Fig. 1: Phylogenetic analysis and transposable element dynamics in tea plant genomes.

a Phylogenetic analysis of 22 tea plant genomes using kiwifruit (ACH) as an outgroup, with a heatmap showing presence/absence of genes in pan-gene families. The genomes cluster into four clades: wild relative CT and cultivated groups (CSA, CSS, CSP). ACH Actinidia chinensis Planch. b LTR content proportions in the genomes assembled in this study, with Gypsy families (44.3%) predominating over Copia (9.6%). c Insertion time distribution of full-length Copia and Gypsy LTRs across the 22 genomes. Each line represents an individual genome from (a), with Gypsy elements shown in blue and Copia in purple. d The expression levels of genes with LTR insertions (n = 1746) versus genes without LTR insertions in their promoters (n = 42,922) across various tissues of C. sinensis cv. Zhongcha102. Box plots show the median (center line), first and third quartiles (box bounds), and whiskers extending to 1.5× the interquartile range, with individual data points overlaid. Statistical significance was assessed using a two-tailed Student’s t-tests. TPM transcripts per million mapped reads. Source data are provided as a Source Data file.