Biodiversity Science ›› 2017, Vol. 25 ›› Issue (10): 1095-1104.doi: 10.17520/biods.2017164

• Original Papers: Plant Diversity • Previous Article     Next Article

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

Ya’nan Wei1, Xiaomei Wang1, Pengcheng Yao1, Xiaoyong Chen2, Hongqing Li1, *()   

  1. 1 School of Life Sciences, East China Normal University, Shanghai 200241
    2 School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241
  • Received:2017-06-02 Accepted:2017-08-30 Online:2018-05-05
  • Li Hongqing E-mail:hqli@bio.ecnu.edu.cn

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

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

Fig. 1

Species resolution rate from all to all BLASTn searches"

Fig. 2

Species resolution rate of 15 genera which contain more than one species"

Fig. 3

Species resolution rate based on the phylogenetic method"

Fig. 4

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

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