银唇珠母贝（Pinctada maxima）的染色体水平基因组组装与注释

The chromosome-level genome assembly and annotation of the silver-lipped pearl oyster, Pinctada maxima.

作者信息

Mu Qianqian, Li Zijian, Liu Mingyang, Zhao Baojun, Yang Zhihui, Bao Zhenmin, Hu Jingjie, Liu Pingping

机构信息

Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, 572000, China.

MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.

出版信息

Sci Data. 2025 Jul 26;12(1):1301. doi: 10.1038/s41597-025-05607-3.

DOI:10.1038/s41597-025-05607-3

PMID:40715147

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12297345/

Abstract

The silver-lipped pearl oyster (Pinctada maxima) is a valuable tropical aquaculture species, playing a crucial economic role in the global pearl industry. However, the lack of genomic reference limits our in-depth understanding of this species in genome-based breeding, conservation, evolution and adaptation. Here, annotated chromosome-level reference genome for P. maxima was generated by integrating PacBio long-read sequencing, Illumina short-read sequencing, and Hi-C sequencing data. The total genome size is 1,264.93 Mb, with contig N50 and scaffold N50 of 649 kb and 89.19 Mb, respectively. The majority (97.94%) of the assembled genome was anchored to the 14 chromosomes by Hi-C analysis. The relatively high genome completeness was observed, with 97.38% (metazoa_odb10 database) and 95.26% (mollusca_odb10 database) in BUSCO analysis. Genome annotation revealed approximately 65.46% of the repeat sequences and 26,315 protein-coding genes. Comparative genome analysis revealed 28 expanded and 48 contracted families (p < 0.05) in P. maxima, with 3.2% of genes (894) being species-specific. This chromosome-level genome serves as an essential resource for research in evolutionary genomics, phylogenetics, and biomineralization.

摘要

银唇珠母贝（Pinctada maxima）是一种重要的热带水产养殖物种，在全球珍珠产业中发挥着关键的经济作用。然而，缺乏基因组参考限制了我们在基于基因组的育种、保护、进化和适应性方面对该物种的深入了解。在此，通过整合PacBio长读长测序、Illumina短读长测序和Hi-C测序数据，生成了银唇珠母贝的注释染色体水平参考基因组。基因组总大小为1264.93 Mb，重叠群N50和支架N50分别为649 kb和89.19 Mb。通过Hi-C分析，组装基因组的大部分（97.94%）被锚定到14条染色体上。观察到相对较高的基因组完整性，在BUSCO分析中，分别为97.38%（后生动物_odb10数据库）和95.26%（软体动物_odb10数据库）。基因组注释揭示了约65.46%的重复序列和26315个蛋白质编码基因。比较基因组分析显示，银唇珠母贝中有28个基因家族扩增，48个基因家族收缩（p < 0.05），其中3.2%的基因（894个）是物种特异性的。这个染色体水平的基因组是进化基因组学、系统发育学和生物矿化研究的重要资源。