比较不同DNA条形码对中国海岸带耐盐植物的识别率

Comparison of species resolution rates of DNA barcoding for Chinese coastal halo-tolerant plants

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(mat K、rbc L、trn H-psb A)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,mat K和trn H-psb A片段表现最好,ITS较差,ITS和mat K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mat K(64.03%)和trn H-psb A(61.21%),rbc L的物种识别率最低,仅为46.41%。系统发育树分析显示mat K的物种识别率最高(82.3%),依据trn H-psb A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+mat K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。

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（mat K, rbc L and trn H-psb A） 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, mat K and trn H-psb A 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 mat K（64.03%）, trn H-psb A（61.21%） and rbc L（46.41%）. Phylogenetic trees（NJ trees） indicated that the species resolution rate of mat K was the highest（82.3%）, but no reliable NJ tree based on trn H-psb A could be acquired because of unequal sequence length. NMDS and PCo A 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 ＋ mat K 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.