Transcriptome profiling and histology changes insights into the molecular mechanisms of reproduction related genes and signal pathways in the Caspian Kutum (Rutilus frisii, Nordmann, 1840)

The Caspian Kutum ( Rutilus frisii , Nordmann, 1840) is an economically significant species among bony fish stocks in the southern basin of Caspian Sea. The autumn and spring strains of R. frisii are the two primary strains of this species and returning to freshwater river habitats for spawning. Nevertheless, information for transcriptome, the physiological differences and the regulatory mechanism of controlling for two strains remain unclear. To address this issue, we performed de novo assembly of liver transcriptome from six female R. frisii , using RNA sequencing (RNA-seq) on the Illumina paired-end sequencing technology. Our aim was to identify potential genes that affect the migratory behavior of the two strains and to better understand the population structure of this endangered species. We used gene ontology (GO) analysis, clusters of orthologous groups (COG) analysis, and Kyoto Encyclopedia of genes and genomes (KEGG) analysis to identify functional differences between the two strains. After quality control, the de novo transcriptome assembly carried out with Trinity software and then 110,381 transcripts were generated. A total of 12,569 unigenes were grouped into three major functional categories (biological process, cellular components and molecular functions) and 62 sub-categories. A total of 9,627 transcripts were assigned at least one GO term. According to the public protein databases, we observed 21 unigenes related to reproduction by comparing the assembled unigenes and then 12849 differentially expressed genes (DEGs) were identified. We compared the histology of ovaries between the two strains to determine the degree of sexual maturation. Additionally, to validate the differential expression of selected genes, qRT-PCR was performed. Our study identified specific genes involved in the migration function of R. frisii , which offers insights into understanding the different migratory behaviors between the two strains. The upregulated genes in autumn and spring strains were identified as well. These results provide a basis for future studies on the genetic differences between these two strains of R. frisii and their impact on population structure. Overall, our findings contribute to the conservation and sustainable management of this economically important species.