Niu Yuling, Li Kan, You Xuerong, Wu Yutao, Du Xue, Zhao Ayong, Wang Zhijun
College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China.
Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
Animals (Basel). 2025 Jul 1;15(13):1942. doi: 10.3390/ani15131942.
The objective of this study was to identify the AlkB family genes in poultry using bioinformatics, and to explore their molecular characteristics, evolutionary relationships, and expression patterns to clarify their potential functions in poultry. (1) Methods: The study utilized the NCBI database to obtain chicken genome data, and screened and validated AlkB family members (ALKBH1-5, ALKBH8, and FTO) by hmmsearch and TBtools. MEGA 11.0 was used for phylogenetic analysis, PHYRE2 and I-TASSER predicted protein structures, and the String database was used to construct an interoperability network. Finally, the tissue expression profiles were analyzed by using The Human Protein Atlas online database and qRT-PCR. (2) Results: Phylogenetic analysis revealed distinct avian and mammalian clusters, with chicken AlkB proteins exhibiting low sequence homology but conserved 3D structures compared to mammals. Chromosomal synteny and conserved domains highlighted evolutionary divergence, with ALKBH4 lacking typical AlkB structural motifs. Protein interaction networks linked ALKBH1/2/3/5/8/FTO, underscoring functional coordination in poultry adaptation. Tissue-specific expression showed high AlkB levels in brain tissues, while ALKBH5 dominated in muscle. During differentiation, ALKBH3, ALKBH5, and FTO expression significantly increased during myoblast differentiation. (3) Conclusions: This study identified seven AlkB family genes in poultry, revealing their phylogenetic classification into two subfamilies, conserved structural domains, chromosomal synteny, and tissue-specific expression patterns.
本研究的目的是利用生物信息学方法鉴定家禽中的AlkB家族基因，并探索其分子特征、进化关系和表达模式，以阐明它们在家禽中的潜在功能。(1)方法：本研究利用NCBI数据库获取鸡的基因组数据，并通过hmmsearch和TBtools筛选和验证AlkB家族成员(ALKBH1-5、ALKBH8和FTO)。使用MEGA 11.0进行系统发育分析，PHYRE2和I-TASSER预测蛋白质结构，并使用String数据库构建互作网络。最后，通过在线数据库The Human Protein Atlas和qRT-PCR分析组织表达谱。(2)结果：系统发育分析揭示了明显的鸟类和哺乳动物聚类，与哺乳动物相比，鸡的AlkB蛋白序列同源性较低，但三维结构保守。染色体共线性和保守结构域突出了进化差异，其中ALKBH4缺乏典型的AlkB结构基序。蛋白质相互作用网络将ALKBH1/2/3/5/8/FTO联系起来，强调了家禽适应过程中的功能协调。组织特异性表达显示脑组织中AlkB水平较高，而ALKBH5在肌肉中占主导地位。在分化过程中，成肌细胞分化期间ALKBH3、ALKBH5和FTO的表达显著增加。(3)结论：本研究鉴定了家禽中的7个AlkB家族基因，揭示了它们的系统发育分类为两个亚家族、保守的结构域、染色体共线性和组织特异性表达模式。
