Using GC content to compare recombination patterns on the sex chromosomes and autosomes of the guppy,<i>Poecilia reticulata</i>, and its close outgroup species

Charlesworth, Deborah; Zhang, Yexin; Bergero, Roberta; Graham, Chay; Gardner, Jim; Yong, Lengxob

doi:10.1101/2020.05.22.110635

Cited by 5 publications

(5 citation statements)

References 59 publications

(28 reference statements)

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“…This study also identified a region of high recombination on the end of the Y chromosome opposite to the centromere, consistent with the findings of Lisachov et al (2015). The localization of crossovers in males to the tips of all chromosomes is consistent with the high GC content found there (Charlesworth et al 2020b). Charlesworth et al (2020a) reported a crossover between the X and Y of P. reticulata in a region previously hypothesized to be a nonrecombining stratum.…”

Section: : Introductionsupporting

confidence: 87%

Evolution of the canonical sex chromosomes of the guppy and its relatives

Kirkpatrick

Dixon

Sardell

et al. 2020

Preprint

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The sex chromosomes of the guppy, Poecilia reticulata, and its close relatives are of particular interest: they are much younger than the highly degenerate sex chromosomes of model systems such as mammals and Drosophila melanogaster, and they carry many of the genes responsible for the males’ dramatic coloration. Over the last decade, several studies have analyzed these sex chromosomes using a variety of approaches including sequencing genomes and transcriptomes, cytology, and linkage mapping. Conflicting conclusions have emerged, in particular concerning the history of the sex chromosomes and the evolution of suppressed recombination between the X and Y. Here we address these controversies by reviewing the evidence and reanalyzing data. We find no support for a nonrecombining sex determining region (SDR) or evolutionary strata in P. reticulata. We confirm that its congener P. picta has evolved dosage compensation across all of its X chromosome. Last, we do not find evidence that the nonrecombining SDRs of P. picta and P. wingei descend from a common ancestral SDR, and suggest instead that suppressed recombination between the X and Y evolved independently after the two species diverged. We identify possible causes of conflicting results in previous studies and suggest best practices going forward.

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Section: : Introductionsupporting

confidence: 87%

Evolution of the canonical sex chromosomes of the guppy and its relatives

Kirkpatrick

Dixon

Sardell

et al. 2020

Preprint

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“…Based on the total size in the published assembly, plus the two unplaced scaffolds, totalling about 815 kb, that we inferred from the X. maculatus assembly and mapped to the guppy PAR (see above), our results do not change the conclusion that the guppy PAR cannot be larger than a couple of megabases ( Bergero et al 2019 ). Assuming that consistent high intronic high GC content of a region reflects a high recombination rate that causes GC-biased gene conversion (see Charlesworth et al 2020 ), the uniformly high GC content (Supplementary Figure S2) of the scaffold that our map reveals to be terminal ( Figure 4 ) suggests that recombination rates are uniformly high throughout the guppy PAR, rather than being clustered into parts of the PAR with very high crossover rates.…”

Section: Resultsmentioning

confidence: 86%

Locating the Sex Determining Region of Linkage Group 12 of Guppy (Poecilia reticulata)

Charlesworth

Bergero

Graham

et al. 2020

G3 Genes|Genomes|Genetics

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Despite over 100 years of study, the location of the fully sex-linked region of the guppy (Poecilia reticulata) carrying the male-determining locus, and the regions where the XY pair recombine, remain unclear. Previous population genomics studies to determine these regions used small samples from recently bottlenecked captive populations, which increase the false positive rate of associations between individuals' sexes and SNPs. Using new data from multiple natural populations, we show that a recently proposed candidate for this species' male-determining gene is probably not completely sex-linked, leaving the maleness factor still unidentified. Variants in the chromosome 12 region carrying the candidate gene sometimes show linkage disequilibrium with the sex-determining factor, but no consistently male-specific variant has yet been found. Our genetic mapping with molecular markers spread across chromosome 12 confirms that this is the guppy XY pair. We describe two families with recombinants between the X and Y chromosomes, which confirm that the male-determining locus is in the region identified by all previous studies, near the terminal pseudo-autosomal region (PAR), which crosses over at a very high rate in males. We correct the PAR marker order, and assign two unplaced scaffolds to the PAR. We also detect a duplication, with one copy in the male-determining region, explaining signals of sex linkage in a more proximal region.

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“…The candidate contig is followed by a GC-rich region, corresponding to the end of the chromosome where recombination is known to be high and shows no evidence for sex-linkage ( Bergero et al. 2019 ; Charlesworth et al. 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata)

Fraser

Whiting

Paris

et al. 2020

Genome Biology and Evolution

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101

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Theory predicts that the sexes can achieve greater fitness if loci with sexually antagonistic polymorphisms become linked to the sex determining loci, and this can favour the spread of reduced recombination around sex determining regions. Given that sex-linked regions are frequently repetitive and highly heterozygous, few complete Y chromosome assemblies are available to test these ideas. The guppy system (Poecilia reticulata) has long been invoked as an example of sex chromosome formation resulting from sexual conflict. Early genetics studies revealed that male colour patterning genes are mostly but not entirely Y-linked, and that X-linkage may be most common in low predation populations. More recent population genomic studies of guppies have reached varying conclusions about the size and placement of the Y-linked region. However, this previous work used a reference genome assembled from short-read sequences from a female guppy. Here, we present a new guppy reference genome assembly from a male, using long-read PacBio single-molecule real-time sequencing (SMRT) and chromosome contact information. Our new assembly sequences across repeat- and GC-rich regions and thus closes gaps and corrects mis-assemblies found in the short-read female-derived guppy genome. Using this improved reference genome, we then employed broad population sampling to detect sex differences across the genome. We identified two small regions that showed consistent male-specific signals. Moreover, our results help reconcile the contradictory conclusions put forth by past population genomic studies of the guppy sex chromosome. Our results are consistent with a small Y-specific region and rare recombination in male guppies.

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Using GC content to compare recombination patterns on the sex chromosomes and autosomes of the guppy,Poecilia reticulata, and its close outgroup species

Cited by 5 publications

References 59 publications

Evolution of the canonical sex chromosomes of the guppy and its relatives

Evolution of the canonical sex chromosomes of the guppy and its relatives

Locating the Sex Determining Region of Linkage Group 12 of Guppy (Poecilia reticulata)

Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata)

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