Dong Zhen, Bai Yitian, Liu Shikai, Yu Hong, Kong Lingfeng, Du Shaojun, Li Qi
Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China.
Institute of Marine and Environmental Technology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, United States.
Genomics. 2023 Mar;115(2):110582. doi: 10.1016/j.ygeno.2023.110582. Epub 2023 Feb 14.
The oyster Ostrea denselamellosa is a live-bearing species with a sharp decline in the natural population. Despite recent breakthroughs in long-read sequencing, high quality genomic data are very limited in O. denselamellosa. Here, we carried out the first whole genome sequencing at the chromosome-level in O. denselamellosa. Our studies yielded a 636 Mb assembly with scaffold N50 around 71.80 Mb. 608.3 Mb (95.6% of the assembly) were anchored to 10 chromosomes. A total of 26,412 protein-coding genes were predicted, of which 22,636 (85.7%) were functionally annotated. By comparative genomics, we found that long interspersed nuclear element (LINE) and short interspersed nuclear element (SINE) made up a larger proportion in O. denselamellosa genome than in other oysters'. Moreover, gene family analysis showed some initial insight into its evolution. This high-quality genome of O. denselamellosa provides a valuable genomic resource for studies of evolution, adaption and conservation in oysters.
密鳞牡蛎（Ostrea denselamellosa）是一种卵胎生物种，其天然种群数量急剧下降。尽管长读长测序最近取得了突破，但密鳞牡蛎的高质量基因组数据非常有限。在此，我们首次对密鳞牡蛎进行了染色体水平的全基因组测序。我们的研究产生了一个636 Mb的基因组组装，支架N50约为71.80 Mb。608.3 Mb（占组装的95.6%）被锚定到10条染色体上。总共预测了26412个蛋白质编码基因，其中22636个（85.7%）具有功能注释。通过比较基因组学，我们发现长散在核元件（LINE）和短散在核元件（SINE）在密鳞牡蛎基因组中所占比例比其他牡蛎的更大。此外，基因家族分析对其进化有了一些初步认识。密鳞牡蛎的这个高质量基因组为牡蛎的进化、适应性和保护研究提供了宝贵的基因组资源。
