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Home / Equine Research Bank / BMC Genomics / Genome collinearity analysis illuminates the evolution of do...
BMC genomics2021; 22(1); 665; doi: 10.1186/s12864-021-07984-6

Genome collinearity analysis illuminates the evolution of donkey chromosome 1 and horse chromosome 5 in perissodactyls: A comparative study.

Abstract: It is important to resolve the evolutionary history of species genomes as it has affected both genome organization and chromosomal architecture. The rapid innovation in sequencing technologies and the improvement in assembly algorithms have enabled the creation of highly contiguous genomes. DNA Zoo, a global organization dedicated to animal conservation, offers more than 150 chromosome-length genome assemblies. This database has great potential in the comparative genomics field. Results: Using the donkey (Equus asinus asinus, EAS) genome provided by DNA Zoo as an example, the scaffold N50 length and Benchmarking Universal Single-Copy Ortholog score reached 95.5 Mb and 91.6%, respectively. We identified the cytogenetic nomenclature, corrected the direction of the chromosome-length sequence of the donkey genome, analyzed the genome-wide chromosomal rearrangements between the donkey and horse, and illustrated the evolution of the donkey chromosome 1 and horse chromosome 5 in perissodactyls. Conclusions: The donkey genome provided by DNA Zoo has relatively good continuity and integrity. Sequence-based comparative genomic analyses are useful for chromosome evolution research. Several previously published chromosome painting results can be used to identify the cytogenetic nomenclature and correct the direction of the chromosome-length sequence of new assemblies. Compared with the horse genome, the donkey chromosomes 1, 4, 20, and X have several obvious inversions, consistent with the results of previous studies. A 4.8 Mb inverted structure was first discovered in the donkey chromosome 25 and plains zebra chromosome 11. We speculate that the inverted structure and the tandem fusion of horse chromosome 31 and 4 are common features of non-caballine equids, which supports the correctness of the existing Equus phylogeny to an extent.
© 2021. The Author(s).
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Publication Date: 2021-09-15 PubMed ID: 34521340PubMed Central: PMC8442440DOI: 10.1186/s12864-021-07984-6Google Scholar: Lookup
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  • Journal Article

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 explores the genome structure of donkeys and horses, particularly focusing on their chromosomes, for the purpose of investigative comparative genomics and a deeper understanding of their evolutionary histories.

Overview of the Research

  • The researchers utilized the donkey genome from a database curated by DNA Zoo, an organization dedicated to animal conservation. This source offers over 150 chromosome-length genome assemblies, making it an excellent tool for comparative genomics research. The donkey genome taken from the database demonstrated impressively high continuity and integrity.
  • Using this immaculate genome as an example, they assessed the Benchmarking Universal Single-Copy Ortholog (BUSCO) score and the scaffold N50 length, arriving at figures of 91.6% and 95.5 Mb respectively.

Investigation and Results

  • The research team looked into cytogenetic nomenclature, or named parts of a chromosome, for identifying and fixing the direction of the chromosome-length sequence of the donkey genome.
  • Although the primary focus was the donkey genome, they also accounted for the horse genome and made an effort to identify and analyze the chromosomal rearrangements that occurred between donkeys and horses on a cellular level.
  • As a part of this comparative genomics study, the researchers successfully outlined the evolution of donkey chromosome 1 and horse chromosome 5 in their respective species.

Key Discoveries and Conclusions

  • Compared to horses, donkeys had noticeable inversions in chromosomes 1, 4, 20, and X. This finding was aligned with what other studies had also revealed.
  • The researchers discovered a 4.8Mb inverted structure in donkey chromosome 25 and plains zebra chromosome 11, which had not been previously exposed.
  • In accordance with the findings from this paper, the scientists theorized that the inverted structure and tandem fusion on horse chromosome 31 and 4 are common properties of non-caballine equids, or donkey-like animals. This finding indirectly supports the correctness of the existing phylogeny of the genus Equus.

Cite This Article

APA
Li S, Zhao G, Han H, Li Y, Li J, Wang J, Cao G, Li X. (2021). Genome collinearity analysis illuminates the evolution of donkey chromosome 1 and horse chromosome 5 in perissodactyls: A comparative study. BMC Genomics, 22(1), 665. https://doi.org/10.1186/s12864-021-07984-6

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 22
Issue: 1
Pages: 665
PII: 665

Researcher Affiliations

Li, Shaohua
  • Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
  • College of Basic Medicine, Inner Mongolia Medical University, Hohhot, 010110, China.
  • Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot, 011517, China.
Zhao, Gaoping
  • Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot, 011517, China.
Han, Hongmei
  • Department of Physical Education, Hohhot Minzu College, Hohhot, 010051, China.
Li, Yunxia
  • Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
  • Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot, 011517, China.
Li, Jun
  • Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot, 011517, China.
Wang, Jinfeng
  • College of Basic Medicine, Inner Mongolia Medical University, Hohhot, 010110, China.
Cao, Guifang
  • College of Veterinary Science, Inner Mongolia Agricultural University, Hohhot, 010018, China.
Li, Xihe
  • Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China. lixh@imu.edu.cn.
  • Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot, 011517, China. lixh@imu.edu.cn.

MeSH Terms

  • Animals
  • Chromosomes / genetics
  • Chromosomes, Human, Pair 1
  • Chromosomes, Human, Pair 5
  • Equidae / genetics
  • Genome
  • Horses / genetics
  • Humans

Conflict of Interest Statement

All authors have no conflict of interest to declare.

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Citations

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