RRC ID 71787
Author Lau Q, Igawa T, Ogino H, Katsura Y, Ikemura T, Satta Y.
Title Heterogeneity of synonymous substitution rates in the Xenopus frog genome.
Journal PLoS One
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 (NA = 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.
Volume 15(8)
Pages e0236515
Published 2020-1-1
DOI 10.1371/journal.pone.0236515
PII PONE-D-20-12594
PMID 32764757
PMC PMC7413554
MeSH Animals Chromosomes Evolution, Molecular* Genetic Heterogeneity Genome / genetics* Hybridization, Genetic In Situ Hybridization, Fluorescence Phylogeny Silent Mutation / genetics* Xenopus laevis / genetics*
IF 2.74
Resource
Clawed frogs / Newts