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. 2020 Jun 15;15(6):e0234504.
doi: 10.1371/journal.pone.0234504. eCollection 2020.

Transcriptome sequencing reveals signatures of positive selection in the Spot-Tailed Earless Lizard

Jose A Maldonado  1 , Thomas J Firneno Jr  1 , Corey E Roelke  1 , Nathan D Rains  2 , Juliet Mwgiri  1 , Matthew K Fujita  1
Affiliations

Transcriptome sequencing reveals signatures of positive selection in the Spot-Tailed Earless Lizard

Jose A Maldonado et al. PLoS One. .

Abstract

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.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Schematic overview of our workflow to assemble the transcriptome of H. lacerata, H. subcaudalis, and H. maculata, and analysis carried out in this study.
Fig 2
Fig 2. Venn diagram showing the number of shared orthologous groups identified by OrthoFinder between all four species assembled transcriptome.
Fig 3
Fig 3
Gene ontology annotations for the liver transcriptome of H. maculata (yellow), H. subcaudalis (red), and H. lacerata (blue).
See this image and copyright information in PMC

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