Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes

Janečka, Jan E.; Davis, Brian W.; Ghosh, S. N.; Paria, Nandina; Das, Pranab Jyoti; Orlando, Ludovic; Schubert, Mikkel; Nielsen, Martin K.; Stout, T.A.E.; Brashear, Wesley; Li, Gang; Johnson, Charles D.; Metz, Richard P.; Zadjali, Al Muatasim Al; Love, Charles C.; Varner, D.D.; Bellott, Daniel W.; Murphy, William J.; Chowdhary, Bhanu P.; Raudsepp, Terje

doi:10.1038/s41467-018-05290-6

Cited by 67 publications

(111 citation statements)

References 69 publications

(162 reference statements)

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“…We observed strong testis-biased expression among genes that had 530 duplicated and translocated to the Y chromosome, similar to patterns observed on other Y 531 chromosomes (Carvalho et al 2000;Skaletsky et al 2003;Murphy et al 2006;Hughes et 532 al. 2010;Paria et al 2011;Soh et al 2014;Mahajan and Bachtrog 2017;Janečka et al 2018).…”

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confidence: 99%

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: 99%

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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“…The cattle X-d2b region contains SRY and is in a telomeric position similar to the X-d2 region of pig. The cattle X-d2b region contains two copies of RBMY, which is also duplicated in the horse X-d2 [20].…”

Section: Comparison Of X-degenerate Y Chromosome Regionsmentioning

confidence: 99%

“…A study of bovine Y chromosome gene expression has contributed information on genes in X-d regions [16], but interpretation of the data is limited by the relatively poor quality of the available Y chromosome assembly. [18], pig [19] and horse [20], 84 have well characterised and assembled Y chromosomes. 85…”

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confidence: 99%

New Insights into Mammalian Sex Chromosome Structure and Evolution from High-quality Bovine X and Y Chromosome Sequences

Liu

Low

Tearle

et al. 2019

Preprint

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Background Mammalian X chromosomes are mainly euchromatic with a similar size and structure among species whereas Y chromosomes are smaller, have undergone substantial evolutionary changes and accumulated male specific genes and genes involved in sex determination. The PAR is conserved on the X and Y and pair during meiosis. The structure, evolution and function of mammalian sex chromosomes is still poorly understood because few species have high quality sex chromosome assemblies. Results Here we report the first bovine sex chromosome assemblies that include the complete pseudoautosomal region (PAR) spanning 6.84 Mb and three Y chromosome X-degenerate (X-d) regions. We show that the ruminant PAR comprises 31 genes and is similar to the PAR of pig and dog but extends further than those of human and horse. Differences in the pseudoautosomal boundaries are consistent with evolutionary divergence times. Conclusions A bovidae-specific expansion of members of the lipocalin gene family in the PAR may reflect immune-modulation and anti-inflammatory responses that contribute to parasite resistance in ruminants. Comparison of the X-d regions of Y chromosomes across species reveal five conserved X-Y gametologs, which are global regulators of gene activity, and may have a fundamental role in mammalian sexual dimorphism.

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“…The timing of this bottleneck is not clear, however, as aDNA studies have revealed that ancient domestic horses had greater Y-chromosome diversity than modern horses (Lippold et al 2011a;Librado et al 2017). The recent publication of the first complete assembly of the horse Y-chromosome should assist in future aDNA studies of male-biased processes in horse domestication (Janečka et al 2018).…”

Section: Horsesmentioning

confidence: 99%

Paleogenomics of Animal Domestication

Irving-Pease

Ryan

Jamieson

et al. 2018

Population Genomics

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Starting with dogs, over 15,000 years ago, the domestication of animals has been central in the development of modern societies. Because of its importance for a range of disciplinesincluding archaeology, biology, and the humanities-domestication has been studied extensively. This chapter reviews how the field of paleogenomics, has, and will continue to, revolutionise our understanding of animal domestication. We discuss how the recovery of ancient DNA from archaeological remains is allowing researchers to overcome inherent shortcomings arising from the analysis of modern DNA alone. In particular, we show how DNA, extracted from ancient substrates, has proven to be a crucial source of information to reconstruct the geographic and temporal origin of domestic species. We also discuss how ancient DNA is being used by geneticists and archaeologists to directly observe evolutionary changes linked to artificial and natural selection to generate a richer understanding of this fascinating process.

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Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes

Cited by 67 publications

References 69 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

New Insights into Mammalian Sex Chromosome Structure and Evolution from High-quality Bovine X and Y Chromosome Sequences

Paleogenomics of Animal Domestication

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