Microsatellite polymorphism and genetic differentiation of different populations screened from genome survey sequencing in red-tail catfish (Hemibagrus wyckioides)

•Polymorphic microsatellites were identified from genome survey sequences.•High genetic diversity was revealed in both wild and hatchery populations by SSR.•The hatchery populations were indicated in the early stage of domestication. The increasing farming scale of red-tail catfish (Hemibagrus wyckioides) in recent years has made great contribution to the sustainable growth of aquaculture in southern China. However, due to the lack of genetic management measures, the long-term domestication process of red-tail catfish was uncertain. In this study, genome survey sequencing at approximately 103 × coverage depth was performed in the species and then SSR markers were screened to assess the genetic variation in two wild and two hatchery populations. The K-mer analysis indicated the genome size of red-tail catfish was about 728 Mb with low heterozygosity. The assembly of 74.85 Gb Illumina data produced 274,929 scaffolds at N50 = 16.3 kb, from which 36,149 genes were annotated using the reference genome of channel catfish (Ictalurus punctatus). A total of 678,251 SSR motifs were detected and 18 polymorphic microsatellite loci were used for population genetics analysis. Genetic diversity levels in four populations were considered to be healthy, with the number of alleles (Na), effective alleles (Ne) and observed heterozygosity (Ho) ranging from 5.44 to 7.56, 3.45 to 4.86 and 0.674 to 0.793, respectively. The genetic differentiation levels among populations were from low to moderate and genetic variations mainly occurred between individuals (98.16 %). Bayesian analysis showed that all populations could be divided into two clusters. All results indicate that the domestication process of the hatchery populations is in an early stage. This study will provide significant guidance for further whole genome sequencing and genetic improvement of red-tail catfish in the future.