Shi Ling, Ng Judy Kin-Wing, Xiong Qing, Ao Kelvin Fu-Kiu, Shin Soo-Kyung, Law Cherie Tsz-Yiu, Mu Weixue, Liu Guang-Ming, Rao Shitao, Tsui Stephen Kwok-Wing
School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.
Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China.
BMC Genomics. 2025 May 26;26(1):529. doi: 10.1186/s12864-025-11719-2.
Ctenopharyngodon idella (grass carp), Mylopharyngodon piceus (black carp), Hypophthalmichthys nobilis (bighead carp), and Hypophthalmichthys molitrix (silver carp), collectively known as the four major domesticated Asian carp, are freshwater fish species from the family Cyprinidae and are widely consumed in China. Current studies on these species primarily focus on immune system regulation and the growth and development of individual species. However, in-depth genomic investigations and comprehensive comparative analysis remained limited.
The complete genomes of Ctenopharyngodon idella, Mylopharyngodon piceus and Hypophthalmichthys nobilis were assembled using a hybrid approach that integrated both next- and third-generation sequencing reads, followed by annotation using the MAKER2 pipeline. Based on the high-quality genomes of Ctenopharyngodon idella, Mylopharyngodon piceus Hypophthalmichthys nobilis, and Hypophthalmichthys molitrix, a comparative genomic analysis was conducted using bioinformatic tools to investigate gene family evolution in these four domesticated Asian carp species.
High-quality genomes of Ctenopharyngodon idella, Mylopharyngodon piceus, and Hypophthalmichthys nobilis were assembled, achieving over 90% completeness. Immune-related gene families, including MHC class I and NLRC3-like genes, have undergone rapid evolution, with Ctenopharyngodon idella exhibiting significant expansion of NLRC3-like genes. Massive tandem duplication events were identified in trace amine-associated receptors (TAARs), and rapid expansion was observed in TAAR16 and TAAR29. Additionally, a novel TAAR gene cluster was identified in all four Asian carp species. Comparative genomic analysis revealed the expansion of type 1 taste receptor genes, particularly in Ctenopharyngodon idella and Mylopharyngodon piceus.
This study has successfully constructed the high-quality genomes of Ctenopharyngodon idella, Mylopharyngodon piceus, and Hypophthalmichthys nobilis. The comparative genomic analysis revealed the evolution of immune-related genes and chemosensory receptors in the four major domesticated Asian carp species. These findings suggested the enhanced immunity and sensory perception in these species, providing valuable insights into their adaptation, survival and reproduction.
草鱼（Ctenopharyngodon idella）、青鱼（Mylopharyngodon piceus）、鳙鱼（Hypophthalmichthys nobilis）和鲢鱼（Hypophthalmichthys molitrix）统称为四大养殖亚洲鲤鱼，它们是鲤科淡水鱼类，在中国被广泛食用。目前对这些物种的研究主要集中在免疫系统调节以及单个物种的生长发育方面。然而，深入的基因组研究和全面的比较分析仍然有限。
采用整合了二代和三代测序读数的混合方法组装草鱼、青鱼和鳙鱼的完整基因组，随后使用MAKER2流程进行注释。基于草鱼、青鱼、鳙鱼和鲢鱼的高质量基因组，利用生物信息学工具进行比较基因组分析，以研究这四种养殖亚洲鲤鱼物种的基因家族进化。
组装得到了草鱼、青鱼和鳙鱼的高质量基因组，完整性超过90%。包括MHC I类和NLRC3样基因在内的免疫相关基因家族经历了快速进化，草鱼中NLRC3样基因有显著扩增。在痕量胺相关受体（TAARs）中鉴定出大量串联重复事件，并且在TAAR16和TAAR29中观察到快速扩增。此外，在所有四种亚洲鲤鱼物种中都鉴定出一个新的TAAR基因簇。比较基因组分析揭示了1型味觉受体基因的扩增，特别是在草鱼和青鱼中。
本研究成功构建了草鱼、青鱼和鳙鱼的高质量基因组。比较基因组分析揭示了四种主要养殖亚洲鲤鱼物种中免疫相关基因和化学感应受体的进化。这些发现表明这些物种的免疫力和感官感知能力增强，为它们的适应、生存和繁殖提供了有价值的见解。
