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Tarim schizothoracin (Schizothorax biddulphi) is an endemic fish species native to the Tarim River system of Xinjiang and has been classified as an extremely endangered freshwater fish species in China. Here, we used a next generation sequencing platform (ion torrent PGM™) to obtain a large number of microsatellites for S. biddulphi, for the first time. A total of 40577 contigs were assembled, which contained 1379 SSRs. In these SSRs, the number of dinucleotide repeats were the most frequent (77.08%) and AC repeats were the most frequently occurring microsatellite, followed by AG, AAT and AT. Fifty loci were randomly selected for primer development; of these, 38 loci were successfully amplified and 29 loci were polymorphic across panels of 30 individuals. The Ho ranged from 0.15 to 0.83, and He ranged from 0.15 to 0.85, with 3.5 alleles per locus on average. Cross-species utility indicated that 20 of these markers were successfully amplified in a related, also an endangered fish species, S. irregularis. This study suggests that PGM™ sequencing is a rapid and cost-effective tool for developing microsatellite markers for non-model species and the developed microsatellite markers in this study would be useful in Schizothorax genetic analysis.

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This paper reports on the morphological variations of six Schizothoracinae species, including Aspiorhynchus laticeps, Schizothorax biddulphi, Schizothorax eurystomus, Schizothorax barbatus, Schizothorax intermedia, and Diptychus maculatus, the first reference to the morphological characters of these species. Based on the results from the cluster analysis, S. biddulphi and S. eurystomus are the most morphologically similar, with their Euclidean distances within 0.0167; their morphological similarity to S. intermedia, A. laticeps, and D. maculatus is gradually reduced, with an increase in the Euclidean distance from 0.0317 to 0.5765. *These authors are equal contributors. U.S.