Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding.
Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding.
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DOI：
10.1371/journal.pone.0035071
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Zhou S
中科院分区：
文献类型：
--
作者：
Dong W;Liu J;Yu J;Wang L;Zhou S
目前，植物分子系统学和DNA条形码技术严重依赖叶绿体基因序列的使用。由于叶绿体基因的进化速率相对较低，适合低分类水平被子植物分子研究和物种 DNA 条形码的选择很少。我们扫描了 12 个属的整个叶绿体基因组，以寻找高度可变的区域。 9个属的序列数据来自GenBank，3个属是我们自己的。我们从每个属叶绿体基因组的所有可变基因座中鉴定出近 5% 的最可变基因座，然后选择了至少三个属中存在的 23 个基因座。 23 个基因座包括 4 个编码区、2 个内含子和 17 个基因间间隔区。在 23 个基因座中，变异最大（按照从最高变异性到最低变异性的顺序）是基因间区域 ycf1-a、trnK、rpl32-trnL 和 trnH-psbA，其次是 trnSUGA-trnGUCC、petA-psbJ、rps16-trnQ、ndhC-trnV、ycf1-b、ndhF、rpoB-trnC、 psbE-petL 和 rbcL-accD。三个基因座，trnSUGA-trnGUCC、trnT-psbD 和 trnW-psaJ，在三个属中每个位点（π 值）显示出非常高的核苷酸多样性。其他基因座可能具有解决物种水平的系统发育和物种鉴定问题的强大潜力。某些属不存在 accD-psal、rbcL-accD、rpl32-trnL、rps16-trnQ 和 ycf1 位点。为了对本研究中确定的高度可变基因座进行扩增和测序，我们从其保守的侧翼区域设计了引物。我们测试了引物在代表基础被子植物、单子叶植物、真双子叶植物、玫瑰花和紫苑的八个物种中扩增靶序列的适用性，并证实引物扩增了这些物种的所需序列。叶绿体基因组序列包含高度可变的区域。在系统发育分析和 DNA 条形码中筛选合适的基因座以解析密切相关的物种或属时，这些区域是首先考虑的因素。
At present, plant molecular systematics and DNA barcoding techniques rely heavily on the use of chloroplast gene sequences. Because of the relatively low evolutionary rates of chloroplast genes, there are very few choices suitable for molecular studies on angiosperms at low taxonomic levels, and for DNA barcoding of species. We scanned the entire chloroplast genomes of 12 genera to search for highly variable regions. The sequence data of 9 genera were from GenBank and 3 genera were of our own. We identified nearly 5% of the most variable loci from all variable loci in the chloroplast genomes of each genus, and then selected 23 loci that were present in at least three genera. The 23 loci included 4 coding regions, 2 introns, and 17 intergenic spacers. Of the 23 loci, the most variable (in order from highest variability to lowest) were intergenic regions ycf1-a, trnK, rpl32-trnL, and trnH-psbA, followed by trnSUGA-trnGUCC, petA-psbJ, rps16-trnQ, ndhC-trnV, ycf1-b, ndhF, rpoB-trnC, psbE-petL, and rbcL-accD. Three loci, trnSUGA-trnGUCC, trnT-psbD, and trnW-psaJ, showed very high nucleotide diversity per site (π values) across three genera. Other loci may have strong potential for resolving phylogenetic and species identification problems at the species level. The loci accD-psaI, rbcL-accD, rpl32-trnL, rps16-trnQ, and ycf1 are absent from some genera. To amplify and sequence the highly variable loci identified in this study, we designed primers from their conserved flanking regions. We tested the applicability of the primers to amplify target sequences in eight species representing basal angiosperms, monocots, eudicots, rosids, and asterids, and confirmed that the primers amplified the desired sequences of these species. Chloroplast genome sequences contain regions that are highly variable. Such regions are the first consideration when screening the suitable loci to resolve closely related species or genera in phylogenetic analyses, and for DNA barcoding.
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影响因子：
11.6
作者：
Alverson, Andrew J.;Rice, Danny W.;Palmer, Jeffrey D.
通讯作者：
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影响因子：
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作者：
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DOI：
10.1073/pnas.0812297106
发表时间：
2009-02-24
影响因子：
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作者：
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DOI：
10.1073/pnas.0603152103
发表时间：
2006-06-20
影响因子：
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作者：
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DOI：
10.1073/pnas.0503123102
发表时间：
2005-06-07
影响因子：
11.1
作者：
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通讯作者：
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