Efficiency of ITS Sequences for DNA Barcoding in Passiflora (Passifloraceae)

Abstract

DNA barcoding is a technique for discriminating and identifying species using short, variable, and standardized DNA regions. Here, we tested for the first time the performance of plastid and nuclear regions as DNA barcodes in Passiflora. This genus is a largely variable, with more than 900 species of high ecological, commercial, and ornamental importance. We analyzed 1034 accessions of 222 species representing the four subgenera of Passiflora and evaluated the effectiveness of five plastid regions and three nuclear datasets currently employed as DNA barcodes in plants using barcoding gap, applied similarity-, and tree-based methods. The plastid regions were able to identify less than 45% of species, whereas the nuclear datasets were efficient for more than 50% using “best match” and “best close match” methods of TaxonDNA software. All subgenera presented higher interspecific pairwise distances and did not fully overlap with the intraspecific distance, and similarity-based methods showed better results than tree-based methods. The nuclear ribosomal internal transcribed spacer 1 (ITS1) region presented a higher discrimination power than the other datasets and also showed other desirable characteristics as a DNA barcode for this genus. Therefore, we suggest that this region should be used as a starting point to identify Passiflora species.

Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae)

“…In this study, sequence analysis of ITS datasets using Bayesian inference (BI) tree-based method gave the highest species resolution based on the topology with the highest product of posterior clade probabilities across all nodes followed by BM and BCM model of TaxonDNA, which too presented equally efficient results either in single or combination of barcodes. Similarly, patterned results have been obtained in different DNA barcoding studies in various plant groups (Yan et al, 2014; Giudicelli, Mäder & De, 2015; Xu et al, 2015; Yan et al, 2015). The clustering algorithm of the Bayesian framework provides a flexible way to model rate variation and obtain reliable estimates of speciation times, provided the assumptions of the models be adequate (Drummond et al, 2012).…”

“…However, ITS region has proved to be a suitable marker in authentication of Cassia species in the commercial herbal market (Seethapathy et al, 2014). The strong identification ability of nuclear region ITS have been verified in many complex groups (Baldwin et al, 1995; Alves et al, 2014; Wang et al, 2014; Giudicelli, Mäder & De, 2015). Therefore, we suggest that ITS1 itself could be the first option for DNA barcoding in subtribe Cassiinae, though ITS2 should not be discarded.…”

Peer Review #2 of "Assessing universality of DNA barcoding in geographically isolated selected desert medicinal species of Fabaceae and Poaceae (v0.1)"

“…DNA barcoding is introduced in 2003 as a molecular based species identification tool by using a short, variable and standardized DNA region, the barcode (Hebert et al, 2003a;Hebert et al, 2003b;Hebert & Gregory, 2005). In order to meet the criteria of DNA barcode, a gene locus must possess enough species level genetic variability, short sequence length, and conserved flanking regions (Giudicelli et al, 2015). Common DNA barcodes proposed for plants are plastidial matK, rbcL, ITS, rpoB and rpoC1, the intergenic plastidial spacers (trnH-psbA, atpF-atpH and psbK-psbI) and the nuclear internal transcribed spacers that have been used singly or in combinations (De Mattia et al, 2011;Saddhe & Kumar, 2017).…”

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“…However, ITS region has proved to be a suitable marker in authentication of Cassia species in the commercial herbal market (Seethapathy et al, 2014). The strong identification ability of nuclear region ITS have been verified in many complex groups (Baldwin et al, 1995;Alves et al, 2014;Wang et al, 2014;Giudicelli et al, 2015). Therefore, we suggest that ITS1 itself could be the first option for DNA barcoding in subtribe Cassiinae, though ITS2 should not be discarded.…”

“…In this study, sequence analysis of ITS datasets using Bayesian inference (BI) tree-based method gave the highest species resolution based on the topology with the highest product of posterior clade probabilities across all nodes followed by BM and BCM model of TaxonDNA, which too presented equally efficient results either in single or combination of barcodes. Similarly, patterned results have been obtained in different DNA barcoding studies in various plant groups (Yan et al, 2014;Giudicelli et al, 2015;Xu et al, 2015;Yan et al, 2015). The clustering algorithm of Bayesian framework provides a flexible way to model rate variation and obtain reliable estimates of speciation times, provided the assumptions of the models be adequate (Drummond et al, 2012).…”