Detection of evolutionary conserved and accelerated genomic regions related to adaptation to thermal niches in Anolis lizards.

Autor: Sakamoto F; Graduate School of Life Sciences Tohoku University Sendai Japan., Kanamori S; Graduate School of Life Sciences Tohoku University Sendai Japan., Díaz LM; National Museum of Natural History of Cuba Havana Cuba., Cádiz A; Faculty of Biology University of Havana Havana Cuba.; Present address: Department of Biology University of Miami Coral Gables Florida USA., Ishii Y; Graduate School of Life Sciences Tohoku University Sendai Japan., Yamaguchi K; Trans-Omics Facility National Institute for Basic Biology Okazaki Japan., Shigenobu S; Trans-Omics Facility National Institute for Basic Biology Okazaki Japan.; Department of Basic Biology, School of Life Science The Graduate University for Advanced Studies, SOKENDAI Okazaki Japan., Nakayama T; Division of Life Sciences, Center for Computational Sciences University of Tsukuba Tsukuba Japan., Makino T; Graduate School of Life Sciences Tohoku University Sendai Japan., Kawata M; Graduate School of Life Sciences Tohoku University Sendai Japan.
Jazyk: angličtina
Zdroj: Ecology and evolution [Ecol Evol] 2024 Mar 07; Vol. 14 (3), pp. e11117. Date of Electronic Publication: 2024 Mar 07 (Print Publication: 2024).
DOI: 10.1002/ece3.11117
Abstrakt: Understanding the genetic basis for adapting to thermal environments is important due to 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 alignment. 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.
Competing Interests: The authors declare no conflicts of interest.
(© 2024 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)
Databáze: MEDLINE
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