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<p><i>Parus major</i> presents profuse physiological and ecological adaptations, serving as a living model for delving into evolutionary processes. We characterized the TGF-beta gene superfamily in <i>P. major</i> at the genome-wide level, revealing a total of 22 homologs in this gene family. TGF-beta homologs depicted fundamental physicochemical properties, excluding BMP1, BMP6, BMP10, INHA, and GDF2. Phylogenetic analysis separated the homologs of the TGF-beta gene superfamily and those of other vertebrate species into two primary clades (TGF-beta and BMP). Except for the Nodal modulator, all TGF-beta homologs’ gene structures showed homogeneity in the domain and motif composition analysis. The TGF-beta propeptide domain and TGF-beta have been identified in all the homologs of TGF-beta genes. Comparative study of gene structures revealed that gene duplications gave rise to the TGF-beta gene superfamily. Eight duplicate gene pairs were identified, out of which the BMP6-BMP7 pair showed segmental duplication. For each pair of genes, the Ka/Ks test ratio results showed that none of the ratios exceeded 1, which means these proteins are subject to purifying selection. Based on Circos analysis, the TGF-beta gene superfamily homologs were segmentally distributed in the genome and organized in scattered clusters. This work provides a molecular foundation for the functional examination of TGF-beta ligand proteins, might be a useful tool for comprehensive phylogenomic studies, and could inspire the development of new strategies to comprehend evolutionary mechanisms.</p>

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Genomic and molecular characterization of TGF-beta superfamily in Parus major

  • 期刊论文

  • 发表日期：

    2025年9月30日

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  • Mehwish Sultana,
  • Shakeela Parveen,
  • Muhammad Farhan Khan,
  • Muhammad Tayyab,
  • Muhammad Hussain,
  • Saman Shabir,
  • Warda Safdar,
  • Laiba Shafique

摘要

Parus major presents profuse physiological and ecological adaptations, serving as a living model for delving into evolutionary processes. We characterized the TGF-beta gene superfamily in P. major at the genome-wide level, revealing a total of 22 homologs in this gene family. TGF-beta homologs depicted fundamental physicochemical properties, excluding BMP1, BMP6, BMP10, INHA, and GDF2. Phylogenetic analysis separated the homologs of the TGF-beta gene superfamily and those of other vertebrate species into two primary clades (TGF-beta and BMP). Except for the Nodal modulator, all TGF-beta homologs’ gene structures showed homogeneity in the domain and motif composition analysis. The TGF-beta propeptide domain and TGF-beta have been identified in all the homologs of TGF-beta genes. Comparative study of gene structures revealed that gene duplications gave rise to the TGF-beta gene superfamily. Eight duplicate gene pairs were identified, out of which the BMP6-BMP7 pair showed segmental duplication. For each pair of genes, the Ka/Ks test ratio results showed that none of the ratios exceeded 1, which means these proteins are subject to purifying selection. Based on Circos analysis, the TGF-beta gene superfamily homologs were segmentally distributed in the genome and organized in scattered clusters. This work provides a molecular foundation for the functional examination of TGF-beta ligand proteins, might be a useful tool for comprehensive phylogenomic studies, and could inspire the development of new strategies to comprehend evolutionary mechanisms.