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Data from: Study of regional differences in GC content values in chromosomes of the guppy and related fish species

Citation

Charlesworth, Deborah (2020), Data from: Study of regional differences in GC content values in chromosomes of the guppy and related fish species, Dryad, Dataset, https://doi.org/10.5061/dryad.ghx3ffbkw

Abstract

Genetic and physical mapping of the guppy (P. reticulata) have shown that recombination patterns differ greatly between males and females. Crossover events occur evenly across the chromosomes in females, but in male meiosis they are restricted to the tip furthest from the centromere of each chromosome, creating very high recombination rates per megabase, similar to the high rates in of pseudo-autosomal regions (PARs) of mammalian sex chromosomes. We here used the intronic GC content to indirectly infer the recombination patterns on guppy chromosomes. This is based on evidence that recombination is associated with GC-biased gene conversion, so that genome regions with high recombination rates should be detectable by high GC content. We used intron sequences and 3rd positions of codons, in order to make comparisons between sequences that are matched, as far as possible, with respect to selective constraints. Both these types of sites are likely to be under weak selection. Almost all guppy chromosomes, including the sex chromosome (LG12), prove to have very high GC values near their assembly ends, suggesting high recombination rates due to strong crossover localisation in male meiosis. Our test does not suggest that the guppy XY pair has stronger crossover localisation than the autosomes, or than the homologous chromosome in a closely related fish, the platyfish (Xiphophorus maculatus). We therefore conclude that the guppy XY pair has not recently undergone an evolutionary change to a different recombination pattern, or reduced its crossover rate, but that the guppy evolved Y-linkage due to acquiring a male-determining factor that also conferred the male crossover pattern. The results also identify the centromere ends of guppy chromosomes, which were not determined in the guppy genome assembly. 

Methods

Python and r code files for intronic GC analyses in the chromosomes of 3 fish species, based on published and unpublished short-read genome sequences and annotated genes.

Usage Notes

No other files are needed. The files include 2 files with scripts for the analysis, and the files with results after analyses.

Funding

European Research Council, Award: 695225