Pangenome-wide characterization of the TCP gene family and its potential role in regulating adventitious shoot regeneration in apple

Chuanjun Chang , Zushu Xie , Shubiao Zhang , Dantong Shao , Xiaoyan Ma , Lu Tong , Muhammad Mobeen Tahir , Zhanling Lu , Ikhtiyor Namozov , Dong Zhang , Juanjuan Ma , Yanrong Lv
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Abstract

With rapid advancements in sequencing technologies, the genomes of numerous plant species have been deciphered. Among these, apple—a globally important fruit crop—has greatly benefited from such progress, with numerous high-quality genome assemblies providing valuable resources for genomic research and gene family studies. In this study, we analyzed the genomic characteristics of 26 Malus accessions, identified and classified their transcription factor (TF) families, and conducted a comprehensive pangenome-wide investigation of the TCP gene family across these accessions. Our findings revealed a strong positive correlation between genome size and transposable element (TE) content, suggesting TEs play a role in genome expansion. TF profiling showed significant variation in the abundance of certain families among different accessions. Specifically, 932 TCP genes were grouped into three subfamilies (PCF, CIN, and CYC/TB1) with a consistent compositional pattern. Orthologous gene group (OGG) analysis among the 26 Malus accessions revealed that core TCP genes were relatively conserved in gene count and possessed longer gene sequences and coding sequences (CDS). Synteny analyses indicated strong evolutionary conservation, with purifying selection acting on most TCP genes. Functional enrichment analysis highlighted the functional diversity within the TCP gene family. Moreover, transcriptomic analyses during adventitious shoot (AS) regeneration showed that core TCP genes were expressed at higher levels than non-core ones and identified some candidate TCP genes potentially involved in regulating AS formation. This study provides valuable insights into the evolutionary conservation and functional diversity of the TCP gene family, revealing its potential regulatory roles in AS regeneration in apple.
TCP基因家族的全基因组特征及其在调控苹果不定芽再生中的潜在作用
随着测序技术的快速发展,许多植物物种的基因组已经被破译。其中,苹果作为一种全球重要的水果作物,其大量高质量的基因组组装为基因组研究和基因家族研究提供了宝贵的资源。本研究分析了26份苹果材料的基因组特征,对其转录因子(TF)家族进行了鉴定和分类,并对这些材料的TCP基因家族进行了全基因组范围的研究。我们的研究结果表明,基因组大小与转座因子(TE)含量呈正相关,表明TE在基因组扩增中起作用。TF谱分析显示,不同种质间某些家族的丰度存在显著差异。具体而言,932个TCP基因被分为三个亚家族(PCF, CIN和CYC/TB1),其组成模式一致。同源基因群(OGG)分析表明,核心TCP基因在基因数量上相对保守,且具有较长的基因序列和编码序列(CDS)。Synteny分析显示了强烈的进化保守性,纯化选择作用于大多数TCP基因。功能富集分析强调了TCP基因家族的功能多样性。此外,转录组学分析表明,核心TCP基因的表达水平高于非核心基因,并确定了一些可能参与调控AS形成的候选TCP基因。该研究为TCP基因家族的进化保护和功能多样性提供了有价值的见解,揭示了其在苹果AS再生中的潜在调控作用。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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