Efficacy of DNA barcode internal transcribed spacer 2 (ITS 2) in phylogenetic study of Alpinia species from Peninsular Malaysia

• Published in: Physiology and molecular biology of plants Vol. 26; no. 9; pp. 1889 - 1896
• Main Authors: Tan, Wei Harn, Chai, Li Chin, Chin, Chiew Foan
• Format: Journal Article
• Language: English
• Published: New Delhi Springer India 01.09.2020; Springer Nature B.V
• Subjects: Alpinia; Biological and Medical Physics; Biomedical and Life Sciences; Biophysics; Cell Biology; Deoxyribonucleic acid; DNA; Gene sequencing; Identification; Life Sciences; Phylogenetics; Phylogeny; Plant Physiology; Plant Sciences; Protein structure; Research Article; Secondary structure; Species; Malaysia; ITS2; Peninsular Malaysia; DNA barcoding; Molecular identification
• ISSN: 0971-5894; 0974-0430
• DOI: 10.1007/s12298-020-00868-1

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.