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

doi:10.17520/biods.2017164

Abstract

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.

http://jtp.cnki.net/bilingual/detail/html/SWDY201710013

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

Ya’nan Wei, Xiaomei Wang, Pengcheng Yao, Xiaoyong Chen, Hongqing Li. Comparison of species resolution rates of DNA barcoding for Chinese coastal halo-tolerant plants[J]. Biodiv Sci, 2017, 25(10): 1095-1104.

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URL: https://www.biodiversity-science.net/EN/10.17520/biods.2017164

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

Figures/Tables 5

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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