Unravelling the thread of Podarcis omics; insights into the genome and transcriptome of the Cretan wall lizard

Abstract

Background Whole genome data are invaluable resources for both conservation and adaptation studies, especially for endemic species, providing insights into the evolution of genes involved in genomic adaptation across different environments. Objective We compare the newly generated genomic and transcriptomic data of the Cretan endemic lizard species Podarcis cretensis to other Podarcis species to obtain an overview of gene family evolution and genome structure within the genus. Methods Comparative genomic and transcriptomic analyses were performed using the newly published genome of P. cretensis . A gene set was predicted using RNA-seq data from 36 samples, comprising three tissues (liver, brain, and muscle) from both male and female individuals across three distinct habitats. Results The main findings revealed that P. cretensis and P. raffonei present the best genome assemblies and the most syntenic among the Podarcis species examined. Moreover, P. cretensis displayed the highest percentage of single-copy genes and the lowest percentage of duplicated genes. These duplicated genes are primarily associated with immune and sensory-related gene families, including chemokines, interleukins, immunoglobulin-like domain proteins, secreted proteins, and vomeronasal type-2 receptors. Conclusions This study deepens our understanding of chromosome structure, gene expression, and genome evolution in the Podarcis genus, representing the most extensive comparative analysis to date. The newly predicted gene set of the insular endemic species P. cretensis offers initial insights into gene expression related to adaptation across environments and tissues. Comparative genomic analyses further revealed gene families potentially involved in environmental adaptation.

Bibliographic Information