Zhong Qiuwei, Cheng Qiangqiang, Du Xuanjin, Xiao Yao, Guo Chunce, Zhang Lu, Ma Jikai
Jiangxi Provincial Key Laboratory of Subtropical Forest Resources Cultivation, 2011 Co-Innovation Center of Jiangxi Typical Trees Cultivation and Utilization, Jiangxi Agricultural University, Nanchang, 330045, China.
Jiangxi Province Key Laboratory of Vegetable Cultivation and Utilization, Jiangxi Agricultural University, Nanchang, 330045, China.
BMC Genomics. 2025 Apr 29;26(1):423. doi: 10.1186/s12864-025-11628-4.
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.
香椿（Toona fargesii A. Chev.）是一种具有木材和药用价值的珍贵树种，属于楝科香椿属。由于包括干旱问题在内的各种因素，它在中国是一种濒危物种。KNOXs（类结瘤同源框）是TALE转录因子的一个子集，在包括抗旱性在内的发育和非生物胁迫中起关键作用。最近公布的香椿基因组表明香椿属发生了一次特定的全基因组复制（WGD）事件，这为揭示KNOX基因在香椿中的作用提供了宝贵资源。在此，我们进行了全基因组分析，包括KNOX基因的鉴定、共线性和复制，以揭示它们的特征和进化。此外，还研究了基因结构、蛋白质-蛋白质相互作用（PPI）、亚细胞定位和表达模式，以验证KNOX基因在香椿干旱响应和发育方面的作用。一般来说，共鉴定出21个推定的TfKNAT（KNAT的直系同源物）基因，并分为三个亚家族。有趣的是，大多数TfKNAT基因在另一条染色体上有一个旁系同源物，在染色体区域分配、序列、结构、顺式元件、亚细胞定位和表达模式上表现出高度共线性和相似性。它们大约在420万至840万年前（MYA）发生分化，接近特定的WGD（221 ~ 501 MYA），这可能是该家族扩张的主要驱动力。更重要的是，顺式元件包含许多与干旱胁迫密切相关的脱落酸响应元件，特别是三个TfKNAT3/4基因，PPI分析表明TfKNAT3/4可以与干旱相关蛋白相互作用。事实上，随着PEG胁迫时间延长，三个TfKNAT3/4成员的表达先急剧增加然后逐渐下降。此外，脱落酸处理显著诱导了三个TfKNAT3/4基因的表达，也增强了它们对干旱胁迫的参与。总体而言，我们的研究结果突出了TfKNAT家族的重要性以及TfKNAT3/4在香椿抗旱性中的潜在作用。
