Genome-wide identification and integrative analysis of KNOX family characterization, duplication and expression provide insights into PEG-induced drought stress in Toona fargesii

Toona fargesii A. Chev. (T. fargesii), a precious tree with timber and medicinal properties, belongs to the Toona genus of the Meliaceae family. It is an endangered species in China, owing to various issues including the concerns about the drought aspect. KNOXs (knotted-like homeoboxes), a subset of TALE transcription factors, play pivotal roles in development and abiotic stress including drought resistance. The recent publication of the T. fargesii genome, indicating a specific whole-genome duplication (WGD) event in the Toona genus, serves as a valuable resource for uncovering the role of KNOX genes in T. fargesii. Here, genome-wide analysis including identification, synteny and duplication of KNOX genes was conducted to unveil their characterization and evolution. Moreover, gene structures, protein-protein interaction (PPI), subcellular localizations and expression patterns were also examined to verify KNOX genes with respect to drought response and development in T. fargesii. Generally, 21 putative TfKNAT (orthologs of KNAT) genes were identified and classified into three subfamilies. Intriguingly, most of TfKNAT gene possessed a paralog on another chromosome exhibiting high collinearity and similarities in chromosome regional assignments, sequences, structures, cis-elements, subcellular localizations and expression patterns. They diverged approximately 4.2 to 8.4 million years ago (MYA) approaching to the specific WGD (22.1 ~ 50.1 MYA) which may predominantly drive the family expansion. More importantly, the cis-elements contained many ABA-responsive elements strongly associated with drought stress, especially three TfKNAT3/4 genes, and PPI analysis suggested that TfKNAT3/4 could interact with proteins related to the drought. Indeed, the expression of three TfKNAT3/4 members sharply increased and then gradually decreased with prolonged PEG stress duration. Additionally, the ABA treatment significantly induced three TfKNAT3/4 genes expression also strengthened their involvement in the drought stress. Collectively, our findings highlight the significance of the TfKNAT family and the potential role of TfKNAT3/4 in drought resistance of T. fargesii.