Assembly of a young vertebrate Y chromosome reveals convergent signatures of sex chromosome evolution

Peichel, Catherine L.; McCann, Shaugnessy R.; Ross, Joseph A.; Naftaly, Alice F.S.; Urton, James R.; Cech, Jennifer N.; Grimwood, Jane; Schmutz, Jeremy; Myers, R; Kingsley, David M.; White, Michael A.

doi:10.1101/2019.12.12.874701

Cited by 7 publications

(24 citation statements)

References 112 publications

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“…High-quality genome assemblies of sex chromosomes are becoming more available (Liu et al 2019;Peichel et al 2019). An assembly of the neo-Y chromosome of Drosophila miranda showed that the neo-Y chromosome has expanded and many of the genes have been amplified to high copy number (Bachtrog et al 2019).…”

Section: Discussionmentioning

confidence: 99%

Evolution of a sex megachromosome

Conte

Clark

Roberts

et al. 2020

Preprint

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AbstractChromosome size and morphology vary within and among species, but little is known about either the proximate or ultimate causes of these differences. Cichlid fish species in the tribe Oreochromini share an unusual megachromosome that is ~3 times longer than any of the other chromosomes. This megachromosome functions as a sex chromosome in some of these species. We explore two hypotheses of how this sex megachromosome may have evolved. The first hypothesis proposes that it developed by the accumulation of repetitive elements as recombination was reduced around a dominant sex-determination locus, as suggested by traditional models of sex chromosome evolution. An alternative hypothesis is that the megachromosome originated via the fusion of an autosome with a highly-repetitive B chromosome, one of which had carried a sex-determination locus. Here we test these hypotheses using comparative analysis of several chromosome-scale cichlid and teleost genomes. We find the megachromosome consists of three distinct regions based on patterns of recombination, gene and transposable element content, and synteny to the ancestral autosome. A WZ sex-determination locus encompasses the last ~105Mbp of the 134Mbp megachromosome and the last 47Mbp of the megachromosome shares no obvious homology to any ancestral chromosome. Comparisons across 69 teleost genomes reveal the megachromosome contains unparalleled amounts of endogenous retroviral elements, immunoglobulin genes, and long non-coding RNAs. Although the origin of this megachromosome remains ambiguous, it has clearly been a focal point of extensive evolutionary genomic conflicts. This megachromosome represents an interesting system for studying sex chromosome evolution and genomic conflicts.

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Section: Discussionmentioning

confidence: 99%

Evolution of a sex megachromosome

Conte

Clark

Roberts

et al. 2020

Preprint

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“…Many chr. Un contigs that were not placed in the v. 4 genome assembly may be represented in the v. assembly if they were contained completely within a PacBio Canu contig (Peichel et al 2019). To test this, we used BLAT to align the 3378 chr.…”

Section: Closing Gaps In the Reference Assemblymentioning

confidence: 99%

“…These annotations combined evidence from multiple RNA-seq transcriptomes, all predicted Ensembl protein sequences (release 95), and ab inito gene predictions from SNAP (v. 2006-07-28) (Korf 2004) and Augustus (v. 3.3.2) (Stanke et al 2006). MAKER was run over three rounds using the RNAseq transcriptomes and methods previously described (Peichel et al 2019).…”

Section: Genome Annotationmentioning

confidence: 99%

“…Y chromosomes in mammals have also been documented to have highly variable centromeric repeats that are divergent from their counterparts across the remainder of the genome (Wolfe et al 1985;Pertile et al 2009;Miga et al 2014). Assembly of segments of the threespine stickleback Y chromosome centromere (Peichel et al 2019) revealed an alpha satellite monomer repeat that was divergent from the consensus monomeric repeat identified from the remainder of the genome (Cech and Peichel 2015). With the assembly of larger tracks of centromeric sequence from the autosomes and the X chromosome, we now show the Y chromosome centromere is also divergent from the remainder of the genome at the level of higher order repeats (Peichel et al 2019), matching other rapidly evolving Y chromosomes.…”

Section: Telomere Repeats and Centromere Repeats Were Identified Withmentioning

confidence: 99%

“…Within the human genome, many highly repetitive regions have been resolved, such as pericentromeres (Vollger et al 2020), complete centromeres (Jain et al 2018b), telomeres (Jain et al 2018a) and the entire major histocompatibility complex (Jain et al 2018a). De novo assemblies of highly repetitive Y chromosomes have also become feasible using long-read sequencing (Mahajan et al 2018;Peichel et al 2019). Overall, long-read sequencing has enabled telomere-to-telomere chromosome assemblies in multiple species (Liu et al 2020;Miga et al 2019).…”

Section: Introductionmentioning

confidence: 99%

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Improved contiguity of the threespine stickleback genome using long-read sequencing

Nath

Shaw

White

2020

Preprint

Self Cite

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AbstractWhile the cost and time for assembling a genome have drastically reduced, it still remains a challenge to assemble a highly contiguous genome. These challenges are rapidly being overcome by the integration of long-read sequencing technologies. Here, we use long sequencing reads to improve the contiguity of the threespine stickleback fish (Gasterosteus aculeatus) genome, a prominent genetic model species. Using Pacific Biosciences sequencing, we were able to fill over 76% of the gaps in the genome, improving contiguity over five-fold. Our approach was highly accurate, validated by 10X Genomics long-distance linked-reads. In addition to closing a majority of gaps, we were able to assemble segments of telomeres and centromeres throughout the genome. This highlights the power of using long sequencing reads to assemble highly repetitive and difficult to assemble regions of genomes. This latest genome build has been released through a newly designed community genome browser that aims to consolidate the growing number of genomics datasets available for the threespine stickleback fish.

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Sexual Dimorphism through the Lens of Genome Manipulation, Forward Genetics, and Spatiotemporal Sequencing

Kasimatis¹,

Sánchez‐Ramírez²,

Stevenson

2020

Genome Biology and Evolution

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Sexual reproduction often leads to selection that favors the evolution of sex-limited traits or sex-specific variation for shared traits. These sexual dimorphisms manifest due to sex-specific genetic architectures and sex-biased gene expression across development, yet the molecular mechanisms underlying these patterns are largely unknown. The first step is to understand how sexual dimorphisms arise across the genotype-phenotype-fitness map. The emergence of “4D genome technologies” allows for efficient, high-throughput, and cost-effective manipulation and observations of this process. Studies of sexual dimorphism will benefit from combining these technological advances (e.g., precision genome editing, inducible transgenic systems, and single-cell RNA sequencing) with clever experiments inspired by classic designs (e.g., bulked segregant analysis, experimental evolution, and pedigree tracing). This perspective poses a synthetic view of how manipulative approaches coupled with cutting-edge observational methods and evolutionary theory are poised to uncover the molecular genetic basis of sexual dimorphism with unprecedented resolution. We outline hypothesis-driven experimental paradigms for identifying genetic mechanisms of sexual dimorphism among tissues, across development, and over evolutionary time.

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Assembly of a young vertebrate Y chromosome reveals convergent signatures of sex chromosome evolution

Cited by 7 publications

References 112 publications

Evolution of a sex megachromosome

Evolution of a sex megachromosome

Improved contiguity of the threespine stickleback genome using long-read sequencing

Sexual Dimorphism through the Lens of Genome Manipulation, Forward Genetics, and Spatiotemporal Sequencing

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