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

Sep 30, 2026

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The HOX gene family orchestrates embryonic development, cell differentiation, and morphogenesis. Using bioinformatics analyses, this study identified 33 HOX genes in the donkey genome. Protein physicochemical characterization showed amino-acid lengths from 94 to 444, with 31 alkaline members, and secondary structures dominated by random coils and alpha helices, with all proteins localized to the nucleus. Conserved motif 1 and 2 were detected across all proteins. Phylogenetic clustering grouped the 33 genes into eight subgroups, while collinearity analyses revealed strong conservation between donkey and horse HOX families. Gene Ontology and tissue expression profiling confirmed roles in embryonic development and skeletal formation, with differential expression across 13 tissues, supporting insights for donkey molecular breeding.

LanguageEnglish

CategoryResearch & Report

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Pages18

Reading Time45 min

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Abstract

1. Introduction

Homeobox and HOX gene organization

HOX genes in vertebral patterning

Article Genome-Wide Characterization of the HOX Gene Family: Evolution and Expression Patterns in Donkey Xiaotong Liu , Anqi Liu, Muhammad Zahoor Khan , Qifei Zhu , Yunfan Zheng, Wenting Chen, Bingbing Cai, Zhiyu Yan , Yongdong Peng * and Changfa Wang * Academic Editor: Jarosław Króliczewski Received: 22 October 2025 Revised: 16 December 2025 Accepted: 17 December 2025 Published: 19 December 2025 Copyright: © 2025 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license. Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, China; [zahoorkhan@lcu.edu.cn](zahoorkhan@lcu.edu.cn) (M.Z.K.) * [Correspondence: pengyongdong@lcu.edu.cn](Correspondence: pengyongdong@lcu.edu.cn) (Y.P.); [wangchangfa@lcu.edu.cn](wangchangfa@lcu.edu.cn) (C.W.) Abstract The HOX 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 HOX 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 HOX genes were clustered into eight phylogenetic subgroups. Furthermore, collinearity analysis indicated a high degree of collinearity between the donkey and horse HOX gene families. Gene Ontology analysis confirmed the significant role of the donkey HOX gene family in regulating embryonic development and skeletal system formation. Tissue expression profile analysis revealed significant differences in the expression levels of the 33 HOX genes across 13 different tissues. This study not only systematically identified and characterized the donkey HOX gene family but also provided valuable insights into the genetic regulation mechanisms of key traits in donkey molecular breeding. Keywords: HOXs; donkey; structure; chromosome mapping; phylogenetic analysis 1. Introduction Homeobox genes are a class of core regulatory genes that are widely distributed across various organisms and encode transcription factors. These genes primarily regulate the expression of downstream target genes through the proteins they produce. Their products play crucial roles in processes such as embryonic development, cell differentiation, and morphogenesis by controlling the spatiotemporal expression of these target genes [1,2] . The HOX gene family is characterized by several distinctive features, including high conservation, clustered organization, and spatiotemporal collinearity. High conservation is exemplified by a shared 180 bp highly conserved DNA sequence (the homeobox) that encodes a protein domain known as the homeodomain, which consists of 60 amino acids [3,4] . The HOX family is extensive and diverse, typically organized into four distinct clusters—HOXA, HOXB, HOXC, and HOXD—each located on different chromosomes. Additionally, HOX gene clusters exhibit a high degree of organizational coherence, with all genes transcribed from the same DNA strand [3,5] . HOX expression demonstrates collinearity, meaning that genes within the cluster activate sequentially along the 3′→5′ direction of the chromosome. The expression regions of HOX genes are strictly partitioned along the anterior–posterior axis of the embryo: genes located at the 3′ -end are expressed in the anterior region, while those at the 5′ -end are expressed in the poster

FAQs

How many HOX gene family members were identified in the donkey genome?

A total of 33 HOX gene family members were identified from the donkey genome.

What do the physicochemical and structural analyses indicate about donkey HOX proteins?

Donkey HOX proteins encode amino acids ranging from 94 to 444, with 31 classified as alkaline proteins. Their secondary structures are mainly random coils and alpha helices, and all members are localized to the nucleus.

How were the donkey HOX genes organized in phylogenetic and collinearity analyses?

Phylogenetic analysis clustered the 33 donkey HOX genes into eight subgroups. Collinearity analysis showed a high degree of collinearity between donkey and horse HOX gene families.

Sep 30, 2026

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