Characteristics and Mutational Hotspots of Plastomes inDebregeasia(Urticaceae)
Characteristics and Mutational Hotspots of Plastomes inDebregeasia(Urticaceae)
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DOI：
10.3389/fgene.2020.00729
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发表时间：
2020-07-08
影响因子：
3.7
通讯作者：
Wu, Zeng-Yuan
中科院分区：
文献类型：
--
作者：
Wang, Ruo-Nan;Milne, Richard, I;Wu, Zeng-Yuan
大麻属是荨麻科植物中一个重要的经济属。以前的基于形态的系统研究，或使用多达四个质体区，都没有令人满意地解决该属之间的关系。在此，我们报道了荨麻科植物的25个新的质体，其中包括来自5个新种的12个质体和来自其他属的13个质体。我们结合一个已发表的Debregeasia的质体组，分析了质体组的结构和特征，确定了选择中的突变热点和位点，并构建了系统发育图。结果表明，大麦的质体非常保守，大小在155,743~156,065个碱基之间，没有结构上的变异。确定了11个突变热点，其中3个(rpoB-trnc-gca、trnT-ggu-psbDandycf1)在DNA条形码、群体遗传学和系统发育重建方面具有很高的潜在应用价值。选择压力分析表明，有9个基因(clpP、ndhF、petB、PSBA、psbK、rbcL、rpl23、ycf2和ycf1)可能经历正选择。系统发育分析结果表明，该属为单系种，在所研究的属中最接近于Boehmeria属。在Debregeasia中，长叶杜鹃为姊妹TOD。Saeneb，在哪里D。Elltica、D.Orientalis with D.鳞片动物形成了另一个亚纲。本研究丰富了荨麻科细胞器基因组资源，突出了质体组数据在检测突变热点、进行进化和系统分析中的作用。
Debregeasiais an economically important genus of the nettle family (Urticaceae). Previous systematic studies based on morphology, or using up to four plastome regions, have not satisfactorily resolved relationships within the genus. Here, we report 25 new plastomes for Urticaceae, including 12 plastomes from fiveDebregeasiaspecies and 13 plastomes from other genera. Together with the one published plastome forDebregeasia, we analyzed plastome structure and character, identified mutation hotspots and loci under selection, and constructed phylogenies. The plastomes ofDebregeasiawere found to be very conservative, with a size from 155,743 bp to 156,065 bp, and no structural variation. Eleven mutation hotspots were identified, including three (rpoB-trnC-GCA,trnT-GGU-psbDandycf1) that are highly variable both withinDebregeasiaand among genera; these show high potential value for future DNA barcoding, population genetics and phylogenetic reconstruction. Selection pressure analysis revealed nine genes (clpP,ndhF,petB,psbA,psbK,rbcL,rpl23,ycf2, andycf1) that may experience positive selection. Phylogenomic analyses results suggest thatDebregeasiawas monophyletic, and closest toBoehmeriaamong genera examined. WithinDebregeasia,D. longifoliawas sister toD. saeneb, whereasD. elliptica,D. orientaliswithD. squamataformed the other subclade. This study enriches organelle genome resources for Urticaceae, and highlights the utility of plastome data for detecting mutation hotspots for evolutionary and systematic analysis.