Li Juanjuan, Zhang Yue
Hubei Province Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Hubei Key Laboratory of Resource Utilization and Quality Control of Characteristic Crops, College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China.
Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
Plants (Basel). 2025 Jun 21;14(13):1909. doi: 10.3390/plants14131909.
The yellow flower lotus () is the sister species of the sacred lotus (). The evolution of gene expression patterns across multiple tissues during the species divergence of these two lotuses remains unexplored. The WUSCHEL-related homeobox () family, a plant-specific transcription factor family, plays a crucial role in tissue development and stress responses. In this study, utilizing a chromosome-level reference genome and a transcriptome database covering multiple tissues, we identified and categorized 11 genes into three subfamilies. We identified seven syntenic gene pairs between s and s that originated from whole-genome duplications. Through conserved motif analysis, we found subfamily-specific motifs in the protein sequences of s and s. Variations in the three-dimensional conformations of homologous genes indicate function divergences between the two lotus species. The gene expression matrix of across tissues reveals expression divergences within and between the two lotus species. By employing a weight gene co-expression network analysis pipeline, we developed eight co-expression networks that differed from the co-expression networks of their syntenic genes. Overall, our findings suggest that genomic variations in the orthologs contribute to the distinct expression patterns and regulatory networks observed during the evolution of these two lotuses.
黄花莲（）是神圣莲（）的姊妹物种。在这两种莲花物种分化过程中，多个组织中基因表达模式的演变仍未得到探索。WUSCHEL相关同源框（）家族是植物特有的转录因子家族，在组织发育和应激反应中起关键作用。在本研究中，利用染色体水平的参考基因组和涵盖多个组织的转录组数据库，我们鉴定并将11个基因分类为三个亚家族。我们在s和s之间鉴定出七对同源基因对，它们起源于全基因组复制。通过保守基序分析，我们在s和s的蛋白质序列中发现了亚家族特异性基序。同源基因的三维构象变化表明这两种莲花物种之间存在功能差异。跨组织的基因表达矩阵揭示了两种莲花物种内部和之间的表达差异。通过采用加权基因共表达网络分析流程，我们构建了八个与它们的同源基因共表达网络不同的共表达网络。总体而言，我们的研究结果表明，直系同源基因中的基因组变异导致了这两种莲花进化过程中观察到的不同表达模式和调控网络。
