中国榕属植物六个候选DNA条形码的评价
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摘要
榕属植物Ficus Linn.(Moraceae),大约有750种,因生境的多样化和榕-榕小蜂复杂的协同进化历史,使其成为分类学中非常棘手的类群。DNA条形码有望对榕属植物的鉴定带来新的曙光,但尚需筛选评估候选DNA片段。本研究针对榕属植物63种,228个样本,基于5个叶绿体基因片段(rbcL,matK,trnH-psbA,psbK-psbⅠ,atpF-atpH)和1个核基因片段(ITS),计算了遗传距离,单个片段和组合片段的"Barcoding Gap",并构建了系统发育树来检验所选取基因片段物种鉴定的能力。结果表明,各基因片段中ITS具有最多的变异位点,较大的种间变异和种内变异,最高的物种分辨率(72%)和较高的引物通用性；ps6K-psbⅠ和trnH-psbA具有适中的变异率和相对较低的物种分别率(约19%),而matK, rbcL和atpF-atpH不能有效地区分榕属物种。在可能的组合片段中,ITS+trnH-psbA表现最好但物种鉴别率与单独的ITS片段相差不大(75%vs72%)。所以,我们建议以ITS作为榕属植物的DNA条形码。
Genus Ficus (Moraceae), with about750species, diverse habits and complicated co-evolutionary history with fig-wasps, is a notoriously difficult group in taxonomy. DNA barcoding is expected to bring light to the identification of Ficus but need evaluation of candidate loci. Based on five plastid loci (rbcL, matK, trnH-psbA, psbK-psbI, atpF-atpH) and a nuclear locus (ITS), we calculated their genetic distances and DNA barcoding gaps individually and in combination, and constructed phylogenetic trees to test their ability to distinguish the species of the genus.228samples representing63putative species in Ficus of China were included in this study. The results demonstrated that ITS has the most variable sites, greater intra-and inter-specific divergences, the highest species discrimination rate (72%) and higher primer universality among the single loci. It is followed by psbK-psbI and trnH-psbA with moderate variation and considerably lower species discrimination rates (about19%), whereas matK, rbcL and atpF-atpH couldn't effectively separate the species. Among the possible combinations of loci, ITS+trnH-psbA performed best but only marginally improved species resolution over ITS alone (75%vs72%). Therefore, we recommend using ITS as a single DNA barcoding locus in Ficus.
Genus Ficus (Moraceae), with about750species, diverse habits and complicated co-evolutionary history with fig-wasps, is a notoriously difficult group in taxonomy. DNA barcoding is expected to bring light to the identification of Ficus but need evaluation of candidate loci. Based on five plastid loci (rbcL, matK, trnH-psbA, psbK-psbI, atpF-atpH) and a nuclear locus (ITS), we calculated their genetic distances and DNA barcoding gaps individually and in combination, and constructed phylogenetic trees to test their ability to distinguish the species of the genus.228samples representing63putative species in Ficus of China were included in this study. The results demonstrated that ITS has the most variable sites, greater intra-and inter-specific divergences, the highest species discrimination rate (72%) and higher primer universality among the single loci. It is followed by psbK-psbI and trnH-psbA with moderate variation and considerably lower species discrimination rates (about19%), whereas matK, rbcL and atpF-atpH couldn't effectively separate the species. Among the possible combinations of loci, ITS+trnH-psbA performed best but only marginally improved species resolution over ITS alone (75%vs72%). Therefore, we recommend using ITS as a single DNA barcoding locus in Ficus.
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