Data from: Detection of evolutionary conserved and accelerated genomic regions related to adaptation to thermal niches in Anolis lizards
Abstract
Understanding the genetic basis for adapting to thermal environments is important due to the serious effects of global warming on ectothermic species. Various genes associated with thermal adaptation in lizards have been identified mainly focusing on changes in gene expression or the detection of positively selected genes using coding regions. Only a few comprehensive genome-wide analyses have included noncoding regions. This study aimed to identify evolutionarily conserved and accelerated genomic regions using whole genomes of eight Anolis lizard species that have repeatedly adapted to similar thermal environments in multiple lineages. Evolutionarily conserved genomic regions were extracted as regions with overall sequence conservation (regions with fewer base substitutions) across all lineages compared with the neutral model. Genomic regions that underwent accelerated evolution in the lineage of interest were identified as those with more base substitutions in the target branch than in the entire background branch. Conserved elements across all branches were relatively abundant in “intergenic” genomic regions among noncoding regions. Accelerated regions (ARs) of each lineage contained a significantly greater proportion of noncoding RNA genes than the entire multiple alignments. Common genes containing ARs within 5 kb of their vicinity in lineages with similar thermal habitats were identified. Many genes associated with circadian rhythms and behavior were found in hot-open and cool-shaded habitat lineages. These genes might play a role in contributing to thermal adaptation and assist future studies examining the function of genes involved in thermal adaptation via genome editing.
Contact: Fuku Sakamoto (fukusakamoto29@gmail.com), Masakado Kawata (kawata@tohoku.ac.jp).
DESCRIPTIONS
The files contained under the "Sakamoto_etal_2024_anole_pairwise_alignment" directory are pairwise alignments of each Anolis species using the 13-chromosome genome of Anolis carolinensis as reference (compressed in gzip format). The alignments were generated by LastZ (Harris, 2007), subjected to the chaining and netting process introduced by Kent et al. (2003), and then filtered by a proprietary script. The naming convention is "pairwise_[target species name]carolinensis[chromosome name of A. carolinensis].maf."
The files in the "Sakamoto_etal_2024_anole_multiple_alignment" directory are multiple alignments of Anolis species using the 13-chromosome genome of Anolis carolinensis as reference (compressed in gzip format). Multiple alignments were generated by integrating pairwise alignments for each species using MultiZ (Blanchette et al., 2004). This dataset contains only alignments that are aligned with at least seven of the eight species covered in this study. The naming convention is "multiple_carolinensis_[chromosome name of A. carolinensis].maf."
The "Sakamoto_etal_2024_anole_neutral_phylogenetic_tree" directory contains the phylogenetic tree data inferred from the modified 4D sites.
The directory "Sakamoto_etal_2024_anole_CONorACC_score" contains the conserved and accelerated scores calculated by phyloP of the PHAST package (Pollard et al., 2010). For each chromosome of Anolis carolinensis, a conservation or acceleration score of the branch on the phylogenetic tree of interest was calculated by comparing a neutral model to each genomic region. The naming convention is "logP_[A. carolinensis chromosome name][target branch name][score calculation options (ACC or CON or CONACC)].gff."
The "Sakamoto_etal_2024_SCRIPTS" directory contains the codes used in this study. Please read the respective README files for details of each script.
REFERENCES
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Blanchette, M., Kent, W.J., Riemer, C., Elnitski, L., Smit, A.F., Roskin, K.M., Baertsch, R., Rosenbloom, K., Clawson, H., Green, E.D., Haussler, D., & Miller, W. (2004). Aligning multiple genomic sequences with the threaded blockset aligner. Genome research, 14(4), 708715. https://doi.org/10.1101/gr.1933104
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Harris, R.S. (2007). Improved Pairwise Alignment of Genomic DNA. PhD thesis, Pennsylvania State Univ.
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Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., & Haussler, D. (2003). Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl. Acad. Sci., 100, 1148411489. https://www.pnas.org/doi/10.1073/pnas.1932072100
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Pollard, K.S., Hubisz, M.J., Rosenbloom, K.R., & Siepel, A. (2010). Detection of nonneutral substitution rates on mammalian phylogenies. Genome research, 20(1), 110121. https://doi.org/10.1101/gr.097857.109