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

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. • Genome size is highly positively correlated with transposable element content across 26 Malus accessions. • Transcription factor families profiling across different apple accessions reveals significant variation in the abundance of specific families, such as TCP and GRAS. • The TCP gene family exhibits a high degree of synteny and is predominantly subject to strong purifying selection among 26 Malus accessions. • Core TCP genes exhibit relative conservation in member count and show long lengths of both gene and coding sequences among 26 Malus accessions. • Transcriptomic analyses identify several candidate TCP genes potentially involved in enhancing adventitious shoot regeneration capacity in apple.