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Scientific reports2023; 13(1); 20180; doi: 10.1038/s41598-023-47583-x

Trio-binning of a hinny refines the comparative organization of the horse and donkey X chromosomes and reveals novel species-specific features.

Abstract: We generated single haplotype assemblies from a hinny hybrid which significantly improved the gapless contiguity for horse and donkey autosomal genomes and the X chromosomes. We added over 15 Mb of missing sequence to both X chromosomes, 60 Mb to donkey autosomes and corrected numerous errors in donkey and some in horse reference genomes. We resolved functionally important X-linked repeats: the DXZ4 macrosatellite and ampliconic Equine Testis Specific Transcript Y7 (ETSTY7). We pinpointed the location of the pseudoautosomal boundaries (PAB) and determined the size of the horse (1.8 Mb) and donkey (1.88 Mb) pseudoautosomal regions (PARs). We discovered distinct differences in horse and donkey PABs: a testis-expressed gene, XKR3Y, spans horse PAB with exons1-2 located in Y and exon3 in the X-Y PAR, whereas the donkey XKR3Y is Y-specific. DXZ4 had a similar ~ 8 kb monomer in both species with 10 copies in horse and 20 in donkey. We assigned hundreds of copies of ETSTY7, a sequence horizontally transferred from Parascaris and massively amplified in equids, to horse and donkey X chromosomes and three autosomes. The findings and products contribute to molecular studies of equid biology and advance research on X-linked conditions, sex chromosome regulation and evolution in equids.
© 2023. The Author(s).
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Publication Date: 2023-11-17 PubMed ID: 37978222PubMed Central: PMC10656420DOI: 10.1038/s41598-023-47583-xGoogle Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research involves the examination of horse and donkey chromosomes through the trio-binning of a hinny hybrid, revealing important genomic data and distinct species-specific features. This new information could significantly aid studies relating to equid biology and evolution.

Genome Assembly and Enhancement

  • The researchers produced single haplotype assemblies using a hinny hybrid – a cross between a female donkey and a male horse.
  • This approach dramatically improved the gapless continuity for the horse and donkey autosomal genomes and the X chromosomes, filling in previous knowledge gaps and correcting errors in the reference genomes.
  • Specifically, the study added over 15 Mb of missing sequence to both X chromosomes and corrected many errors in the donkey genome and some in the horse’s genome.

New Insights into X-Linked Repeats

  • The research resolved previously challenging X-linked repeats like the DXZ4 macrosatellite and the Equine Testis Specific Transcript Y7 (ETSTY7).
  • ETSTY7 is a sequence that was transferred horizontally from Parascaris and has been heavily amplified in equids. In this study, the sequence was assigned to horse and donkey X chromosomes and three autosomes.

Clarification of Pseudoautosomal Boundaries and Regions

  • The study clarified the location of pseudoautosomal boundaries (PABs) and determined the size of the pseudoautosomal regions (PARs) in both horse (1.8Mb) and donkey (1.88Mb).
  • The research also found differences between the horse and the donkey PABs. In the case of the horse, a testis-expressed gene, XKR3Y, spans the PAB with parts located in both Y and the X-Y PAR. For the donkey, the XKR3Y is Y-specific.
  • DXZ4 also showed a similarity in both animals with an ~8kb monomer, but with twice as many copies in the donkey than in the horse.

Contribution to Equid Biology and Evolution Research

  • The data and insights generated from this study contribute to molecular studies on equid biology, and further research into X-linked conditions, sex chromosome regulation, and evolution in equids.

Cite This Article

APA
Jevit MJ, Castaneda C, Paria N, Das PJ, Miller D, Antczak DF, Kalbfleisch TS, Davis BW, Raudsepp T. (2023). Trio-binning of a hinny refines the comparative organization of the horse and donkey X chromosomes and reveals novel species-specific features. Sci Rep, 13(1), 20180. https://doi.org/10.1038/s41598-023-47583-x

Publication

Scientific reports
ISSN: 2045-2322
NlmUniqueID: 101563288
Country: England
Language: English
Volume: 13
Issue: 1
Pages: 20180
PII: 20180

Researcher Affiliations

Jevit, Matthew J
  • School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA.
Castaneda, Caitlin
  • School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA.
Paria, Nandina
  • Texas Scottish Rite Hospital for Children, Dallas, TX, 75219, USA.
Das, Pranab J
  • ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India.
Miller, Donald
  • Baker Institute for Animal Health, Cornell University, Ithaca, NY, 14853, USA.
Antczak, Douglas F
  • Baker Institute for Animal Health, Cornell University, Ithaca, NY, 14853, USA.
Kalbfleisch, Theodore S
  • Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY, 40546, USA.
Davis, Brian W
  • School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA. bdavis@cvm.tamu.edu.
Raudsepp, Terje
  • School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA. traudsepp@cvm.tamu.edu.

MeSH Terms

  • Male
  • Horses / genetics
  • Animals
  • Equidae / genetics
  • X Chromosome / genetics
  • Sex Chromosomes
  • Genome

Conflict of Interest Statement

The authors declare no competing interests.

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