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タイトル: | Heterogeneity of synonymous substitution rates in the Xenopus frog genome |
著者: | Lau, Quintin Igawa, Takeshi Ogino, Hajime Katsura, Yukako Ikemura, Toshimichi Satta, Yoko |
著者名の別形: | 桂, 有加子 |
キーワード: | Xenopus Amphibian genomics Centromeres Frogs Genetic loci Chromosome mapping Invertebrate genomics Mammalian genomics |
発行日: | Aug-2020 |
出版者: | Public Library of Science (PLoS) |
誌名: | PLoS ONE |
巻: | 15 |
号: | 8 |
論文番号: | e0236515 |
抄録: | With the increasing availability of high quality genomic data, there is opportunity to deeply explore the genealogical relationships of different gene loci between closely related species. In this study, we utilized genomes of Xenopus laevis (XLA, a tetraploid species with (L) and (S) sub-genomes) and X. tropicalis (XTR, a diploid species) to investigate whether synonymous substitution rates among orthologous or homoeologous genes displayed any heterogeneity. From over 1500 orthologous/homoeologous genes collected, we calculated proportion of synonymous substitutions between genomes/sub-genomes (k) and found variation within and between chromosomes. Within most chromosomes, we identified higher k with distance from the centromere, likely attributed to higher substitution rates and recombination in these regions. Using maximum likelihood methods, we identified further evidence supporting rate heterogeneity, and estimated species divergence times and ancestral population sizes. Estimated species divergence times (XLA.L-XLA.S: ~25.5 mya; XLA-XTR: ~33.0 mya) were slightly younger compared to a past study, attributed to consideration of population size in our study. Meanwhile, we found very large estimated population size in the ancestral populations of the two species (N[A] = 2.55 x 10⁶). Local hybridization and population structure, which have not yet been well elucidated in frogs, may be a contributing factor to these possible large population sizes. |
著作権等: | © 2020 Lau et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
URI: | http://hdl.handle.net/2433/265370 |
DOI(出版社版): | 10.1371/journal.pone.0236515 |
PubMed ID: | 32764757 |
出現コレクション: | 学術雑誌掲載論文等 |
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