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.
Highlights
IntroductionSchluter 2008; Tigano & Friesen 2016) and is important for natural populations to maximize their potential to adapt to changes in their environment
Standing genetic variation is widely recognized as the main source of adaptation (Barrett &Schluter 2008; Tigano & Friesen 2016) and is important for natural populations to maximize their potential to adapt to changes in their environment
We generated a chromosome-level assembly of the Atlantic silverside genome by integrating long-range information from synthetic long reads from 10X Genomics, in vitro proximity ligation data from Chicago libraries, and Hi-C proximity ligation data from whole cells
Summary
Schluter 2008; Tigano & Friesen 2016) and is important for natural populations to maximize their potential to adapt to changes in their environment. Quantification of standing genetic variation has been based on sequence variation, often across a limited number of genetic markers, or small microsatellite repeats. Structural variation, including changes in the position, orientation, and number of copies of DNA sequence, is generally neglected as a type of standing genetic variation. Structural variation has been associated directly or indirectly with many traits involved in speciation and adaptation and is abundant in the few genomes in which they have been catalogued (Wellenreuther & Bernatchez 2018; Catanach et al 2019; Lucek et al 2019; Mérot et al 2020; Tigano et al 2020; Weissensteiner et al 2020). Structural variants can directly affect phenotypic traits, such as the insertion of a repeated transposable element in the iconic case of industrial melanism in the peppered moth
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