Floristic Diversity Research Group, Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada. N1G 2W1 Botanical Research Institute of Texas (BRIT), 509 Pecan Street, Suite 101, Fort Worth, Texas 76102-4060, USA.
Mol Ecol Resour. 2008 May;8(3):480-90. doi: 10.1111/j.1471-8286.2007.02002.x.
The concept and practice of DNA barcoding have been designed as a system to facilitate species identification and recognition. The primary challenge for barcoding plants has been to identify a suitable region on which to focus the effort. The slow relative nucleotide substitution rates of plant mitochondria and the technical issues with the use of nuclear regions have focused attention on several proposed regions in the plastid genome. One of the challenges for barcoding is to discriminate closely related or recently evolved species. The Myristicaceae, or nutmeg family, is an older group within the angiosperms that contains some recently evolved species providing a challenging test for barcoding plants. The goal of this study is to determine the relative utility of six coding (Universal Plastid Amplicon - UPA, rpoB, rpoc1, accD, rbcL, matK) and one noncoding (trnH-psbA) chloroplast loci for barcoding in the genus Compsoneura using both single region and multiregion approaches. Five of the regions we tested were predominantly invariant across species (UPA, rpoB, rpoC1, accD, rbcL). Two of the regions (matK and trnH-psbA) had significant variation and show promise for barcoding in nutmegs. We demonstrate that a two-gene approach utilizing a moderately variable region (matK) and a more variable region (trnH-psbA) provides resolution among all the Compsonuera species we sampled including the recently evolved C. sprucei and C. mexicana. Our classification analyses based on nonmetric multidimensional scaling ordination, suggest that the use of two regions results in a decreased range of intraspecific variation relative to the distribution of interspecific divergence with 95% of the samples correctly identified in a sequence identification analysis.
DNA 条形码的概念和实践旨在设计一个系统，以促进物种鉴定和识别。植物条形码的主要挑战是确定一个合适的区域作为研究重点。植物线粒体核苷酸替代率相对较慢，以及核区使用的技术问题，使得人们将注意力集中在质体基因组的几个拟议区域上。条形码技术的一个挑战是区分密切相关或最近进化的物种。肉豆蔻科（Myristicaceae），或肉豆蔻科，是被子植物中较老的一组，其中包含一些最近进化的物种，这为植物条形码提供了一个具有挑战性的测试。本研究的目的是确定六个编码（通用质体扩增子 - UPA、rpoB、rpoc1、accD、rbcL、matK）和一个非编码（trnH-psbA）叶绿体基因座在使用单区域和多区域方法对 Compsoneura 属进行条形码时的相对有效性。我们测试的五个区域在物种间主要是不变的（UPA、rpoB、rpoC1、accD、rbcL）。两个区域（matK 和 trnH-psbA）具有显著的变异性，有望用于肉豆蔻的条形码。我们证明，利用一个中等变异性区域（matK）和一个更具变异性的区域（trnH-psbA）的双基因方法，可以在我们采样的所有 Compsonuera 物种中提供分辨率，包括最近进化的 C. sprucei 和 C. mexicana。我们基于非度量多维标度排序的分类分析表明，与种间差异的分布相比，使用两个区域会导致种内变异范围减小，在序列鉴定分析中，95%的样本得到正确识别。
