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

Abstract

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.

Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies

“…Selection scans may overlook some of our association outlier windows because differentiation at these loci may be moderate, but rather we are detecting consistent allele frequency changes in the same direction between HP-LP comparisons. Many of the associated windows mapped to a previously unplaced scaffold in the genome (000094F), but we were able to place this at the start of chromosome 20 along with some local rearrangements (Figure S6) using previously published HiC data [61]. From here on and in Figure 2C-D, we refer to this new arrangement for chromosome 20 and scaffold 000094F as chromosome 20.…”

“…LITE libraries were sequenced on an Illumina HiSeq4000 with a 150bp paired-end metric and a target insert size of 300bp, and were pooled across several lanes so as to avoid technical bias with a sequencing coverage target of ≥10x per sample. Data from the Guanapo and Oropouche rivers has been previously published as part of Fraser et al [61].…”

“…Paired-end reads were quality-controlled with fastQC (v0.11.7) and trimmed with trim_galore (v0.4.5) before being aligned to the long-read, male guppy genome assembly [61] with bwa mem (v0.7.17). Appropriate read groups were added followed by alignment indexing, deduplication and merging to produce final bams.…”

“…Appropriate read groups were added followed by alignment indexing, deduplication and merging to produce final bams. Merged, deduplicated alignments were recalibrated using a truth-set of variants generated from high-coverage, PCR-free sequencing data from 12 individuals [61]. GVCFs were produced using GATK’s (v4.0.5.1) HaplotypeCaller and consolidated to chromosome/scaffold intervals with GenomicsDBImport prior to genotyping with GenotypeGVCFs.…”

The Genomic Architecture and Evolutionary Fates of Supergenes

“…For instance, a comparative study showed that in Neurospora tetrasperma large inversions present in the mat chromosome are a consequence instead of a cause of suppressed recombination ( Sun et al 2017 ; and see additional examples in Vicoso et al 2013 and Yan et al 2020 ). Likewise, population-level studies of young supergenes ( table 1 ) can contribute to a more refined characterization of the early stages of supergene evolution, as has been the case for young sex chromosomes (for instance, in guppies: Bergero et al 2019 ; Fraser et al 2020 , see also reviews by Charlesworth 2019 and Furman et al 2020 ).…”