Department of Biology, Amphibian and Reptile Diversity Research Center, The University of Texas at Arlington, Arlington, TX, United States of America.
Texas Parks and Wildlife Department, Austin, Texas, TX, United States of America.
PLoS One. 2020 Jun 15;15(6):e0234504. doi: 10.1371/journal.pone.0234504. eCollection 2020.
The continual loss of threatened biodiversity is occurring at an accelerated pace. High-throughput sequencing technologies are now providing opportunities to address this issue by aiding in the generation of molecular data for many understudied species of high conservation interest. Our overall goal of this study was to begin building the genomic resources to continue investigations and conservation of the Spot-Tailed Earless lizard. Here we leverage the power of high-throughput sequencing to generate the liver transcriptome for the Northern Spot-Tailed Earless Lizard (Holbrookia lacerata) and Southern Spot-Tailed Earless Lizard (Holbrookia subcaudalis), which have declined in abundance in the past decades, and their sister species, the Common Lesser Earless Lizard (Holbrookia maculata). Our efforts produced high quality and robust transcriptome assemblies validated by 1) quantifying the number of processed reads represented in the transcriptome assembly and 2) quantifying the number of highly conserved single-copy orthologs that are present in our transcript set using the BUSCO pipeline. We found 1,361 1-to-1 orthologs among the three Holbrookia species, Anolis carolinensis, and Sceloporus undulatus. We carried out dN/dS selection tests using a branch-sites model and identified a dozen genes that experienced positive selection in the Holbrookia lineage with functions in development, immunity, and metabolism. Our single-copy orthologous sequences additionally revealed significant pairwise sequence divergence (~.73%) between the Northern H. lacerata and Southern H. subcaudalis that further supports the recent elevation of the Southern Spot-Tailed Earless Lizard to full species.
受威胁的生物多样性持续不断地大量丧失，而且这种丧失的速度正在加快。高通量测序技术现在提供了机会，可以通过帮助生成许多研究不足的具有高度保护意义的物种的分子数据来解决这个问题。我们这项研究的总体目标是开始构建基因组资源，以继续对斑点尾无耳蜥蜴进行调查和保护。在这里，我们利用高通量测序的强大功能，为北方斑点尾无耳蜥蜴（Holbrookia lacerata）和南方斑点尾无耳蜥蜴（Holbrookia subcaudalis）生成肝脏转录组，这两个物种在过去几十年中数量减少，以及它们的姐妹种普通小耳无耳蜥蜴（Holbrookia maculata）。我们的努力产生了高质量和稳健的转录组组装，通过以下两种方法进行了验证：1）量化转录组组装中代表的处理读取数量，以及 2）使用 BUSCO 管道量化我们的转录组中存在的高度保守的单拷贝直系同源物的数量。我们在三种 Holbrookia 物种、卡罗莱纳蜥（Anolis carolinensis）和波纹蜥（Sceloporus undulatus）中发现了 1361 个 1:1 直系同源物。我们使用分支位点模型进行了 dN/dS 选择测试，鉴定出十几个在 Holbrookia 谱系中经历正选择的基因，这些基因具有发育、免疫和代谢功能。我们的单拷贝直系同源序列还揭示了北方 H. lacerata 和南方 H. subcaudalis 之间存在显著的成对序列差异（约 73%），这进一步支持了南方斑点尾无耳蜥蜴最近被提升为完整物种。
