The low copy nuclear region, RPB2 as a novel DNA barcode region for species identification in the rattan genus Calamus (
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RESEARCH ARTICLE
The low copy nuclear region, RPB2 as a novel DNA barcode region for species identification in the rattan genus Calamus (Arecaceae) Anoja Kurian1 • Suma Arun Dev1 • Vadakkethil Balakrishnan Sreekumar2 E. M. Muralidharan1
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Received: 17 October 2019 / Revised: 30 July 2020 / Accepted: 10 August 2020 Ó Prof. H.S. Srivastava Foundation for Science and Society 2020
Abstract Taxonomic complexities, like environmental plasticity and homoplasy, make precise identification challenging in Calamus, the genus of spiny climbing palms of the subfamily Calamoideae (Arecaceae). In the present study, the species discriminatory power of twelve potential DNA barcode regions (rbcL, matK, psbA-trnH, rpoC, rpoB, psbK-psbI, atpF-atpH, psbZ-trnfM, ITS1, ITS2, PRK, and RPB2) were evaluated in 21 species of Calamus from the Western Ghats region of India, using distance, tree, and similarity based statistical methods. Except for the low copy nuclear region, RPB2, none of the tested plastid loci or nuclear loci ITS, either singly or in combinations, could discriminate all the species of Calamus due to low substitution rate of plastid regions and multiple copies of ITS respectively. The RPB2 locus showed highest species resolution with 96% accuracy in similarity based analysis, indicating its potential and efficiency as a barcode locus for the genus. The putative ‘‘Calamus gamblei complex’’ based on overlapping morphology was successfully resolved as six distinct, though closely related, species. The analysis also indicates that C. delessertianus is a morphological variant of C. dransfieldii. In spite of being a low copy nuclear gene region, RPB2 provided an efficient
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12298-020-00864-5) contains supplementary material, which is available to authorized users. & E. M. Muralidharan [email protected] 1
Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala 680653, India
2
Forest Ecology and Biodiversity Conservation Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala 680653, India
barcode to delineate Calamus species and has the potential to further extend its use as a prospective barcode to other Palm genera. Keywords Calamus Species complex Rattans DNA barcoding Low copy nuclear region RPB2
Introduction DNA barcoding, a species identification method using standardized short sequences of DNA, called DNA barcode (Hebert et al. 2003) is widely used in various fields of research, such as conservation biology (Stoeckle 2003), timber forensics and tracking (Asif and Cannon 2005; Fuji 2007), identification of adulterants (Baker et al. 2012; Dev et al. 2014), phylogeography (Kuppu et al. 2019), and in biosystematics (Gao et al. 2010; Pang et al. 2010) due to its high species discriminatory ability. Mitochondrial DNA barcodes for animals using cox1/CO1 (Hebert et al. 2004) turned out to be successful having the necessary universality and variability, unlike in
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