Chromosome-Level Genome Assembly and Genomic Analysis of the Hybrid Grouper ShanHu (Epinephelus fuscoguttatus ♀ × Epinephelus polyphekadion ♂)

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 (Epinephelus fuscoguttatus ♀ × Epinephelus polyphekadion ♂) 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.