The Pacific oyster (Crassostrea gigas) genome is highly polymorphic and affluent in structural variations (SVs), a significant source of genetic variation underlying inter-individual differences. Here, we used two genome assemblies and 535 individuals of genome re-sequencing data to construct a comprehensive landscape of structural variations in the Pacific oyster. Through whole-genome alignment, 11,087 short SVs and 11,561 copy number variations (CNVs) were identified. While analysis of re-sequencing data revealed 511,170 short SVs and 979,486 CNVs, a total of 63,100 short SVs and 58,182 CNVs were identified in at least 20 samples and regarded as common variations. Based on the common short SVs, both Fst and Pi ratio statistical methods were employed to detect the selective sweeps between 20 oyster individuals from the fast-growing strain and 20 individuals from their corresponding wild population. A total of 514 overlapped regions (8.76 Mb), containing 746 candidate genes, were identified by both approaches, in addition with 103 genes within 61 common CNVs only detected in the fast-growing strains. The GO enrichment and KEGG pathway analysis indicated that the identified candidate genes were mostly associated with apical part of cell and were significantly enriched in several metabolism-related pathways, including tryptophan metabolism and histidine metabolism. This work provided a comprehensive landscape of SVs and revealed their responses to selection, which will be valuable for further investigations on genome evolution under selection in the oysters.

太平洋牡蛎 ( Crassostrea gigas ) 基因组具有高度多态性和丰富的结构变异 (SV)，这是个体差异背后遗传变异的重要来源。在这里，我们使用两个基因组组装和 535 个基因组重测序数据来构建太平洋牡蛎结构变异的综合景观。通过全基因组比对，确定了 11,087 个短 SV 和 11,561 个拷贝数变异 (CNV)。虽然对重测序数据的分析揭示了 511,170 个短 SV 和 979,486 个 CNV，但在至少 20 个样本中总共鉴定了 63,100 个短 SV 和 58,182 个 CNV，并被视为常见变异。基于常见的短 SV，Fst和Pi比率统计方法被用来检测来自快速生长菌株的20个牡蛎个体与其对应的野生种群的20个个体之间的选择性扫描。两种方法共鉴定了 514 个重叠区域 (8.76 Mb)，包含 746 个候选基因，此外，61 个常见 CNV 中的 103 个基因仅在快速生长的菌株中检测到。GO富集和KEGG通路分析表明，鉴定出的候选基因主要与细胞的顶端部分相关，并且在几种代谢相关通路中显着富集，包括色氨酸代谢和组氨酸代谢。这项工作提供了 SV 的全面景观，并揭示了他们对选择的反应，