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Home / Equine Research Bank / Int J Mol Sci / Genome-Wide Characterization of the HOX Gene Family: Evoluti...
International journal of molecular sciences2025; 27(1); 38; doi: 10.3390/ijms27010038

Genome-Wide Characterization of the HOX Gene Family: Evolution and Expression Patterns in Donkey.

Abstract: The gene family plays an indispensable role in regulating embryonic development, cell differentiation, and morphogenesis. This study employed bioinformatics approaches for systematic analysis, ultimately identifying 33 gene family members from the donkey genome. Physicochemical property analysis revealed that the number of amino acids encoded ranged from 94 to 444, with 31 members classified as alkaline proteins. Their secondary structure was predominantly composed of random coils and alpha helices, and all members were localized to the nucleus. Conserved motif analysis further demonstrated that all donkey HOX family proteins contained highly conserved motifs 1 and 2. Along with three other species, the 33 donkey genes were clustered into eight phylogenetic subgroups. Furthermore, collinearity analysis indicated a high degree of collinearity between the donkey and horse gene families. Gene Ontology analysis confirmed the significant role of the donkey gene family in regulating embryonic development and skeletal system formation. Tissue expression profile analysis revealed significant differences in the expression levels of the 33 genes across 13 different tissues. This study not only systematically identified and characterized the donkey gene family but also provided valuable insights into the genetic regulation mechanisms of key traits in donkey molecular breeding.
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Publication Date: 2025-12-19 PubMed ID: 41515917PubMed Central: PMC12785281DOI: 10.3390/ijms27010038Google 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.

Overview

  • This research systematically identified and analyzed the HOX gene family in donkeys, exploring their evolutionary relationships, structural properties, and expression patterns across different tissues.
  • The study provides insights into the genetic basis of embryonic development and important traits, with implications for donkey breeding programs.

Introduction to the HOX Gene Family

  • The HOX gene family is crucial for regulating embryonic development, guiding cell differentiation, and shaping the morphology of organisms.
  • These genes encode transcription factors that influence the development of body plans by controlling the expression of other genes during early stages of growth.

Identification and Characterization of HOX Genes in Donkey

  • Using bioinformatics techniques, researchers identified 33 HOX genes in the donkey genome.
  • Physicochemical analyses showed that these genes encode proteins ranging from 94 to 444 amino acids in length.
  • Out of the 33, 31 proteins were categorized as alkaline, indicating their basic nature.
  • Secondary structure prediction revealed that these proteins predominantly consist of random coils and alpha helices, typical features that support their function as transcription factors.
  • All HOX proteins were predicted to localize in the nucleus, consistent with their role in gene regulation.

Conserved Motifs and Phylogenetic Analysis

  • Motif analysis found highly conserved motifs 1 and 2 across all donkey HOX proteins, highlighting critical sequence elements important for their function.
  • Phylogenetic clustering grouped the 33 donkey HOX genes into eight distinct subgroups alongside HOX genes from three other species, demonstrating evolutionary relationships and conservation.

Comparative Genomics and Collinearity

  • Comparative collinearity analysis revealed that donkey HOX genes show a high degree of synteny with those of the horse, indicating strong conservation between these closely related species.
  • This suggests that the genetic mechanisms governing developmental processes are preserved within the equid family.

Functional Annotation and Expression Profiling

  • Gene Ontology (GO) analysis confirmed that donkey HOX genes are significantly involved in embryonic development and skeletal system formation, reaffirming their key biological roles.
  • Tissue expression profiling across 13 different tissues showed significant variation in expression levels of the 33 HOX genes, indicating their differential roles depending on tissue type and developmental stage.

Significance and Implications

  • This systematic characterization advances understanding of the HOX gene family in donkeys at the molecular level.
  • The findings offer valuable genetic insights that can aid future donkey breeding programs aimed at improving key traits, particularly those related to development and morphology.
  • Overall, the study contributes foundational knowledge for exploring gene regulation mechanisms in donkeys and related species.

Cite This Article

APA
Liu X, Liu A, Khan MZ, Zhu Q, Zheng Y, Chen W, Cai B, Yan Z, Peng Y, Wang C. (2025). Genome-Wide Characterization of the HOX Gene Family: Evolution and Expression Patterns in Donkey. Int J Mol Sci, 27(1), 38. https://doi.org/10.3390/ijms27010038

Publication

International journal of molecular sciences
ISSN: 1422-0067
NlmUniqueID: 101092791
Country: Switzerland
Language: English
Volume: 27
Issue: 1
PII: 38

Researcher Affiliations

Liu, Xiaotong
  • Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China.
Liu, Anqi
  • Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China.
Khan, Muhammad Zahoor
  • Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China.
Zhu, Qifei
  • Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China.
Zheng, Yunfan
  • Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China.
Chen, Wenting
  • Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China.
Cai, Bingbing
  • Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China.
Yan, Zhiyu
  • Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China.
Peng, Yongdong
  • Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China.
Wang, Changfa
  • Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China.

MeSH Terms

  • Animals
  • Equidae / genetics
  • Phylogeny
  • Evolution, Molecular
  • Multigene Family
  • Homeodomain Proteins / genetics
  • Homeodomain Proteins / chemistry
  • Homeodomain Proteins / metabolism
  • Genes, Homeobox
  • Genome
  • Gene Expression Profiling
  • Gene Expression Regulation, Developmental

Grant Funding

  • GDWZ202401 / Liaocheng Municipal Bureau of Science and Technology, High-talented Foreign Expert Introduction Program
  • SDAIT-27 / The Shandong Province Modern Agricultural Technology System Donkey Industrial Innovation Team
  • 19211162 / Livestock and Poultry Breeding Industry Project of the Ministry of Agriculture and Rural Affairs
  • 31671287 / The National Natural Science Foundation of China
  • 319312101-14 / The Open Project of Liaocheng University Animal Husbandry Discipline
  • 3193308 / The Open Project of Shandong Collaborative Innovation Center for Donkey Industry Technology
  • K20LC0901 / Research on Donkey Pregnancy Improvement
  • 318052025 / Liaocheng University scientific research fund
  • 2025LZGC033 / Key R&D Program of Shandong Province，China

Conflict of Interest Statement

The authors declare no conflicts of interest.

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