TY - JOUR
T1 - Evaluation of chloroplast DNA markers for distinguishing Phalaenopsis species
AU - Lin, Jhong Yi
AU - Lin, Bo Yen
AU - Chang, Ching Dong
AU - Liao, Sin Chung
AU - Liu, Yu Chang
AU - Wu, Wen Luan
AU - Chang, Ching Chun
N1 - Publisher Copyright:
© 2015 Elsevier B.V.
PY - 2015/8/1
Y1 - 2015/8/1
N2 - Comparative analysis of chloroplast DNA (cpDNA) between two endemic moth orchids in Taiwan, Phalaenopsis aphrodite subsp. formosana and P. equestris, previously revealed many evolutionary hotspots. In this study, we explored 27 pre-screened cpDNA regions to evaluate molecular markers for distinguishing Phalaenopsis species. Fifteen cpDNA markers were highly variable among moth orchids, with polymorphic information contents ≥8.0. The rps16-. trnQ marker showed the best discrimatory power which 15 endemic moth orchids could be successfully separated into 13 groups. From the sequences of the seven selected cpDNA regions, the rps16-. trnQ intergenic spacer was the best DNA barcode which 19 endemic moth orchids could be completely distinguished. The petN-. psbM intergenic spacer could be better used as a DNA barcode to differentiate P. aphrodite subsp. formosana and P. amabilis. Additionally, the inheritance mode of cpDNA in moth orchids was maternally predominated. Phylogenetic analysis revealed non-monophyletic relationships below the Phalaenopsis genus level. In summary, we have revealed a set of cpDNA markers that could be used for identification and phylogenetic study of Phalaenopsis orchids.
AB - Comparative analysis of chloroplast DNA (cpDNA) between two endemic moth orchids in Taiwan, Phalaenopsis aphrodite subsp. formosana and P. equestris, previously revealed many evolutionary hotspots. In this study, we explored 27 pre-screened cpDNA regions to evaluate molecular markers for distinguishing Phalaenopsis species. Fifteen cpDNA markers were highly variable among moth orchids, with polymorphic information contents ≥8.0. The rps16-. trnQ marker showed the best discrimatory power which 15 endemic moth orchids could be successfully separated into 13 groups. From the sequences of the seven selected cpDNA regions, the rps16-. trnQ intergenic spacer was the best DNA barcode which 19 endemic moth orchids could be completely distinguished. The petN-. psbM intergenic spacer could be better used as a DNA barcode to differentiate P. aphrodite subsp. formosana and P. amabilis. Additionally, the inheritance mode of cpDNA in moth orchids was maternally predominated. Phylogenetic analysis revealed non-monophyletic relationships below the Phalaenopsis genus level. In summary, we have revealed a set of cpDNA markers that could be used for identification and phylogenetic study of Phalaenopsis orchids.
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U2 - 10.1016/j.scienta.2015.06.019
DO - 10.1016/j.scienta.2015.06.019
M3 - Article
AN - SCOPUS:84933506157
SN - 0304-4238
VL - 192
SP - 302
EP - 310
JO - Scientia Horticulturae
JF - Scientia Horticulturae
ER -