ArticleBMC plant biology2026
Evolution of the TCP gene family and pan-genome analysis in tea (Camellia sinensis).
Article in BMC plant biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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1 citing paper in PubMed.
- Evolutionary and pan-genomic analysis of theFrontiers in plant science · 2026Article
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6 authors.
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Abstract
TCP transcription factors are key regulators of plant architecture and development, yet their evolution is often inferred from a single reference genome. Using a dataset of 1,015 plant genomes, we observed a pronounced clade-level gradient in TCP copy number, including complete absence in algae and expanded repertoires in angiosperms, with retention after WGD/segmental duplication emerging as a major contributor. We then leveraged a tea pangenome of nine Camellia genomes (three wild species and six cultivated Camellia sinensis varieties) to resolve pangenome-scale TCP dynamics. A total of 292 TCP genes were identified and grouped into three lineages (PCF, CIN and CYC/TB1). Cultivated accessions in this sampled panel harbored fewer annotated TCP genes than the sampled wild relatives, with an average reduction of approximately 27%. Orthogroup analysis revealed a compact core (4 orthogroups; 57 genes, 19.5%) and a large dispensable component (25 orthogroups; 235 genes, 80.5%) that showed extensive copy-number variation and lineage-specific loss/expansion; core enrichment was strongest in CYC/TB1, whereas PCF was biased toward dispensable genes. Tea TCP expansion was mainly attributed to WGD/segmental duplication (60.3%) and dispersed duplication (26.7%). Most homologous pairs evolved under purifying selection, but dispensable pairs exhibited higher Ka/Ks than core pairs, consistent with relaxed constraint. Pan-transcriptome comparisons across eight tissues showed generally higher TCP expression in cultivated materials, particularly in apical bud and stem/fruit-related tissues. Together, these results establish a pangenome-informed TCP resource and suggest that dosage remodeling and structural variation may have contributed to lineage diversification in tea and provide candidates for future studies of domestication-related evolution.
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