NADP-malic enzyme (NAPD-ME), and pyruvate orthophosphate dikinase (PPDK) are important enzymes that participate in C4 photosynthesis. However, the evolutionary history and forces driving evolution of these genes in C4 plants are not completely understood. We identified 162 NADP-ME and 35 PPDK genes in 25 species and constructed respective phylogenetic trees. We classified NADP-ME genes into four branches, A1, A2, B1 and B2, whereas PPDK was classified into two branches in which monocots were in branch I and dicots were in branch II. Analyses of selective pressure on the NAPD-ME and PPDK gene families identified four positively selected sites, including 94H and 196H in the a5 branch of NADP-ME, and 95A and 559E in the e branch of PPDK at posterior probability thresholds of 95%. The positively selected sites were located in the helix and sheet regions. Quantitative RT-PCR (qRT-PCR) analyses revealed that expression levels of 6 NADP-ME and 2 PPDK genes from foxtail millet were up-regulated after exposure to light. This study revealed that positively selected sites of NADP-ME and PPDK evolution in C4 plants. It provides information on the classification and positive selection of plant NADP-ME and PPDK genes, and the results should be useful in further research on the evolutionary history of C4 plants.

中文翻译：

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植物中C ₄光合途径基因的鉴定与进化

NADP-苹果酸酶（NAPD-ME）和丙酮酸正磷酸二激酶（PPDK）是参与C4光合作用的重要酶。但是，尚未完全了解C4植物中这些基因的进化历史和驱动这些基因进化的力量。我们鉴定了25个物种中的162个NADP-ME和35个PPDK基因，并分别构建了系统树。我们将NADP-ME基因分为四个分支：A1，A2，B1和B2，而PPDK被分为两个分支，其中单子叶植物位于分支I，双子叶植物位于分支II。对NAPD-ME和PPDK基因家族的选择性压力分析确定了四个阳性选择位点，包括NADP-ME的a5分支中的94H和196H以及PPDK的e分支中的95A和559E（后验概率阈值为95％）。阳性选择的位点位于螺旋区和片区。定量RT-PCR（qRT-PCR）分析显示，狐尾谷子中的6个NADP-ME和2个PPDK基因的表达水平在暴露于光照后被上调。这项研究揭示了在C4植物中NADP-ME和PPDK进化的阳性选择位点。它提供了有关植物NADP-ME和PPDK基因的分类和阳性选择的信息，其结果对于进一步研究C4植物的进化史应该是有用的。