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Divergence in the non-recombining regions leads to the accumulation of Y or W specific sequence useful for developing sex-linked markers. Here we use in silico whole-genome subtraction to identify putative sex-linked sequences in the scincid lizard\n                      <jats:italic>Bassiana duperreyi<\/jats:italic>\n                      which has heteromorphic XY sex chromosomes.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      We generated 96.7\u2009\u00d7\u200910\n                      <jats:sup>9<\/jats:sup>\n                      150\u2009bp paired-end genomic sequence reads from a XY male and 81.4\u2009\u00d7\u200910\n                      <jats:sup>9<\/jats:sup>\n                      paired-end reads from an XX female for in silico whole genome subtraction to yield Y enriched contigs. We identified 7 reliable markers which were validated as Y chromosome specific by polymerase chain reaction (PCR) against a panel of 20 males and 20 females.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      The sex of\n                      <jats:italic>B. duperreyi<\/jats:italic>\n                      can be reversed by low temperatures (XX genotype reversed to a male phenotype). We have developed sex-specific markers to identify the underlying genotypic sex and its concordance or discordance with phenotypic sex in wild populations of\n                      <jats:italic>B. duperreyi<\/jats:italic>\n                      . Our pipeline can be applied to isolate Y or W chromosome-specific sequences of any organism and is not restricted to sequence residing within single-copy genes. This study greatly improves our knowledge of the Y chromosome in\n                      <jats:italic>B. duperreyi<\/jats:italic>\n                      and will enhance future studies of reptile sex determination and sex chromosome evolution.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12864-020-07071-2","type":"journal-article","created":{"date-parts":[[2020,9,29]],"date-time":"2020-09-29T08:03:11Z","timestamp":1601366591000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":27,"title":["Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtraction"],"prefix":"10.1186","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7307-4639","authenticated-orcid":false,"given":"Duminda Sampath Bandara","family":"Dissanayake","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5257-0019","authenticated-orcid":false,"given":"Clare Ellen","family":"Holleley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura Kate","family":"Hill","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7749-9506","authenticated-orcid":false,"given":"Denis","family":"O\u2019Meally","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1259-3531","authenticated-orcid":false,"given":"Janine Eileen","family":"Deakin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2428-0361","authenticated-orcid":false,"given":"Arthur","family":"Georges","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,9,29]]},"reference":[{"key":"7071_CR1","first-page":"593","volume":"17","author":"K D\u00fcsing","year":"1884","unstructured":"D\u00fcsing K. 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