Sakulsathaporn Arpakorn, Wonnapinij Passorn, Suttangkakul Anongpat, Apisitwanich Somsak, Vuttipongchaikij Supachai
Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand.
Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand.
Genet Mol Biol. 2020 Jan 13;42(4):e20180371. doi: 10.1590/1678-4685-GMB-2018-0371. eCollection 2020.
We have identified 46 RNA editing sites located in 20 chloroplast (cp) genes of Borassus flabellifer (Asian Palmyra palm), family Arecaceae, and tested these genes for supporting phylogenetic study among the commelinids. Among the 46 sites, 43 sites were found to cause amino acid alterations, which were predicted to increase the hydrophobicity and transmembrane regions of the proteins, and one site was to cause a premature stop codon. Analysis of these editing sites with data obtained from seed plants showed that a number of shared-editing sites depend on the evolutionary relationship between plants. We reconstructed a deep phylogenetic relationship among the commelinids using seven RNA edited genes that are orthologous among monocots. This tree could represent the relationship among subfamilies of Arecaceae family, but was insufficient to represent the relationship among the orders of the commelinid. After adding eight gene sequences with high parsimony-informative characters (PICs), the tree topology was improved and could support the topology for the commelinid orders ((Arecales,Dasypogenaceae) (Zingiberales+Commelinales,Poales)). The result provides support for inherent RNA editing along the evolution of seed plants, and we provide an alternative set of loci for the phylogenetic tree reconstruction of Arecaceae's subfamilies.
我们在棕榈科扇叶树头榈（亚洲扇叶棕榈）的20个叶绿体（cp）基因中鉴定出46个RNA编辑位点，并对这些基因进行了测试，以支持鸭跖草类植物之间的系统发育研究。在这46个位点中，发现43个位点会导致氨基酸改变，预计这些改变会增加蛋白质的疏水性和跨膜区域，还有一个位点会导致提前终止密码子。利用从种子植物获得的数据对这些编辑位点进行分析表明，许多共享编辑位点取决于植物之间的进化关系。我们使用单子叶植物中直系同源的7个RNA编辑基因重建了鸭跖草类植物之间的深层系统发育关系。这棵树可以代表棕榈科亚科之间的关系，但不足以代表鸭跖草类目之间的关系。在添加了8个具有高简约信息特征（PIC）的基因序列后，树的拓扑结构得到了改进，能够支持鸭跖草类目（（棕榈目，刺葵科）（姜目+鸭跖草目，禾本目））的拓扑结构。该结果为种子植物进化过程中固有的RNA编辑提供了支持，并且我们为棕榈科亚科的系统发育树重建提供了一组替代位点。
