Development of Genetic Novel SSR Markers by Transcriptome Sequencing in Ophicephalus argus Cantor

Abstract

Northern snakehead Ophiocephalus argus Cantor is an endemic freshwater species in China. This species is widely distributed in the lower Yellow and Yangtze river systems in eastern China. In the present study, six cDNA libraries of Ophiocephalus argus were sequenced using Illumina HiSeq4000 paired-end sequencing technology. 67 564 sequences from 79 500 964 paired-end reads were generated. A total of 7182 unigenes were clustered into 25 functional categories by searching against the COG database, and BLAST2GO search assigned 33 710 unigenes to 59 GO terms. From the 67 564 assembled unique sequences, 21 464 SSRs were identified in 14 997 unique sequences. Among the 7992 with compound formation (SSRs), 100 primer pairs were successfully designed for further validation, and 42 of them produced polymorphic products in Ophiocephalus argus individuals. The number of alleles per locus ranged from 5 to 19, the observed and expected heterozygosity estimates ranged from 0.178 to 0.985 and from 0.421 to 0.929, respectively. The generation of such larges cale sequence data in the present study provides a valuable resource for gene discovery and molecular marker development.