Wang Chengxin, Luo Site, Song Yong, Yang Liting, Wang Xinyue, Chen Shengao
College of Life Science and Technology/Tarim Research Center of Rare Fishes, Tarim University, CN-0997, Alar 843300, Xinjiang Uygur Autonomous Region, Xinjiang, China.
School of Life Sciences, Xiamen University, Xiamen, 361102, China.
Sci Data. 2024 Dec 31;11(1):1451. doi: 10.1038/s41597-024-04340-7.
Triplophysa bombifrons, a species of bony fish localized in China, has largely been understudied genetically, with limited data available beyond its mitochondrial genome. This study introduces a chromosome-level genome assembly for T. bombifrons, achieved through the integration of PacBio long-read sequencing and Hi-C chromatin interaction mapping. The assembly reveals a genome structure comprising 25 chromosomes and an overall size of 655.95 Mb. The quality of this assembly is demonstrated by a scaffold N50 length of 24.25 Mb, and a genome completeness evaluation via BUSCO, which shows that 97.4% of the Vertebrata Benchmarking Universal Single-Copy Orthologs are present. Gene prediction methods including de novo, homology-based, and transcript-based, identified 34,211 genes, with 34,151 being functionally annotated. These findings may provide valuable resources in conservation, functional genomics, and molecular breeding of T. bombifrons, as well as the molecular phylogenetics and evolutionary patterns in Triplophysa.
高原鳅属鱼类（Triplophysa bombifrons）是一种分布于中国的硬骨鱼类，在遗传学方面的研究很大程度上还不够深入，除了线粒体基因组外，可用数据有限。本研究通过整合PacBio长读长测序和Hi-C染色质相互作用图谱，介绍了高原鳅（T. bombifrons）的染色体水平基因组组装。该组装揭示了一个由25条染色体组成的基因组结构，总大小为655.95 Mb。该组装的质量通过支架N50长度为24.25 Mb以及通过BUSCO进行的基因组完整性评估得到证明，该评估表明存在97.4%的脊椎动物基准通用单拷贝直系同源基因。包括从头预测、基于同源性和基于转录本的基因预测方法，共鉴定出34,211个基因，其中34,151个具有功能注释。这些发现可能为高原鳅的保护、功能基因组学和分子育种，以及高原鳅属的分子系统发育和进化模式提供有价值的资源。
