Table1_Genome-Wide Identification and Comparative Analysis of WOX Genes in Four Euphorbiaceae Species and Their Expression Patterns in Jatropha curcas.DOCX

The WUSCHEL-related homeobox (WOX) proteins are widely distributed in plants and play important regulatory roles in growth and development processes such as embryonic development and organ development. Here, series of bioinformatics methods were utilized to unravel the structural basis and genetic hierarchy of WOX genes, followed by regulation of the WOX genes in four Euphorbiaceae species. A genome-wide survey identified 59 WOX genes in Hevea brasiliensis (H. brasiliensis: 20 genes), Jatropha curcas (J. curcas: 10 genes), Manihot esculenta (M. esculenta: 18 genes), and Ricinus communis (R. communis: 11 genes). The phylogenetic analysis revealed that these WOX members could be clustered into three close proximal clades, such as namely ancient, intermediate and modern/WUS clades. In addition, gene structures and conserved motif analyses further validated that the WOX genes were conserved within each phylogenetic clade. These results suggested the relationships among WOX members in the four Euphorbiaceae species. We found that WOX genes in H. brasiliensis and M. esculenta exhibit close genetic relationship with J. curcas and R. communis. Additionally, the presence of various cis-acting regulatory elements in the promoter of J. curcas WOX genes (JcWOXs) reflected distinct functions. These speculations were further validated with the differential expression profiles of various JcWOXs in seeds, reflecting the importance of two JcWOX genes (JcWOX6 and JcWOX13) during plant growth and development. Our quantitative real-time PCR (qRT-PCR) analysis demonstrated that the JcWOX11 gene plays an indispensable role in regulating plant callus. Taken together, the present study reports the comprehensive characteristics and relationships of WOX genes in four Euphorbiaceae species, providing new insights into their characterization.WUSCHEL相关同源盒（WUSCHEL-related homeobox, WOX）蛋白广泛分布于植物中，在胚胎发育、器官发育等生长发育进程中发挥重要调控功能。本研究采用一系列生物信息学方法，解析了WOX基因的结构基础与遗传层级，并对4种大戟科植物的WOX基因调控模式进行了探究。通过全基因组范围的鉴定，共在巴西橡胶树（Hevea brasiliensis，简称H. brasiliensis，含20个WOX基因）、麻疯树（Jatropha curcas，简称J. curcas，含10个WOX基因）、木薯（Manihot esculenta，简称M. esculenta，含18个WOX基因）以及蓖麻（Ricinus communis，简称R. communis，含11个WOX基因）中得到59个WOX基因。系统发育分析显示，这些WOX家族成员可划分为3个紧密相关的进化枝，分别为古老进化枝、中间进化枝以及现代/WUS进化枝。此外，基因结构与保守基序分析进一步验证了各系统发育进化枝内的WOX基因具有保守性。上述结果阐明了4种大戟科植物中WOX家族成员的进化关系。研究发现，巴西橡胶树与木薯的WOX基因与麻疯树、蓖麻的WOX基因具有较近的遗传亲缘关系。此外，麻疯树WOX基因（JcWOXs）启动子区域存在多种顺式作用调控元件，提示其功能具有多样性。麻疯树各JcWOX基因在种子中的差异表达谱进一步验证了上述推测，同时揭示了2个JcWOX基因（JcWOX6与JcWOX13）在植物生长发育过程中的重要作用。实时荧光定量PCR（quantitative real-time PCR, qRT-PCR）分析结果显示，JcWOX11基因在调控植物愈伤组织形成过程中发挥不可或缺的作用。综上，本研究全面解析了4种大戟科植物WOX基因的特征及其相互关系，为该家族基因的功能鉴定提供了新的研究思路。