Liu Yiqun, Mao Yunxiang
Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institute, Ocean University of China, Sanya 572000, China.
Yazhou Bay Innovation Institute, Hainan Tropical Ocean University, Sanya 572022, China.
Int J Mol Sci. 2025 May 23;26(11):5036. doi: 10.3390/ijms26115036.
Groupers are important aquaculture species, and hybridization is an effective breeding method for genetic improvement and to enhance production efficiency in groupers. The ShanHu grouper ( ♀ × ♂) is a hybrid grouper with potential for aquaculture development and research value. Using Illumina and PacBio sequencing platforms, as well as PacBio SMRT technology and Hi-C auxiliary mounting technology, the whole genome sequencing and assembly of the ShanHu grouper were completed, resulting in a chromosome-level genome information for this hybrid grouper. The genome assembly has a total length of 1.17 Gb with a scaffold N50 of 46.12 Mb, and 171 contigs were anchored into 24 chromosomes. Additionally, its repeat sequences and non-coding RNAs were annotated and 26,102 genes were predicted. Through comparative genomic analysis of the hybrid species ShanHu grouper and its parents, we found that comparative genomic analyses revealed centric inversion structural variations on the chromosomes of the hybrid ShanHu grouper in relation to the brown-marbled grouper and the camouflage grouper. Furthermore, the gene families of the hybrid species have expanded in pathways related to immunity and growth development. This study is the first to provide complete genomic information for a hybrid grouper, offering its full genetic information, exploring the genetic variations in the genomes of hybrid offspring, and providing data references for foundational theoretical research and grouper production practices.
石斑鱼是重要的水产养殖品种，杂交是石斑鱼遗传改良和提高生产效率的有效育种方法。珊瑚石斑鱼（♀×♂）是一种具有水产养殖发展潜力和研究价值的杂交石斑鱼。利用Illumina和PacBio测序平台以及PacBio SMRT技术和Hi-C辅助挂载技术，完成了珊瑚石斑鱼的全基因组测序和组装，获得了该杂交石斑鱼的染色体水平基因组信息。基因组组装总长1.17 Gb，支架N50为46.12 Mb，171个重叠群被锚定到24条染色体上。此外，对其重复序列和非编码RNA进行了注释，并预测了26102个基因。通过对杂交种珊瑚石斑鱼及其亲本的比较基因组分析，我们发现比较基因组分析揭示了杂交珊瑚石斑鱼与棕点石斑鱼和豹纹鳃棘鲈染色体上的着丝粒倒位结构变异。此外，杂交种的基因家族在免疫和生长发育相关途径中有所扩展。本研究首次为杂交石斑鱼提供了完整的基因组信息，提供了其完整的遗传信息，探索了杂交后代基因组中的遗传变异，为基础理论研究和石斑鱼生产实践提供了数据参考。
