Efficacy of DNA barcode internal transcribed spacer 2 (ITS 2) in phylogenetic study of Alpinia species from Peninsular M
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RESEARCH ARTICLE
Efficacy of DNA barcode internal transcribed spacer 2 (ITS 2) in phylogenetic study of Alpinia species from Peninsular Malaysia Wei Harn Tan1 • Li Chin Chai1 • Chiew Foan Chin1
Received: 18 January 2020 / Revised: 1 August 2020 / Accepted: 14 August 2020 / Published online: 29 August 2020 Ó Prof. H.S. Srivastava Foundation for Science and Society 2020
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.
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12298-020-00868-1) contains supplementary material, which is available to authorized users. & Chiew Foan Chin [email protected] 1
University of Nottingham Malaysia Campus, Semenyih, Malaysia
Keywords Alpinia Peninsular Malaysia DNA barcoding ITS2 Molecular identification
Introduction The genus Alpinia Roxb. is the largest genus in the Zingiberaceae (ginger) family with approximately 235 species (Govaerts et al. 2017). Several traits distinguish the genus from other genera in the Zingiberaceae family namely terminally borne inflorescence on the leafy stem, poorly developed or absence of lateral staminodes and typically attractive labellum. The genus has an extensive distribution range, which can be found growing in Japan, tropical and sub-tropical Asia, Australia and the Pacific Islands. There are currently 27 recognised Alpinia species in Peninsular Malaysia, 13 of which are endemic to the region (Govaerts et al. 2017). Alpinia species are small or large herbaceous plants, up to 2 m in height. Most species are found in understory of rainforest while some favour disturbed habitats (e.g. A. mutica and A. javanica) or wetlands (A. aquatica). Many species of Alpinia are rich in phytochemicals making t
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