Zhang Xinmiao, Xiong Dongmei, Jian Shenglong, Jiang Yu, Wang Lixin
College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
Qinghai Provincial Fishery Technology Extension Center, Xining, 810000, China.
BMC Genomics. 2025 Sep 26;26(1):839. doi: 10.1186/s12864-025-12057-z.
The Sichuan taimen (Hucho bleekeri Kimura) is a critically endangered fish species that has attracted significant attention and is classified as a national first-level protected species in China. Despite its ecological importance, genomic resources for the Sichuan taimen and its closely related species are limited, which hampers effective conservation efforts. A comprehensive understanding of the genomic characteristics of this species, particularly those related to its evolutionary adaptations and population dynamics, is essential for improving conservation strategies.
We present the first chromosome-level genome of the Sichuan taimen, with a final genome size of approximately 3.45 Gb. Notably, tandem repetitive sequences constitute 44.47% of the genome and significantly influence its genomic architecture and functional organization. Among these, VNTRs account for the majority of the tandem repeats, which Likely contributes to the relatively large genome size. Positive selection analysis revealed genes associated with immune responses and neurobiological functions, potentially facilitating adaptation to the unique environmental conditions of mountain stream habitats. Additionally, the divergence time between the Siberian taimen and the Sichuan taimen was estimated to be approximately 2.34 Mya, with a notable decline in their effective population size occurring around 1 Mya.
The genome assembly of the Sichuan taimen provides insights into its evolutionary adaptations, highlighting the functional significance of tandem repeats and positively selected genes. These findings establish a genomic foundation for elucidating its survival mechanisms in a unique habitat, and emphasize the critical role of integrating genomic data into conservation strategies to enhance the management of Sichuan taimen populations and contribute to the conservation of other endangered salmonid species.
四川哲罗鲑（Hucho bleekeri Kimura）是一种极度濒危的鱼类物种，已引起广泛关注，并被列为中国国家一级保护动物。尽管其具有重要的生态意义，但四川哲罗鲑及其近缘物种的基因组资源有限，这阻碍了有效的保护工作。全面了解该物种的基因组特征，特别是与其进化适应和种群动态相关的特征，对于改进保护策略至关重要。
我们展示了首个四川哲罗鲑的染色体水平基因组，最终基因组大小约为3.45Gb。值得注意的是，串联重复序列占基因组的44.47%，并对其基因组结构和功能组织产生显著影响。其中，可变数目串联重复序列（VNTRs）占串联重复序列的大部分，这可能是导致基因组相对较大的原因。正选择分析揭示了与免疫反应和神经生物学功能相关的基因，可能有助于适应山溪栖息地的独特环境条件。此外，估计西伯利亚哲罗鲑和四川哲罗鲑之间的分化时间约为234万年前，其有效种群大小在约100万年前显著下降。
四川哲罗鲑的基因组组装为其进化适应提供了见解，突出了串联重复序列和正选择基因的功能重要性。这些发现为阐明其在独特栖息地的生存机制奠定了基因组基础，并强调了将基因组数据整合到保护策略中的关键作用，以加强四川哲罗鲑种群的管理，并为其他濒危鲑科物种的保护做出贡献。
