Fig. 6: Evolutionary characteristics of orphan genes in Theaceae.

A Protein sequence, exon number, and GC content distributions for orphan genes and TFs in CSS ‘Shuchazao’, CSA ‘Yunkang10’, C. DASZ, C. chekiangoleosa, and S. sinensis at different evolutionary nodes. Gray bars represent TFs identified in various Theaceae plants, while other colors indicate orphan genes at different nodes. B Gene family dynamics of orphan genes and TFs in 13 Theaceae plants. The left side represents gene family dynamics in orphan genes, while the right side shows TFs. The numbers in the box indicate the count of gene families, with “+” for gains, “-” for losses, and “N” for nodes in the evolutionary tree. C Ka/Ks values comparison in orthologous gene pairs between orphan genes and TFs at different nodes, namely N-11 (ancestor node of Theaceae), N-10 (ancestor node of the Camellia genus), and N-6 (ancestor node of cultivated tea). D TAI (Transcriptome Aage Index) profiles. A high TAI value indicates that the sample expresses a high number of evolutionarily young genes. E Orphan gene duplication types: The left side shows the phylogenetic relationships of 13 Theaceae plants. Above the horizontal line, the number of gene duplications (GDs) in orphan genes at ancestral nodes is indicated. The “+” symbol denotes gene families that have been gained, while the “-” symbol represents those that have been lost in orphan genes. The bar chart on the right side displays the number of orphan gene duplications and other types of orphan genes at different nodes. Blue represents the number of orphan gene duplications, while orange indicates other types of orphan genes. The pie chart demonstrates the proportion of orphan genes in different duplication types: yellow for tandem duplication, gray for syntenic duplication, and green for other duplication types. “N” denotes nodes, and “Tips” indicates gene duplications occurring during the formation of the 13 Theaceae plants. Species abbreviations: SCZ: Camellia sinensis var. sinensis ‘Shuchazao’, LJ: Camellia sinensis var. sinensis ‘Longjing’, TGY: Camellia sinensis var. sinensis ‘Tieguanyin’, HD: Camellia sinensis var. sinensis ‘Huangdan’, DY: Camellia sinensis var. sinensis ‘Duyun’, BY: Camellia sinensis var. sinensis ‘Biyun’, YH9: Camellia sinensis var. assamica ‘Yinghong9’, YK10: Camellia sinensis var. assamica ‘Yunkang10’, DASZ: Camellia DASZ, CLA: Camellia lanceoleosa, CON: Camellia oleifera var. Nanyongensis, CCH: Camellia chekiangoleosa, ZJ: Stewartia sinensis.