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

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.

SUBMITTER: Tan WH

PROVIDER: S-EPMC7468033 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundDNA barcoding offers an efficient way to determine species identification and to measure biodiversity. For dinoflagellates, an ancient alveolate group of about 2000 described extant species, DNA barcoding studies have revealed large amounts of unrecognized species diversity, most of which is not represented in culture collections. To date, two mitochondrial gene markers, Cytochrome Oxidase I (COI) and Cytochrome b oxidase (COB), have been used to assess DNA barcoding in dinoflagellates, and both failed to amplify all taxa and suffered from low resolution. Nevertheless, both genes yielded many examples of morphospecies showing cryptic speciation and morphologically distinct named species being genetically similar, highlighting the need for a common marker. For example, a large number of cultured Symbiodinium strains have neither taxonomic identification, nor a common measure of diversity that can be used to compare this genus to other dinoflagellates.Methodology/principal findingsThe purpose of this study was to evaluate the Internal Transcribed Spacer units 1 and 2 (ITS) of the rDNA operon, as a high resolution marker for distinguishing species dinoflagellates in culture. In our study, from 78 different species, the ITS barcode clearly differentiated species from genera and could identify 96% of strains to a known species or sub-genus grouping. 8.3% showed evidence of being cryptic species. A quarter of strains identified had no previous species identification. The greatest levels of hidden biodiversity came from Scrippsiella and the Pfiesteriaceae family, whilst Heterocapsa strains showed a high level of mismatch to their given species name.Conclusions/significanceThe ITS marker was successful in confirming species, revealing hidden diversity in culture collections. This marker, however, may have limited use for environmental barcoding due to paralogues, the potential for unidentifiable chimaeras and priming across taxa. In these cases ITS would serve well in combination with other markers or for specific taxon studies.

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

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