Lau Q et al. (2020), Heterogeneity of synonymous substitution rates ...

XB-ART-57247

PLoS One 2020 Aug 07;158:e0236515. doi: 10.1371/journal.pone.0236515.

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Heterogeneity of synonymous substitution rates in the Xenopus frog genome.

Lau Q , Igawa T , Ogino H , Katsura Y , Ikemura T , Satta Y .

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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.

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	Fig 1. Boxplots depicting proportion of synonymous substitutions (k) for each chromosome.Between (A) X. laevis L (XLA.L) and S (XLA.S) sub-genomes, (B) X. tropicalis (XTR) and XLA.L, and (C) XTR and XLA.S. p < 0.01, *p < 0.0001 (adjusted p-values from Tukey multiple comparisons of means).
	Fig 2. Relationship patterns between proportion of synonymous substitutions (k) and chromosome location.Representative figures displaying different relationship patterns for each genome pair combination (XTR-XLA.L in red, XTR-XLA.S in green, and XLA.L-XLA.S in blue). (A) Chromosome 1 (e.g. XTR1) showed a common non-linear relationship between k and location. This higher k in distal parts of the chromosome was also seen in chromosomes 2 to 7, irrespective of the genome used for location in the x-axis (S1 Fig). (B, C) Chromosome 8 showed contrasting patterns based on the genome used for location reference: (B) XTR8 (S1 Fig) and XLA8L showed higher k in the distal part of chromosome, while (C) XLA8S had no marked relationship between k and location, likely due to intra-chromosomal rearrangements [6]. (D) In XTR9, k increased distally with location, while (E) it decreased in XTR10; (F) in the homoeologous XLA9_10, k decreased with location. Centromere positions are indicated by dotted vertical line and estimated based on position of frog centromeric repeat 1 (Fcr1) [21] or centromeric markers from X. tropicalis [22]. Full results are shown in S1 Fig.
	Fig 3. Best maximum likelihood estimates of X = 4Nμ and Y = 2μt.Estimates were used to calculate ancestral population size and species divergence time, respectively (in ancestor of XLA-XTR or XLA.S-XLA.L). These estimates were significantly different compared to those using infinitely large α (**p < 0.0001, t-test). Line bars represent mean ± s.d.; each point represents each chromosome, with genome-wide results indicated by dark circles.

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