The pig X and Y chromosomes: structure, sequence and evolution

Skinner, Benjamin M.; Sargent, Carole A.; Churcher, Carol; Hunt, Toby; Herrero, Javier; Loveland, Jane; Dunn, Matt; Louzada, Sandra; Fu, Beiyuan; Chow, William; Gilbert, James; Austin-Guest, Siobhan; Beal, Kathryn; Carvalho-Silva, Denise; Cheng, William; Gordon, Daria; Grafham, Darren; Hardy, Matt; Harley, Joanna; Hauser, Heidi; Howden, Philip; Howe, Kerstin; Lachani, Kim; Ellis, Peter J.I.; Kelly, Daniel; Kerry, Giselle; Kerwin, James; Ng, Bee Ling; Threadgold, Glen; Wileman, Thomas; Wood, Jonathan; Yang, Fengtang; Harrow, Jennifer; Affara, Nabeel A.; Tyler‐Smith, Chris

doi:10.1101/012914

Cited by 7 publications

(7 citation statements)

References 83 publications

(92 reference statements)

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“…We did not detect massive amplification of gene families as observed on mammalian sex chromosomes Murphy et al 2006;Hughes et al 2010;Paria et al 2011;Soh et al 2014; Janečka numbers we observed are on the same order as the duplicated genes on the sex chromosomes 519 of multiple species of Drosophila (Chang and Larracuente 2018;Ellison and Bachtrog 2019). The 520 gene duplications on the threespine stickleback sex chromosomes may reflect selection on the 521 early amplification of genes important for male fertility (Gvozdev et al 2005) or to prevent 522 degradation by providing a repair template through gene conversion (Rozen et al 2003;Skaletsky 523 et al 2003;Backström et al 2005;Bhowmick et al 2007;Connallon and Clark 2010;Davis et al 524 2010;Marais et al 2010;Hallast et al 2013;Soh et al 2014;Skinner et al 2016;Peneder et al 525 2017;Trombetta and Cruciani 2017;Chang and Larracuente 2018). Alternatively, the duplications 526 we observe on the threespine stickleback Y chromosome may simply reflect recent translocations 527 and duplications that have yet to degenerate and pseudogenize.…”

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confidence: 53%

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

Peichel

McCann

Ross

et al. 2019

Preprint

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Heteromorphic sex chromosomes have evolved repeatedly across diverse species. Suppression of recombination between X and Y chromosomes leads to rapid degeneration of the Y chromosome. However, these early stages of degeneration are not well understood, as complete Y chromosome sequence assemblies have only been generated across a handful of taxa with ancient sex chromosomes. Here we describe the assembly of the threespine stickleback (Gasterosteus aculeatus) Y chromosome, which is less than 26 million years old. Our previous work identified that the non-recombining region between the X and the Y spans ∼17.5 Mb on the X chromosome. Here, we combined long-read PacBio sequencing with a Hi-C-based proximity guided assembly to generate a 15.87 Mb assembly of the Y chromosome. Our assembly is concordant with cytogenetic maps and Sanger sequences of over 90 Y chromosome clones from a bacterial artificial chromosome (BAC) library. We found three evolutionary strata on the Y chromosome, consistent with the three inversions identified by our previous cytogenetic analyses. The young threespine stickleback Y shows convergence with older sex chromosomes in the retention of haploinsufficient genes and the accumulation of genes with testis-biased expression, many of which are recent duplicates. However, we found no evidence for large amplicons found in other sex chromosome systems. We also report an excellent candidate for the master sex-determination gene: a translocated copy of Amh (Amhy). Together, our work shows that the same evolutionary forces shaping older sex chromosomes can cause remarkably rapid changes in the overall genetic architecture on young Y chromosomes.

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confidence: 53%

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

Peichel

McCann

Ross

et al. 2019

Preprint

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“…Despite its importance, the sequence of the Y Chromosome has so far been determined only for a handful of mammals-human, chimpanzee, rhesus macaque, mouse, and pig Hughes et al 2010Hughes et al , 2012aSoh et al 2014;Skinner et al 2016), as well as partially sequenced for bull, dog, cat, marmoset, opossum, and rat (Chang et al 2013;Li et al 2013;Bellott et al 2014).…”

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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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“…Moreover, many mammalian genome projects have focused on females to obtain reliable X chromosome sequences (Hughes et al 2012). As a consequence, the complete sequences of Y chromosome have only been determined for a handful of mammals, such as humans (Homo sapiens) (Skaletsky et al 2003), chimpanzees (Pan troglodytes) (Hughes et al 2010), rhesus macaques (Macaca mulatta) (Hughes et al 2012), gorillas (Tomaszkiewicz et al 2016) (Western lowland gorilla), pigs (Sus scrofa) (Skinner et al 2016) and mice (Mus musculus) (Soh et al 2014), as well as partially sequenced for cattle (Bos taurus) (Chang et al 2013), dogs (Canis lupus familiaris), cats (Felis catus) (Li et al 2013), polar bears (Ursus maritimus) (Bidon et al 2015), horse (Equus caballus) (Wallner et al 2017), marmosets (Callithrix jacchus), opossums (Monodelphis domestica) and rats (Rattus norvegicus) (Bellott et al 2014).…”

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confidence: 99%

Synteny search identifies carnivore Y chromosome for evolution of male specific genes

Fan

Liu

et al. 2019

Integrative Zoology

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The explosively accumulated mammalian genomes have provided a valuable resource to characterize the evolution of the Y chromosome. Unexpectedly, the Y-chromosome sequence has been characterized in only a small handful of species, with a majority of them being model organisms. Thus, identification of Y-linked scaffolds from unordered genome sequences is becoming more important. Here, we used a syntenic-based approach to generate the scaffolds of male specific region in Y chromosome (MSY) from the genome sequence of 6 male carnivore species. Our results identified 14, 15, 9, 28, 14 and 11 Y-linked scaffolds in polar bear, pacific walrus, red panda, cheetah, ferret and tiger, covering 1.55Mbp, 2.62Mbp, 964Kb, 1.75Mb, 2.17Mbp and 1.84Mb MSY, respectively. All of the candidate Y-linked scaffolds in three selected species (red panda, polar bear and tiger) were successfully verified using PCR. We re-annotated these Y-linked scaffolds plus with domestic dog and cat MSY, a total of 11 orthologous genes conserved in at least 7 of the 8 carnivores were identified. These 11 Y-linked genes have significantly higher evolutionary rates compared with their X-linked counterparts, indicating less purifying selection for MSY genes. Taken together, our study shows that the approach of synteny search is a reliable and easily affordable strategy to identify Y-linked scaffolds from unordered carnivore genome and provides a preliminary evolutionary study for carnivore MSY genes. This article is protected by copyright. All rights reserved.

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The pig X and Y chromosomes: structure, sequence and evolution

Cited by 7 publications

References 83 publications

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

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

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

Synteny search identifies carnivore Y chromosome for evolution of male specific genes

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