Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource; Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China.
Key Laboratory of Forest Ecology and Environment of State Forestry Administration; Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, 100091, China.
Sci Rep. 2017 Oct 2;7(1):12564. doi: 10.1038/s41598-017-13057-0.
DNA barcoding is a useful tool for species identification and phylogenetic construction. But present studies have far reached a consistent result on the universality of DNA barcoding. We tested the universality of tree species DNA barcodes including rbcL, matK, trnH-psbA and ITS, and examined their abilities of species identification and phylogenetic construction in three tropical cloud forests. Results showed that the success rates of PCR amplification of rbcL, matK, trnH-psbA and ITS were 75.26% ± 3.65%, 57.24% ± 4.42%, 79.28% ± 7.08%, 50.31% ± 6.64%, and the rates of DNA sequencing were 63.84% ± 4.32%, 50.82% ± 4.36%, 72.87% ± 11.37%, 45.15% ± 8.91% respectively, suggesting that both rbcL and trnH-psbA are universal for tree species in the tropical cloud forests. The success rates of species identification of the four fragments were higher than 41.00% (rbcL: 41.50% ± 2.81%, matK: 42.88% ± 2.59%, trnH-psbA: 46.16% ± 5.11% and ITS: 47.20% ± 5.76%), demonstrating that these fragments have potentiality in species identification. When the phylogenetic relationships were built with random fragment combinations, optimal evolutionary tree with high supporting values were established using the combinations of rbcL + matK + trnH-psbA in tropical cloud forests.
DNA 条形码是物种鉴定和系统发育构建的有用工具。但目前的研究远未在 DNA 条形码的通用性上达成一致的结果。我们测试了包括 rbcL、matK、trnH-psbA 和 ITS 在内的树种 DNA 条形码的通用性，并在三个热带云雾林中检验了它们的物种鉴定和系统发育构建能力。结果表明，rbcL、matK、trnH-psbA 和 ITS 的 PCR 扩增成功率分别为 75.26%±3.65%、57.24%±4.42%、79.28%±7.08%和 50.31%±6.64%，DNA 测序率分别为 63.84%±4.32%、50.82%±4.36%、72.87%±11.37%和 45.15%±8.91%，表明 rbcL 和 trnH-psbA 对热带云雾林的树种都是通用的。四个片段的物种鉴定成功率均高于 41.00%（rbcL：41.50%±2.81%，matK：42.88%±2.59%，trnH-psbA：46.16%±5.11%和 ITS：47.20%±5.76%），表明这些片段具有物种鉴定的潜力。当使用随机片段组合构建系统发育关系时，使用 rbcL+matK+trnH-psbA 的组合在热带云雾林中建立了具有高支持值的最佳进化树。
