Identification and analysis of gene families expansion and contraction in Coilia nasus

Coilia nasus belongs to genus Coilia, family Engraulidae, order Clupeiformes, which is migratory fish with high nutritional and economic value in China. C. nasus has both migratory and land-locked populations, which is an excellent model for studying reproductive migration and adaptive evolution. This study identified and analyzed the expansion and contraction of gene families in C. nasus, in order to explore the special mechanism of C. nasus caused by changes in the core gene families in the evolutionary process. Comparative genomology was used to identify the C. nasus’s gene families by using the genomes of Danio rerio, Gasterosteus aculeatus, Oryzias latipes, Takifugu rubripes and Tetraodon nigroviridis. Then CAFE V4.2 software was used for gene family expansion and contraction analysis. Finally, GO, KEGG and other database were applied for annotations and pathway analysis of the significantly expanded gene families’ genes. 11 872 gene families were identified in C. nasus, including 16 470 genes. Besides, 2 963 unclustered genes were identified. Compared with the other 5 species, 150 gene families containing 419 genes were found unique to C. nasus. In addition, 1 200 gene families of C. nasus expanded and 7 543 gene families contracted. P values of 39 expanded gene families (including 508 genes) and 36 contracted gene families (including 21 genes) are less than 0.05. 508 genes of significantly expanded gene families were utilized for pathway analysis. Metabolic process, catalytic activity, cell and cell part are the top GO terms. Tight junctions, adrenergic signaling in cardiomyocytes, cardiac muscle contraction, cell adhesion molecules (CAMs), etc. are the top KEGG pathways. Tight junctions and cardiac muscle contraction pathways are related to osmoregulation. GnRH signaling pathway and olfactory transduction pathway are involved in reproductive migration behavior. Furthermore, we mapped 508 genes of significantly expansion gene families on the genome, and found that chromosome 23 had much more genes than other chromosomes. And the genes of significantly expanded gene families located on chromosome 23 were mostly histone genes, which were related to the regulation of chromatin structure. Pathway analysis of the expansion and exclusive gene families of C. nasus indicate that the osmotic regulation, signal transduction, metabolism, gonad development and olfactory transduction may have undergone adaptive evolution, and the regulation of its chromatin structure may also have been altered. These results have strengthened our understanding of the adaptive evolution of C. nasus.