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Background  Chinese giant salamander  Andrias davidianus  is an endangered species. The success of artificial breeding provides a useful way to protect this species. However, the method to identify the sex and mechanism of sex determination were unclear which hinder the improvement of the artificial breeding. Detection of a sex specific marker provides an effective approach to identify genetic sex and investigate the sex determination mechanism.    Results  We used restriction-site-associated DNA (RAD) sequencing to isolate a sex-specific genetic marker in  A. davidianus  to expand knowledge of the sex determination mechanism. Four male and four female specimens were subjected to RAD sequencing, which generated 934,072,989 reads containing approximately 134.4 Gb of sequences. The first round of comparison of the assembled sequence against the opposite sex raw reads revealed 19,097 female and 17,994 male unmatched sequences. Subsequently, 19,097 female sequences were subjected to a BLAST search against male genomic data, which revealed 308 sequences unmapped to the male genome. One hundred of these were randomly selected and validated by PCR in five male and five female specimens, and four putative sex-specific sequences were produced. Further validation was performed by PCR in another 24 females and 24 males, and all female individuals exhibited the expected specific bands, while the males did not. To apply the sex-specific marker, three specimens reversed from genetic female to physiological male were found in a group exposed to elevated temperature, and 13 individuals reversed from genetic male to physiological female were obtained in a 17β-estradiol exposed group.    Conclusion  This is the first report of a sex-specific marker in  A. davidianus  and may have potential for elucidation of its sex determination mechanism and, hence, its conservation .Electronic supplementary material  The online version of this article (10.1186/s12864-019-5771-5) contains supplementary material, which is available to authorized users.

Genome-wide RAD sequencing to identify a sex-specific marker in Chinese giant salamander Andrias davidianus