Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtraction
Abstract Background Homologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lack differential influence on the sexes and sequence divergence on the he...
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doaj-ed52b77f416d4d4b9a7fd57d1fdfbeb92020-11-25T03:39:59ZengBMCBMC Genomics1471-21642020-09-0121111210.1186/s12864-020-07071-2Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtractionDuminda Sampath Bandara Dissanayake0Clare Ellen Holleley1Laura Kate Hill2Denis O’Meally3Janine Eileen Deakin4Arthur Georges5Institute for Applied Ecology, University of CanberraInstitute for Applied Ecology, University of CanberraInstitute for Applied Ecology, University of CanberraInstitute for Applied Ecology, University of CanberraInstitute for Applied Ecology, University of CanberraInstitute for Applied Ecology, University of CanberraAbstract Background Homologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lack differential influence on the sexes and sequence divergence on the hemizygous homolog. 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 Bassiana duperreyi which has heteromorphic XY sex chromosomes. Results We generated 96.7 × 109 150 bp paired-end genomic sequence reads from a XY male and 81.4 × 109 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. Conclusions The sex of B. duperreyi 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 B. duperreyi. 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 B. duperreyi and will enhance future studies of reptile sex determination and sex chromosome evolution.http://link.springer.com/article/10.1186/s12864-020-07071-2Sex-specific markersSex reversalGenotypic sex determinationY chromosome |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Duminda Sampath Bandara Dissanayake Clare Ellen Holleley Laura Kate Hill Denis O’Meally Janine Eileen Deakin Arthur Georges |
spellingShingle |
Duminda Sampath Bandara Dissanayake Clare Ellen Holleley Laura Kate Hill Denis O’Meally Janine Eileen Deakin Arthur Georges Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtraction BMC Genomics Sex-specific markers Sex reversal Genotypic sex determination Y chromosome |
author_facet |
Duminda Sampath Bandara Dissanayake Clare Ellen Holleley Laura Kate Hill Denis O’Meally Janine Eileen Deakin Arthur Georges |
author_sort |
Duminda Sampath Bandara Dissanayake |
title |
Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtraction |
title_short |
Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtraction |
title_full |
Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtraction |
title_fullStr |
Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtraction |
title_full_unstemmed |
Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtraction |
title_sort |
identification of y chromosome markers in the eastern three-lined skink (bassiana duperreyi) using in silico whole genome subtraction |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2020-09-01 |
description |
Abstract Background Homologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lack differential influence on the sexes and sequence divergence on the hemizygous homolog. 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 Bassiana duperreyi which has heteromorphic XY sex chromosomes. Results We generated 96.7 × 109 150 bp paired-end genomic sequence reads from a XY male and 81.4 × 109 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. Conclusions The sex of B. duperreyi 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 B. duperreyi. 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 B. duperreyi and will enhance future studies of reptile sex determination and sex chromosome evolution. |
topic |
Sex-specific markers Sex reversal Genotypic sex determination Y chromosome |
url |
http://link.springer.com/article/10.1186/s12864-020-07071-2 |
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