DOI: 10.5061/dryad.z8w9ghxnc
title: Comparative genomics sheds new light on the convergent evolution of infrared vision in snakes

description: Infrared vision is a highly specialized sensory system that evolved
 independently in three clades of snakes. Apparently, convergent evolution
 occurred in the transient receptor potential ankyrin 1 (TRPA1) proteins of
 infrared-sensing snakes. However, this gene can only explain how infrared
 signals are received, and not the transduction and processing of those
 signals. We sequenced the genome of Xenopeltis unicolor, a key outgroup
 species for pythons, and performed a genome-wide analysis of convergence
 between two clades of infrared-sensing snakes. Our results revealed
 pervasive molecular adaptation in pathways associated with neural
 development and other functions, with parallel selection on loci
 associated with trigeminal nerve structural organization. Additionally, we
 found evidence of convergent amino acid substitutions in a set of genes,
 including TRPA1 and TRPM2. Analysis also identified convergent accelerated
 evolution in non-coding elements near 12 genes involved in facial nerve
 structural organization and optic nerve development. Thus, convergent
 evolution occurred across multiple dimensions of infrared vision in vipers
 and pythons, as well as amino acid substitutions, non-coding elements,
 genes, and functions. These changes enabled independent groups of snakes
 to develop and utilize infrared vision.
description: # Comparative genomics sheds new light on the convergent evolution of
 infrared vision in snakes
 [https://doi.org/10.5061/dryad.z8w9ghxnc](https://doi.org/10.5061/dryad.z8w9ghxnc) Scripts, and data used to detect convergence in multiple dimensions of sequence evolution, including changes in amino acid sequences, gene sequences, gene function, and non-coding regions. ## Description of the data and file structure We have submitted genome sequence of sunbeam snake (SK_yunnan.fasta), orthologous sequence for python (03.Python_bivittatus.zip), orthologous sequence for vipers (04.Viper.zip), scripts (GenomicPipelines-master.zip), and supplementary information (SI.docx). SK_yunnan.fasta #  genome sequence of sunbeam snake, assembled by NextDenovo v2.4.0 using PacBio and Hi-C reads. 03.Python_bivittatus.zip # orthologous gene sequences for *Python bivittatus,* generated using reciprocal best hit approach. 04.Viper.zip # orthologous gene sequences that containing at least one of the two vipers, generated using reciprocal best hit approach. ## Sharing/Access information Links to other publicly accessible locations of the data: * [https://github.com/BIGtigr/GenomicPipelines/tree/master](http://...) * [https://ngdc.cncb.ac.cn/gwh/](https://ngdc.cncb.ac.cn/gwh/) * accession number GWHETGS00000000.1 and BioProject number PRJCA025085 * [https://www.ncbi.nlm.nih.gov/genbank/](https://www.ncbi.nlm.nih.gov/genbank/) * BioProject number PRJNA1113417 ## Code/Software GenomicPipelines-master.zip (on Zenodo as Software) \|--CNE # this pipline was used to conduct genome alignment, multiple genome alignment, and identification of CNEs.\ |  |--[CNE2.1.py](https://github.com/BIGtigr/GenomicPipelines/blob/master/CNE/CNE2.1.py "CNE2.1.py") \|--Clusterprofiler # this two scripts were used to conduct GO and KEGG enrichment analysis. |  |--[GO.py](https://github.com/BIGtigr/GenomicPipelines/blob/master/Clusterprofiler/GO.py "GO.py") [| |--clusterprofiler.pl](https://github.com/BIGtigr/GenomicPipelines/blob/master/Clusterprofiler/clusterprofiler.pl "clusterprofiler.pl")  \|--Convergent_evolution # this script was used to parepare input files for convCal ([https://github.com/BIGtigr/convCal](https://github.com/BIGtigr/convCal)). [| |--convgent_1.2.py](https://github.com/BIGtigr/GenomicPipelines/blob/master/Convergent_evolution/convgent_1.2.py "convgent_1.2.py") \|--Gene_prediction # this scricpt was used to conduct homology based gene prediction for the genome of sunbeam snake |  |--[homology2.2.pl](https://github.com/BIGtigr/GenomicPipelines/blob/master/Gene_prediction/homology2.2.pl "homology2.2.pl") \|--selection [| |--FDR.pl](https://github.com/BIGtigr/GenomicPipelines/blob/master/Selection/FDR.pl "FDR.pl") # script used to conduct FDR adjustment for results generated by [pamlpip.2.3.pl](https://github.com/BIGtigr/GenomicPipelines/blob/master/Selection/pamlpip.2.3.pl "pamlpip.2.3.pl") [| |--pamlpip.2.3.pl](https://github.com/BIGtigr/GenomicPipelines/blob/master/Selection/pamlpip.2.3.pl "pamlpip.2.3.pl") # script used to identify PSGs and REGs