Efficient identification of Y chromosome sequences in the human and <i>Drosophila</i> genomes

Carvalho, Antonio Bernardo; Clark, Andrew G.

doi:10.1101/gr.156034.113

Cited by 105 publications

(194 citation statements)

References 58 publications

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“…S1). In contrast, when this approach was used to identify Y Chromosome scaffolds in species with differentiated sex chromosomes (Drosophila and humans), a substantial number of Y Chromosome scaffolds were completely unmatched by female sequencing reads (Carvalho and Clark 2013). These results suggest that there are not large segments of the house fly Y Chromosome that are unique from the X Chromosome or autosomes.…”

Section: Resultsmentioning

confidence: 91%

“…It was necessary to assemble a male genome because the genome project sequenced gDNA from XX female flies (Scott et al 2014). Then we used a k-mer comparison approach to identify male-specific sequences by searching for male genomic scaffolds that are not matched by female sequencing reads (Carvalho and Clark 2013). Most of the scaffolds in the male genome assembly were (nearly) completely matched by female sequencing reads, and none of the male scaffolds were completely unmatched by female sequencing reads (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…We only considered assembled scaffolds from the male genome that were ≥1 kb. We implemented a k-mer comparison approach to identify male-specific sequences (Carvalho and Clark 2013). In our implementation, we used a k-mer size of 15 bp, used the male sequencing reads to construct a validating bit-array, and implemented the options described by Carvalho and Clark (2013) for identifying Y Chromosome sequences in Drosophila genomes (Supplemental Methods S1, S2).…”

Section: Identifying X and Y Chromosome Sequencesmentioning

confidence: 99%

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The house fly Y Chromosome is young and minimally differentiated from its ancient X Chromosome partner

2017

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Canonical ancient sex chromosome pairs consist of a gene rich X (or Z) Chromosome and a male-limited (or female-limited) Y (or W) Chromosome that is gene poor. In contrast to highly differentiated sex chromosomes, nascent sex chromosome pairs are homomorphic or very similar in sequence content. Nascent sex chromosomes can arise if an existing sex chromosome fuses to an autosome or an autosome acquires a new sex-determining locus/allele. Sex chromosomes often differ between closely related species and can even be polymorphic within species, suggesting that nascent sex chromosomes arise frequently over the course of evolution. Previously documented sex chromosome transitions involve changes to both members of the sex chromosome pair (X and Y, or Z and W). The house fly has sex chromosomes that resemble the ancestral fly karyotype that originated ∼100 million yr ago; therefore, the house fly is expected to have X and Y Chromosomes with different gene content. We tested this hypothesis using whole-genome sequencing and transcriptomic data, and we discovered little evidence for genetic differentiation between the X and Y in house fly. We propose that the house fly has retained the ancient X Chromosome, but the ancestral Y was replaced by an X Chromosome carrying a new male determining gene. Our proposed hypothesis provides a mechanism for how one member of a sex chromosome pair can experience evolutionary turnover while the other member remains unaffected.

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Section: Resultsmentioning

confidence: 91%

Section: Resultsmentioning

confidence: 99%

Section: Identifying X and Y Chromosome Sequencesmentioning

confidence: 99%

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The house fly Y Chromosome is young and minimally differentiated from its ancient X Chromosome partner

2017

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“…The Y chromosome genome scan (YGS) approach was designed to operate on scaffolds from a genome assembly derived from mixed sexes or males; after identification and masking of identical repeats, scaffolds are classified as Y-linked if they have few or no kmer-length matches to female Illumina sequences (40). As applied to An.…”

Section: Resultsmentioning

confidence: 99%

Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes

Hall

Papathanos

Sharma

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

100

152

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Y chromosomes control essential male functions in many species, including sex determination and fertility. However, because of obstacles posed by repeat-rich heterochromatin, knowledge of Y chromosome sequences is limited to a handful of model organisms, constraining our understanding of Y biology across the tree of life. Here, we leverage long single-molecule sequencing to determine the content and structure of the nonrecombining Y chromosome of the primary African malaria mosquito, Anopheles gambiae. We find that the An. gambiae Y consists almost entirely of a few massively amplified, tandemly arrayed repeats, some of which can recombine with similar repeats on the X chromosome. Sex-specific genome resequencing in a recent species radiation, the An. gambiae complex, revealed rapid sequence turnover within An. gambiae and among species. Exploiting 52 sex-specific An. gambiae RNA-Seq datasets representing all developmental stages, we identified a small repertoire of Y-linked genes that lack X gametologs and are not Y-linked in any other species except An. gambiae, with the notable exception of YG2, a candidate male-determining gene. YG2 is the only gene conserved and exclusive to the Y in all species examined, yet sequence similarity to YG2 is not detectable in the genome of a more distant mosquito relative, suggesting rapid evolution of Y chromosome genes in this highly dynamic genus of malaria vectors. The extensive characterization of the An. gambiae Y provides a long-awaited foundation for studying male mosquito biology, and will inform novel mosquito control strategies based on the manipulation of Y chromosomes.

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“…Novel sequencing technologies have opened opportunities to make Y Chromosome sequencing faster and more affordable. One such approach sequences both male and female genomes and uses a differential analysis to identify Y-linked contigs (Carvalho and Clark 2013;). However, this approach still requires substantial amounts of whole-genome sequencing.…”

mentioning

confidence: 99%

A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y

et al. 2016

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The mammalian Y Chromosome sequence, critical for studying male fertility and dispersal, is enriched in repeats and palindromes, and thus, is the most difficult component of the genome to assemble. Previously, expensive and labor-intensive BAC-based techniques were used to sequence the Y for a handful of mammalian species. Here, we present a much faster and more affordable strategy for sequencing and assembling mammalian Y Chromosomes of sufficient quality for most comparative genomics analyses and for conservation genetics applications. The strategy combines flow sorting, short-and long-read genome and transcriptome sequencing, and droplet digital PCR with novel and existing computational methods. It can be used to reconstruct sex chromosomes in a heterogametic sex of any species. We applied our strategy to produce a draft of the gorilla Y sequence. The resulting assembly allowed us to refine gene content, evaluate copy number of ampliconic gene families, locate species-specific palindromes, examine the repetitive element content, and produce sequence alignments with human and chimpanzee Y Chromosomes. Our results inform the evolution of the hominine (human, chimpanzee, and gorilla) Y Chromosomes. Surprisingly, we found the gorilla Y Chromosome to be similar to the human Y Chromosome, but not to the chimpanzee Y Chromosome. Moreover, we have utilized the assembled gorilla Y Chromosome sequence to design genetic markers for studying the male-specific dispersal of this endangered species.

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Efficient identification of Y chromosome sequences in the human and Drosophila genomes

Cited by 105 publications

References 58 publications

The house fly Y Chromosome is young and minimally differentiated from its ancient X Chromosome partner

The house fly Y Chromosome is young and minimally differentiated from its ancient X Chromosome partner

Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes

A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y

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