Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.
Australian National Wildlife Collection, CSIRO, Canberra, ACT, 2911, Australia.
BMC Genomics. 2020 Sep 29;21(1):667. doi: 10.1186/s12864-020-07071-2.
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.
We generated 96.7 × 10 150 bp paired-end genomic sequence reads from a XY male and 81.4 × 10 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.
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.
同源性性染色体随着时间的推移而发生分化，因为重组在性别决定基因座的区域受到抑制，导致重复序列的积累，缺乏对两性差异影响的基因的逐渐丧失，以及半合子同源物的序列分化。非重组区域的分化导致积累了有用的 Y 或 W 特异性序列，用于开发性连锁标记。在这里，我们使用计算机整体基因组消减来鉴定具有异型 XY 性染色体的石龙子 Bassiana duperreyi 中的假定性连锁序列。
我们从 XY 雄性中生成了 96.7 × 10 150 bp 配对末端基因组序列读段，从 XX 雌性中生成了 81.4 × 10 配对末端读段，用于计算机整体基因组消减，以产生 Y 富集的重叠群。我们鉴定了 7 个可靠的标记，这些标记通过聚合酶链反应（PCR）针对 20 个雄性和 20 个雌性的面板进行验证，证明是 Y 染色体特异性的。
B. duperreyi 的性别可以通过低温逆转（XX 基因型逆转为雄性表型）。我们已经开发了性特异性标记来识别 B. duperreyi 野生种群中潜在的基因型性别及其与表型性别的一致性或不一致性。我们的流水线可以用于分离任何生物体的 Y 或 W 染色体特异性序列，并且不限于位于单拷贝基因内的序列。这项研究极大地提高了我们对 B. duperreyi 的 Y 染色体的认识，并将增强未来对爬行动物性别决定和性染色体进化的研究。
