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Title: Heterogeneity of synonymous substitution rates in the Xenopus frog genome
Authors: Lau, Quintin
Igawa, Takeshi
Ogino, Hajime
Katsura, Yukako  kyouindb  KAKEN_id
Ikemura, Toshimichi
Satta, Yoko
Author's alias: 桂, 有加子
Keywords: Xenopus
Amphibian genomics
Centromeres
Frogs
Genetic loci
Chromosome mapping
Invertebrate genomics
Mammalian genomics
Issue Date: Aug-2020
Publisher: Public Library of Science (PLoS)
Journal title: PLoS ONE
Volume: 15
Issue: 8
Thesis number: e0236515
Abstract: 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.
Rights: © 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(Published Version): 10.1371/journal.pone.0236515
PubMed ID: 32764757
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