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PloS one2023; 18(6); e0286861; doi: 10.1371/journal.pone.0286861

Ancient segmentally duplicated LCORL retrocopies in equids.

Abstract: LINE-1 is an active transposable element encoding proteins capable of inserting host gene retrocopies, resulting in retro-copy number variants (retroCNVs) between individuals. Here, we performed retroCNV discovery using 86 equids and identified 437 retrocopy insertions. Only 5 retroCNVs were shared between horses and other equids, indicating that the majority of retroCNVs inserted after the species diverged. A large number (17-35 copies) of segmentally duplicated Ligand Dependent Nuclear Receptor Corepressor Like (LCORL) retrocopies were present in all equids but absent from other extant perissodactyls. The majority of LCORL transcripts in horses and donkeys originate from the retrocopies. The initial LCORL retrotransposition occurred 18 million years ago (17-19 95% CI), which is coincident with the increase in body size, reduction in digit number, and changes in dentition that characterized equid evolution. Evolutionary conservation of the LCORL retrocopy segmental amplification in the Equidae family, high expression levels and the ancient timeline for LCORL retrotransposition support a functional role for this structural variant.
Copyright: © 2023 Batcher et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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Publication Date: 2023-06-08 PubMed ID: 37289743PubMed Central: PMC10249811DOI: 10.1371/journal.pone.0286861Google 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 article focuses on investigating an ancient gene duplication event in horses and related species, known as equids, and its effects on the evolution of these species. The researchers found the gene duplication of LCORL retrocopies plays a prominent role in equids’ evolution, potentially affecting their size, digit number, and dentition.

Transcription of LINE-1 and Retrocopy Variants

  • The research investigates a transposable element known as LINE-1, a part of the genome that can alter its position in the DNA sequence. LINE-1 has the ability to encode proteins that can insert host gene duplicates, known as retrocopies, into the genome.
  • Variations in the number of these retrocopies, or retroCNVs, can occur between different individuals of a species.
  • The study included 86 equids and through this, they identified 437 retrocopy insertions.

Diversity of RetroCNVs Among Equids

  • The research showed that only 5 of these retroCNVs were shared between horses and other equids. This indicates that most retroCNVs were inserted into the genome after the different equid species diverged from a common ancestor.
  • A significant number of these retrocopies were segmented duplications of a specific gene known as Ligand Dependent Nuclear Receptor Corepressor Like (LCORL).
  • These LCORL retrocopies were found in all equids but were absent in other closely related perissodactyl species.

The Role of LCORL Retrocopies in Equid Evolution

  • The majority of LCORL transcripts, the intermediate products between the DNA sequence of a gene and the protein it codes for, originate from these retrocopies in both horses and donkeys.
  • The researchers determined that the initial event where LCORL was retrotransposed (copied and inserted into another part of the genome) occurred approximately 18 million years ago.
  • This timing correlates with significant changes in the evolutionary history of equids, including an increase in body size, a reduction in the number of digits, and changes in teeth structure. These changes imply that the LCORL retrocopies may have had a significant effect on equid evolution.

Functional Role of LCORL Retrocopies

  • The conservation of the LCORL retrocopy through time, its high expression levels, and the ancient timeline of the LCORL segmental amplification in the Equidae family suggest that these structures have a functional role.
  • While the precise functionality wasn’t specified, it is implied that the structural variants may be instrumental for the functioning or development of some traits in these species.

Cite This Article

APA
Batcher K, Varney S, Raudsepp T, Jevit M, Dickinson P, Jagannathan V, Leeb T, Bannasch D. (2023). Ancient segmentally duplicated LCORL retrocopies in equids. PLoS One, 18(6), e0286861. https://doi.org/10.1371/journal.pone.0286861

Publication

PloS one
ISSN: 1932-6203
NlmUniqueID: 101285081
Country: United States
Language: English
Volume: 18
Issue: 6
Pages: e0286861
PII: e0286861

Researcher Affiliations

Batcher, Kevin
  • Department of Population Health and Reproduction, University of California Davis, Davis, CA, United States of America.
Varney, Scarlett
  • Department of Population Health and Reproduction, University of California Davis, Davis, CA, United States of America.
Raudsepp, Terje
  • Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America.
Jevit, Matthew
  • Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America.
Dickinson, Peter
  • Department of Surgical and Radiological Sciences, University of California Davis, Davis, CA, United States of America.
Jagannathan, Vidhya
  • Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
Leeb, Tosso
  • Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
Bannasch, Danika
  • Department of Population Health and Reproduction, University of California Davis, Davis, CA, United States of America.

MeSH Terms

  • Animals
  • Horses / genetics
  • Long Interspersed Nucleotide Elements
  • Equidae / genetics
  • DNA Transposable Elements
  • Proteins

Conflict of Interest Statement

The authors have declared that no competing interests exist.

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Citations

This article has been cited 5 times.
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