De novoassembly and annotation of the eastern fence lizard (Sceloporus undulatus) transcriptome

Background The eastern fence lizard ( Sceloporus undulatus ) has been a model species for ecological and evolutionary research. Genomic and transcriptomic resources for this species would promote investigation of genetic mechanisms that underpin plastic responses to environmental stress, such as climate warming. Moreover, such resources would aid comparative studies of complex traits at the molecular level, such as the transition from oviparous to viviparous reproduction, which happened at least four times within Sceloporus . Findings A de novo transcriptome assembly for Sceloporus undulatus , Sund_v1.0, was generated using over 179 million Illumina reads obtained from three tissues (whole brain, skeletal muscle, and embryo) as well as previously reported liver sequences. The Sund_v1.0 assembly had an average contig length of 782 nucleotides and an E90N50 statistic of 2,550 nucleotides. Comparing S. undulatus transcripts with the benchmarking universal single-copy orthologs (BUSCO) for tetrapod species yielded 97.2% gene representation. A total of 13,422 protein-coding orthologs were identified in comparison to the genome of the green anole lizard, Anolis carolinensis , which is the closest related species with genomic data available. Conclusions The multi-tissue transcriptome of S. undulatus is the first for a member of the family Phrynosomatidae, offering an important resource to advance studies of adaptation in this species and genomic research in reptiles.