ScholarWorks@중앙대학교

초록

Next-generation sequencing has significantly advanced omics and post-omics technologies, facilitating detailed analysis of whole-genome profiles through comparative genomics and reshaping our understanding of evolutionary and ecological dynamics for more precise biotechnological applications. Specifically, analyzing genomic similarities and differences through synteny and structural variations (SVs) has clarified the relationship between genetic variations and phenotypic changes. This study represents the first instance of employing chromosome-level comparative genomics and long-read SV detection in the Pacific oyster Crassostrea gigas, a species crucial for both ecology and economy, aiming to pinpoint genes and genomic regions linked to growth and disease. Utilizing the latest Pacific oyster genomes and their PacBio long reads, we uncovered significant genetic variability that explains differences between individuals. By integrating results from five state-of-the-art read mappers (LRA, Minimap2, NGMLR, Vulcan, and WinnowMap) and two SV callers (cuteSV and Sniffles2), we identified between 193 355 and 219 501 SVs, accounting for 183 Mb (31.2%) and 228 Mb (35.2%) of the total genome in two distinct reference genomes, respectively. This approach, leveraging PacBio long reads, surpassed short-read technologies in identifying candidate genes associated with SVs, such as bone morphogenetic proteins and superoxide dismutase, thereby highlighting their potential roles in growth and disease resistance. Our findings offer a comprehensive view of comparative genomics and long-read SVs, revealing their significance in oyster genome evolution and providing valuable insights for future marine biotechnological research, including the development of genome editing and surrogate broodstock technologies.

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