热带紫海胆厚刺海胆的染色体水平基因组组装

A chromosome-level genome assembly of tropical purple sea urchin Heliocidaris crassispina.

作者信息

Liu Yang, Chen Ting, Ma Bo, Yin Jiayue, Ren Chunhua, Jiang Xiao, Wang Yanhong, Pan Wenjie, Huang Jiasheng, Yu Suzhong, Luo Peng

机构信息

Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, CAS, Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.

University of Chinese Academy of Sciences, Beijing, 100049, China.

出版信息

Sci Data. 2024 Dec 18;11(1):1382. doi: 10.1038/s41597-024-04255-3.

DOI:10.1038/s41597-024-04255-3

PMID:39695201

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11655880/

Abstract

Heliocidaris crassispina is a tropical sea urchin that holds both ecological and economic value and serves as an ideal experimental animal. This study first employed a combination of PacBio HiFi and Hi-C sequencing data to present a high-quality, chromosome-level assembly of H. crassispina genome. This assembled genome spanned 709.77 Mb, with a contig N50 length of 4.98 Mb and a scaffold N50 length of 33.23 Mb. The assembly was anchored on 21 pseudo-chromosomes, covering 98.32% of the genome. A total of 18,665 protein-coding genes were identified, and BUSCO analysis revealed a completeness score of 97.1%. Additionally, non-coding RNAs (ncRNAs) were annotated, including miRNAs, rRNAs, tRNAs and snRNAs, providing a more complete functional understanding of the genome. The high-quality reference genome will enrich the current echinoderm genomic resources and provide a solid foundation for future studies on H. crassispina, including resource surveys, genomic breeding, and marine ranch management.

摘要

厚刺海胆是一种具有生态和经济价值的热带海胆，是理想的实验动物。本研究首次结合PacBio HiFi和Hi-C测序数据，呈现了高质量的厚刺海胆基因组染色体水平组装。该组装基因组跨度为709.77 Mb，重叠群N50长度为4.98 Mb，支架N50长度为33.23 Mb。该组装定位于21条假染色体上，覆盖了98.32%的基因组。共鉴定出18,665个蛋白质编码基因，BUSCO分析显示完整性得分97.1%。此外，还注释了非编码RNA（ncRNAs），包括miRNA、rRNA、tRNA和snRNA，从而对基因组有了更完整的功能理解。高质量的参考基因组将丰富当前的棘皮动物基因组资源，并为厚刺海胆未来的研究，包括资源调查、基因组育种和海洋牧场管理，提供坚实的基础。