Abstract
Alpinia belongs to a large genus with many species found in Peninsular Malaysia. Several species of Alpinia exhibit important medicinal potential. However, progressive studies on the genus Alpinia were hampered by difficulties encountered in species identification. With the advancement achieved in genomic technology, more sensitive tools such as DNA barcoding were developed, which can be used for species identification. Internal Transcribe Spacer 2 (ITS2) is a DNA barcode which has proven to be a promising tool for species identification. The criterions of ITS2 efficacy namely universality and efficacy for species identification were tested on Alpinia species collected from Peninsular Malaysia. The results showed that a success rate of 96.97% was achieved using ITS2 for screening 11 species of Alpinia and an outgroup sample (Zingiber specatabile). Combined with 15 additional sequences from the Genbank for five Alpinia species, ITS2 demonstrated high species identification efficacy with 88.2% of species identified using phylogenetic and distance analysis. The analysis was further improved with the use of ITS2 secondary structure. The results of both criterions demonstrated the ability of ITS2 to successfully discriminate Alpinia species, which will help to improve species identification of Alpinia species in Peninsular Malaysia.
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Acknowledgements
We would like to thank Datuk Seri Dr Lim Chong Keat from the Suriana Botanical Gardens, Penang, Malaysia, for kindly provided us with the Alpinia plant samples. This work was supported by the University of Nottingham Malaysia campus internal grant. Many thanks to volunteers, Boey Jian Sheng, Stephane Arul Mariampilai, Kartik Kanasarmurthy, Kong Wei Yang and Henrik Seyersted for participating in the field sampling.
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CCF conceptualized and designed the experiments. WHT performed the experiments with assistance from LCC. WHT, LCC and CCF analysed the data. WHT and CCF wrote and edited the manuscript.
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Tan, W.H., Chai, L.C. & Chin, C.F. Efficacy of DNA barcode internal transcribed spacer 2 (ITS 2) in phylogenetic study of Alpinia species from Peninsular Malaysia. Physiol Mol Biol Plants 26, 1889–1896 (2020). https://doi.org/10.1007/s12298-020-00868-1
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DOI: https://doi.org/10.1007/s12298-020-00868-1