Tao Peng, Guo Weiling, Li Biyuan, Wang Wuhong, Yue Zhichen, Lei Juanli, Zhao Yanting, Zhong Xinmin
Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
Zhejiang University of Media and Communications, Hangzhou, 310018, China.
Mol Genet Genomics. 2016 Jun;291(3):1167-80. doi: 10.1007/s00438-016-1174-3. Epub 2016 Feb 2.
NADP-dependent malic enzymes (NADP-MEs) play essential roles in both normal development and stress responses in plants. Here, genome-wide analysis was performed to identify 65 putative NADP-ME genes from 12 crucifer species. These NADP-ME genes were grouped into five categories of syntenic orthologous genes and were divided into three clades of a phylogenic tree. Promoter motif analysis showed that NADP-ME1 genes in Group IV were more conserved with each other than the other NADP-ME genes in Groups I and II. A nucleotide motif involved in ABA responses, desiccation and seed development was found in the promoters of most NADP-ME1 genes. Generally, the NADP-ME genes of Brassica rapa, B. oleracea and B. napus had less introns than their corresponding Arabidopsis orthologs. In these three Brassica species, the NADP-ME genes derived from the least fractionated subgenome have lost less introns than those from the medium fractionated and most fractionated subgenomes. BrNADP-ME1 showed the highest expression in petals and mature embryos. Two paralogous NADP-ME2 genes (BrNADP-ME2a and BrNADP-ME2b) shared similar expression profiles and differential expression levels. BrNADP-ME3 showed down-regulation during embryogenesis and reached its lowest expression in early cotyledonary embryos. BrNADP-ME4 was expressed widely in multiple organs and showed high expression during the whole embryogenesis process. Different NADP-ME genes of B. rapa showed differential gene expression profiles in young leaves after ABA treatment or cold stress. Our genome-wide identification and characterization of NADP-ME genes extend our understanding of the evolution or function of this family in Brassicaceae.
依赖于烟酰胺腺嘌呤二核苷酸磷酸（NADP）的苹果酸酶（NADP-MEs）在植物的正常发育和应激反应中都起着至关重要的作用。在此，我们进行了全基因组分析，以从12种十字花科植物中鉴定出65个假定的NADP-ME基因。这些NADP-ME基因被分为五类同线直系同源基因，并被分为系统发育树的三个分支。启动子基序分析表明，第四组中的NADP-ME1基因彼此之间比第一组和第二组中的其他NADP-ME基因更为保守。在大多数NADP-ME1基因的启动子中发现了一个与脱落酸反应、干燥和种子发育有关的核苷酸基序。一般来说，白菜、甘蓝和油菜的NADP-ME基因的内含子比其相应的拟南芥直系同源基因少。在这三种芸苔属植物中，来自最少分化亚基因组的NADP-ME基因比来自中等分化和高度分化亚基因组的基因丢失的内含子更少。BrNADP-ME1在花瓣和成熟胚中表达最高。两个旁系同源的NADP-ME2基因（BrNADP-ME2a和BrNADP-ME2b）具有相似的表达谱和差异表达水平。BrNADP-ME3在胚胎发生过程中表达下调，并在子叶早期胚中达到最低表达水平。BrNADP-ME4在多个器官中广泛表达，并在整个胚胎发生过程中高表达。白菜不同的NADP-ME基因在脱落酸处理或冷胁迫后的幼叶中表现出不同的基因表达谱。我们对NADP-ME基因的全基因组鉴定和表征扩展了我们对十字花科中该家族进化或功能的理解。
