Chen, K., R. Guo, L. Xia, Y. Mei, C. Chen & J. Yang

Genome survey and characterization of new microsatellite markers in Hynobius amjiensis (Caudata: Hynobiidae). pp. 117-124 plus Supplementary Table S1 and Table S2.

Abstract. The Anji Salamander, Hynobius amjiensis Gu, 1992, is a critically endangered amphibian only known from a few mountain tops in the Zhejiang and Anhui Provinces of China. Along with tremendous efforts to breed this species in captivity, there have been attempts to understand the causes for its endangered status from a genetic perspective, which was limited to a few markers from earlier studies. Here we used next-generation sequencing technology on the DNASEQ platform to investigate the characteristics of the salamander’s genome. Based on k-mer analysis, the 19-mer frequency distribution yielded the optimal estimation that suggested a genome size of ~17.54 Gb, 70.77% of which consist of repetitive sequences. Filtered sequences were assembled in 8,852,165 contigs with N50 at 1052 bp; GC rate was 45.3%. We identified 1,441,045 microsatellite loci across the assembled partial genome. Mono-nucleotide microsatellites accounted for 61.4% of all loci, and 2 to 6-base repeat motifs are present at a frequency of 19.59.67.91.5and 0.06%, respectively. PCR primers were developed for 98 microsatellite loci with 2 to 6-base motifs. Our work provides an overview of the genome characteristics of H. amjiensis that can serve subsequent studies on the evolutionary history of this endangered salamander.

Key words. Anji Salamander, endangered species, genome size, microsatellite.