比较不同DNA条形码对中国海岸带耐盐植物的识别率

doi:10.17520/biods.2017164

摘要/Abstract

摘要：

海岸带耐盐植物是一个生态和经济价值独特的庞杂类群, 人们对其DNA条形码特性的了解甚少。本文对我国从辽宁到海南10个沿海省(市)大陆及岛屿海岸带耐盐植物广泛采样, 从采集获得的样品中筛选出53科97属116个物种共562个样品进行DNA条形码研究。对3个叶绿体片段(matK、rbcL、trnH-psbA)和1个核基因片段(ITS)进行了扩增和测序, 统计各个片段的引物通用性和序列获得率, 并检验了物种识别率。从序列获得率来看, matK和trnH-psbA片段表现最好, ITS较差, ITS和matK的引物通用性比其他2个片段差。序列相似性分析表明, 单个片段ITS物种识别率最高(73.36%), 其次为matK (64.03%)和trnH-psbA (61.21%), rbcL的物种识别率最低, 仅为46.41%。系统发育树分析显示matK的物种识别率最高(82.3%), 依据trnH-psbA片段难以获得可靠的系统发育树。多维度非度量分析(non-metric multidimensional scaling, NMDS)表明在进行海岸带区域性植物的DNA条形码研究时, 叶绿体片段和核基因片段均应该考虑。综合上述研究结果, 推荐联合片段ITS + matK作为中国海岸带耐盐植物DNA条形码。本文为海岸带耐盐植物研究提供了总计1,939条DNA条形码基础数据, 为构建耐盐植物DNA条形码数据库奠定了基础。

关键词: DNA条形码, 海岸带, 耐盐植物, 物种识别率, ITS, matK

Abstract

Halo-tolerant plants compose a huge group of plants with unique ecological and economical value. Little is known about their DNA barcoding speciality. In this study, 562 samples of coastal halo-tolerant plants (including 53 families, 97 genera and 116 species) were collected from 10 coastal provinces, ranging from Liaoning to Hainan. Three chloroplast DNA markers (matK, rbcL and trnH-psbA) and one nuclear DNA marker (ITS) were amplified and sequenced. Primer universality and sequence availability of each locus were examined and species resolution rates were tested. When considering sequence availability, matK and trnH- psbA were among the best. But the primer universality of ITS was marginally worse than expected. The all-to-all BLASTn searches indicated that the species resolution rate of ITS was the highest (73.36%), followed by those of matK (64.03%), trnH-psbA (61.21%) and rbcL (46.41%). Phylogenetic trees (NJ trees) indicated that the species resolution rate of matK was the highest (82.3%), but no reliable NJ tree based on trnH-psbA could be acquired because of unequal sequence length. NMDS and PCoA results demonstrated that both chloroplast DNA markers and nuclear DNA markers should be considered when conducting coastal plant DNA barcoding studies. Based on the above results, we suggest that the combination of ITS + matK should be regarded as the barcode for halo-tolerant plants in Chinese coastal regions. In total, the 1939 newly acquired sequences in this study lay the foundation for a DNA barcode database of costal halo-tolerant plants.

Key words: DNA barcoding, coastal region, halo-tolerant plants, species resolution rate, ITS, matK

魏亚男, 王晓梅, 姚鹏程, 陈小勇, 李宏庆 (2017) 比较不同DNA条形码对中国海岸带耐盐植物的识别率. 生物多样性, 25, 1095-1104. DOI: 10.17520/biods.2017164.

Ya’nan Wei, Xiaomei Wang, Pengcheng Yao, Xiaoyong Chen, Hongqing Li (2017) Comparison of species resolution rates of DNA barcoding for Chinese coastal halo-tolerant plants. Biodiversity Science, 25, 1095-1104. DOI: 10.17520/biods.2017164.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2017164

https://www.biodiversity-science.net/CN/Y2017/V25/I10/1095

图/表 5

表1 序列获得率及片段长度

Table 1 Summary of the sequencing success rate and length of candidate barcoding fragments

片段名称 Locus	获得序列数 Species resolution rate	序列获得率 Sequence availability	测序成功物种数 Species successfully sequenced	片段长度 Fragment length (bp)
ITS	481	85.59%	106	304-632
matK	502	89.32%	116	611-721
rbcL	465	83.04%	109	371-650
trnH-psbA	491	87.36%	116	142-907

图1 序列相似性方法的物种识别率统计

Fig. 1 Species resolution rate from all to all BLASTn searches

图2 属内物种数目多于1的15个属的物种识别率统计

Fig. 2 Species resolution rate of 15 genera which contain more than one species

图3 系统发育方法的物种识别率统计

Fig. 3 Species resolution rate based on the phylogenetic method

图4 候选DNA条形码片段的NMDS分析(Stress值: 0.011)

Fig. 4 Multivariate analysis of non-metric multidimensional scaling for the four barcode markers NMDS. Stress value: 0.011.

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