Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China.
Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
Comp Biochem Physiol Part D Genomics Proteomics. 2023 Mar;45:101045. doi: 10.1016/j.cbd.2022.101045. Epub 2022 Nov 29.
The European flat oyster (Ostrea edulis) is an endangered and economically important marine bivalve species that plays a critical role in the coastal ecosystem. Here, we report a high-quality chromosome-level genome assembly of O. edulis, generated using PacBio HiFi-CCS long reads and annotated with Nanopore full-length transcriptome. The O. edulis genome covers 946.06 Mb (scaffold N50 94.82 Mb) containing 34,495 protein-coding genes and a high proportion of repeat sequences (58.49 %). The reconstructed demographic histories show that O. edulis population might be shaped by breeding habit (embryo brooding) and historical climatic change. Comparative genomic analysis indicates that transposable elements may drive lineage-specific evolution in oysters. Notably, the O. edulis genome has a Hox gene cluster rearrangement that has never been reported in bivalves, making this species valuable for evolutionary studies of molluscan diversification. Moreover, genome expansion of O. edulis is probably central to its adaptation to filter-feeding and sessile lifestyles, as well as embryo brooding and pathogen resistance, in coastal ecosystems. This chromosome-level genome assembly provides new insights into the genome feature of oysters, and presents an important resource for genetic research, evolutionary studies, and biological conservation of O. edulis.
欧洲扁牡蛎（Ostrea edulis）是一种濒危的、具有重要经济价值的海洋双壳贝类，在沿海生态系统中起着至关重要的作用。在这里，我们报道了一种高质量的欧洲扁牡蛎染色体水平基因组组装，该组装使用 PacBio HiFi-CCS 长读长和 Nanopore 全长转录组进行注释。O. edulis 基因组覆盖 946.06 Mb（scaffold N50 为 94.82 Mb），包含 34495 个蛋白质编码基因和大量重复序列（58.49%）。重建的种群历史表明，O. edulis 的种群可能受到繁殖习惯（胚胎孵育）和历史气候变化的影响。比较基因组分析表明，转座元件可能驱动牡蛎的谱系特异性进化。值得注意的是，O. edulis 基因组存在 Hox 基因簇重排，这在双壳类动物中从未报道过，这使得该物种成为研究软体动物多样化的进化的有价值的材料。此外，O. edulis 的基因组扩张可能是其适应滤食和固着生活方式、胚胎孵育和抗病原体的关键，在沿海生态系统中。这个染色体水平的基因组组装为牡蛎的基因组特征提供了新的见解，并为 O. edulis 的遗传研究、进化研究和生物保护提供了重要资源。
