DOI: 10.5061/dryad.64fg4
title: Data from: Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae)

description: Premise of the Study The internal transcribed spacer (ITS) region is
 situated between 18S and 26S in a polycistronic rRNA precursor transcript.
 It had been proved to be the most commonly sequenced region across plant
 species to resolve phylogenetic relationships ranging from shallow to deep
 taxonomic levels. Despite several taxonomical revisions in Cassiinae, a
 stable phylogeny remains elusive at the molecular level, particularly
 concerning the delineation of species in the genera Cassia, Senna and
 Chamaecrista. This study addresses the comparative potential of ITS
 datasets (ITS1, ITS2 and concatenated) in resolving the underlying
 morphological disparity in the highly complex genera, to assess their
 discriminatory power as potential barcode candidates in Cassiinae.
 Methodology A combination of experimental data and an in-silico approach
 based on threshold genetic distances, sequence similarity based and
 hierarchical tree-based methods was performed to decipher the
 discriminating power of ITS datasets on 18 different species of Cassiinae
 complex. Lab-generated sequences were compared against those available in
 the GenBank using BLAST and were aligned through MUSCLE 3.8.31 and
 analysed in PAUP 4.0 and BEAST1.8 using parsimony ratchet, maximum
 likelihood and Bayesian inference (BI) methods of gene and species tree
 reconciliation with bootstrapping. DNA barcoding gap was realized based on
 the Kimura two-parameter distance model (K2P) in TaxonDNA and MEGA.
 Principal Findings Based on the K2P distance, significant divergences
 between the inter- and intra-specific genetic distances were observed,
 while the presence of a DNA barcoding gap was obvious. The ITS1 region
 efficiently identified 81.63% and 90% of species using TaxonDNA and BI
 methods, respectively. The PWG-distance method based on simple pairwise
 matching indicated the significance of ITS1 whereby highest number of
 variable (210) and informative sites (206) were obtained. The BI
 tree-based methods outperformed the similarity-based methods producing
 well-resolved phylogenetic trees with many nodes well supported by
 bootstrap analyses. Conclusion The reticulated phylogenetic hypothesis
 using the ITS1 region mainly supported the relationship between the
 species of Cassiinae established by traditional morphological methods. The
 ITS1 region showed a higher discrimination power and desirable
 characteristics as compared to ITS2 and ITS1 + 2, thereby concluding to be
 the locus of choice. Considering the complexity of the group and the
 underlying biological ambiguities, the results presented here are
 encouraging for developing DNA barcoding as a useful tool for resolving
 taxonomical challenges in corroboration with morphological framework.
description: AlignmentS1The aligned sequences matrix of ITS1.AlignmentS2The aligned sequences matrix of ITS2.AlignmentS3Concatenated aligned sequences matrix of ITS1+2.Figure S1Phylogenetic consensus tree obtained for Cassia, Senna, and Chamaecrista species based on nrITS datasets constructed using maximum likelihood algorithm.