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

Abstract

The continual loss of threatened biodiversity is occurring at an accelerated pace. Highthroughput 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.

Insights into the species evolution of Calanus copepods in the northern seas revealed by de novo transcriptome sequencing

“…According to Orthofinder, most protein-coding genes are conserved among the seven Calanus species with only 1.3% of the genes being species-specific. This percentage of species-specific genes is a bit higher than what was reported for five species of bats in the recent study of (Moreno-Santillán et al, 2019) and for five species of lizards in (Maldonado et al, 2020). The number of duplication events are expected to be high for Calanus copepods due to their large genomes (McLaren et al, 1988) et al, 1988).…”

Transcriptome‐derived molecular resources for the conservation of threatened butterflies in Korea

“…Moreover, the length of the smallest and largest unigenes was also higher when using the TransDecoder software. The TransDecoder output file can be utilized directly for protein searches and structural annotation (Maldonado et al 2020;Gomes-dos-Santos et al 2022;Hwang et al 2023).…”

“…The TransDecoder output file can be utilized directly for protein searches and structural annotation (Maldonado et al . 2020; Gomes‐dos‐Santos et al . 2022; Hwang et al .…”