Genome-Wide Identification and Comparative Analysis of the TGA Gene Family in Theaceae Reveals Evolutionary Conservation and Lineage-Specific Expression Divergence

Authors:
Preprint
Publisher website
Google Scholar
Abstract
TGA (TGACG motif-binding factor) proteins are plant-specific group D basic leucine zipper (bZIP) transcription factors that bind as-1/TGACG elements. They integrate jasmonic acid (JA) and salicylic acid (SA) signaling with growth, development and stress responses. Tea (Camellia sinensis) and oil tea (Camellia oleifera) are Theaceae crops grown for beverages and edible oil, and anthracnose, drought and chilling reduce their yield and quality. TGA genes had not been characterized in either crop. We therefore identified TGA genes ge-nome-wide in six representative Theaceae species: Camellia chekiangoleosa, C. oleifera, C. sinensis, Camellia crapnelliana, Camellia japonica and Stewartia sinensis. We then examined their phylogeny, gene structure and conserved motifs, codon usage, duplication and col-linearity, and promoter cis-elements. Transcriptome data and qRT-PCR provided expres-sion evidence for C. oleifera TGA (ColeTGA) genes after inoculation with Colletotrichum fruc-ticola. The survey yielded 68 non-redundant TGA genes, 10 to 13 per species, each with in-tact bZIP and DOG1 domains and a predicted nuclear localization. Phylogenetic analysis resolved five groups, and Theaceae members clustered mainly in Groups II and IV, where motif composition and exon–intron structure were conserved. Codon usage bias was weak (effective number of codons 52–54; codon adaptation index 0.77–0.80). The mean Ka/Ks was 0.25, indicating purifying selection. Whole-genome and segmental duplication drove most family expansion (60–91.67%), while tandem duplication was rare. Promoters were enriched in cis-elements responsive to light, JA, SA and abscisic acid (ABA). Expres-sion varied among tissues, and several genes were enriched in fruit and leaves. Salt, drought and cold each induced subsets of TGA genes. After inoculation with C. fructicola, the 12 ColeTGA genes showed four expression patterns. ColeTGA2, ColeTGA3, ColeTGA4, ColeTGA6, ColeTGA10 and ColeTGA12 were strongly activated. Together, these compari-sons clarify how TGA genes have been conserved and how they diverged among Theaceae lineages. They also identify candidates for functional tests of anthracnose resistance and for stress-tolerance breeding in tea and oil tea.

This publication has 57 references indexed in Scilit: