Identification of Immune Related Genes and Associated Simple Sequence Repeats from Kidney Transcriptome of Cyprinus carpio, Exposed to Two Different Temperature Conditions

Abstract

Common carp is a widely farmed and economically important freshwater fish species that thrives in diverse aquatic habitats. In the present study, two temperature conditions were used to maximise and capture the transcript repertoire. High-throughput transcriptome sequencing data were used to identify transcriptome and immune related genes, as well as associated simple sequence repeats (SSRs). A total of 67.44 GB of high-quality paired-end reads were generated, which were then assembled and clustered into 133,419 transcripts with a GC content of 51.63%. SSRs were identified in 6,245 genes, with the highest number of dinucleotide repeats (33.42%), followed by tri-nucleotide repeats (13.24%) and tetra/penta/hexa/septa/nona/deca nucleotide repeats (2.43%). Further classification analysis identified 1,355 immune genes, of which the largest groups under innate immune response were co-stimulatory molecules (234), followed by cytokines (203) and RIG-I-like receptors (186). Adaptive immune genes included Immunoglobulins (104) and Interleukin (106), followed by negative regulators of immune system (60). Among the immune categories, 142 SSRs were identified in innate immune genes, 67 in adaptive immune genes and 6 in negative regulators. The generated data of transcriptome-derived SSRs in this study offer a wealth of marker resources related to immune mechanisms for molecular marker development and characterization of germplasm, which will aid in understanding genetic diversity and their application in molecular marker assisted breeding of C. carpio for improving aquaculture sustainability.