mitogenome Assembly of an Abundant Coastal Tropical and Subtropical Fish, Atherinomorus stipes.Genome biology and evolution · 2022Article
- Chromosome size affects sequence divergence between species through the interplay of recombination and selection.Evolution; international journal of organic evolution · 2022Article
- Expanding the conservation genomics toolbox: Incorporating structural variants to enhance genomic studies for species of conservation concern.Molecular ecology · 2021Article
- A candidate chromosome inversion in Arctic charr (Salvelinus alpinus) identified by population genetic analysis techniques.G3 (Bethesda, Md.) · 2021Article
Corrections and comments
- Erratum issued
Authors and funding
7 authors at 5 institutions in 1 country.
Funding
Abstract
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 ∼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.
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