Exceptional genome-wide copy number variation in the eastern oyster (Crassostrea virginica)

Authors: MODAK, TEJASHREE - University Of Rhode Island; LITTERMAN, ROBERT - University Of Rhode Island; PURITZ, JONATHAN - University Of Rhode Island; JOHNSON, KEVIN - Louisiana State University; ROBERTS, ERIN - University Of Rhode Island; Proestou, Dina; GUO, XIMING - Rutgers University; GOMEZ-CHIARRI, MARTA - University Of Rhode Island; SCHWARTZ, RACHEL - University Of Rhode Island

Submitted to: Philosophical Transactions of the Royal Society B
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/28/2021
Publication Date: 4/15/2021
Citation: Modak, T., Litterman, R., Puritz, J., Johnson, K., Roberts, E., Proestou, D.A., Guo, X., Gomez-Chiarri, M., Schwartz, R. 2021. Exceptional genome-wide copy number variation in the eastern oyster (Crassostrea virginica). Philosophical Transactions of the Royal Society B. https://doi.org/royalsocietypublishing.org/doi/10.1098/rstb.2020.0164.
DOI: https://doi.org/10.1098/rstb.2020.0164

Interpretive Summary: The recent sequencing and assembly of the Eastern oyster genome and subsequent resequencing of wild oysters collected from multiple regions along the Eastern US coast has enabled the examination of polymorphism and structural genomic variation within and across oyster populations. Copy number variation (CNV), or the number of times a specific sequence or gene is represented in the genome, can have tremendous impacts on how the genome and corresponding phenome evolve in response to environmental change, natural, and artificial selection. Here we report an extraordinary degree of CNV within the genome of this commercially important aquaculture species. Extensive CNV contributes to standing genetic variation and should facilitate selection for commercially important traits. Furthermore, CNV was reduced in inbred, selected oyster lines compared to wild populations.

Technical Abstract: Genomic structural variation is an important source of genetic and phenotypic diversity, playing a critical role in evolution. The recent availability of a high-quality reference genome for the eastern oyster, Crassostrea virginica, and whole genome sequence data of samples from across the species range in the United States of America, provides an opportunity to explore structural variation across the genome of this species. Our analysis shows copy number variation at a rate many times more (16.5%) than that of most model vertebrate species (2.1-14.6%). Duplications are widespread across all ten chromosomes with variation in frequency per chromosome ranging from 1.568e-05 on chr6 to 4.08E-05 on chr5. CNVs show large interindividual copy number variation and highlight chromosomal regions with higher density of duplications and copy number variation. A high percentage of duplications seen in C. virginica lie completely within (40.3%) genes and (5.05%) exons. These results support the hypothesis that structural changes can play a significant role in standing genetic variation in C. virginica, and potentially have a role in their adaptive and evolutionary success. In contrast, reduced standing variation is seen in inbred samples, suggesting that inbreeding reduces this form of diversity. Altogether, these results suggest that copy number variation accounts for an extensive amount of genetic variation in C. virginica