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      The establishment of the species-delimits and varietal-identities of the cultivated germplasm of Luffa acutangula and Luffa aegyptiaca in Sri Lanka using morphometric, organoleptic and phylogenetic approaches

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          Abstract

          Luffa acutangula and L. aegyptiaca are two vegetable species commonly found in South and South East Asia. L. acutangula is widely grown; however, L. aegyptiaca is considered as an underutilized crop. The species delimits, phylogenetic positions, and the varietal identities of L. acutangula and L. aegyptiaca in Sri Lanka are not known. Thus, in the present study, we aimed to establish the species delimits and varietal identities of L. acutangula and L. aegyptiaca varieties grown in Sri Lanka using morphometric, phylogenetic and organoleptic assessments. We assessed five varieties of L. acutangula and three varieties of L. aegyptiaca. The vegetative and reproductive data were collected for the morphometric analysis and DNA sequence polymorphism of the makers rbcL, trnH-psbA and ITS for the phylogenetic analysis. We also conducted an organoleptic assessment based on taste parameters; aroma, bitterness, color, texture, and overall preference using the dishes prepared according to the most common Sri Lankan recipe for Luffa. The variation of the vegetative and reproductive traits grouped L. acutangula varieties into two distinct clusters. The trnH-psbA polymorphism provided the basis for the species delimits of L. acutangula and L. aegyptiaca. The rbcL and ITS polymorphisms provided the basis for the identities of the varieties of L. aegyptiaca and L. acutangula respectively. In the phylogeny, the L. acutangula varieties of Sri Lanka formed a unique clade and the L. aegyptiaca varieties formed a reciprocal monophyletic group in comparison to worldwide L. aegyptiaca reported. The taste parameters aroma, texture, color, and overall preference were significantly different among the Luffa varieties. The L. aegyptiaca varieties received lower preference in the organoleptic assessment. The present study sets the species delimits, phylogenetic positions and the varietal identities of the cultivated germplasm of Luffa and revealed the distinct morphological and organoleptic properties of each variety.

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          SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information

          We present SequenceMatrix, software that is designed to facilitate the assembly and analysis of multi-gene datasets. Genes are concatenated by dragging and dropping FASTA, NEXUS, or TNT files with aligned sequences into the program window. A multi-gene dataset is concatenated and displayed in a spreadsheet; each sequence is represented by a cell that provides information on sequence length, number of indels, the number of ambiguous bases ("Ns"), and the availability of codon information. Alternatively, GenBank numbers for the sequences can be displayed and exported. Matrices with hundreds of genes and taxa can be concatenated within minutes and exported in TNT, NEXUS, or PHYLIP formats, preserving both character set and codon information for TNT and NEXUS files. SequenceMatrix also creates taxon sets listing taxa with a minimum number of characters or gene fragments, which helps assess preliminary datasets. Entire taxa, whole gene fragments, or individual sequences for a particular gene and species can be excluded from export. Data matrices can be re-split into their component genes and the gene fragments can be exported as individual gene files. SequenceMatrix also includes two tools that help to identify sequences that may have been compromised through laboratory contamination or data management error. One tool lists identical or near-identical sequences within genes, while the other compares the pairwise distance pattern of one gene against the pattern for all remaining genes combined. SequenceMatrix is Java-based and compatible with the Microsoft Windows, Apple MacOS X and Linux operating systems. The software is freely available from http://code.google.com/p/sequencematrix/. © The Willi Hennig Society 2010.
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            The general stochastic model of nucleotide substitution.

            DNA sequence evolution through nucleotide substitution may be assimilated to a stationary Markov process. The fundamental equations of the general model, with 12 independent substitution parameters, are used to obtain a formula which corrects the effect of multiple and parallel substitutions on the measure of evolutionary divergence between two homologous sequences. We show that only reversible models, with six independent parameters, allow the calculation of the substitution rates. Simulation experiments on DNA sequence evolution through nucleotide substitution call into question the effectiveness of the general model (and of any other more detailed description); nevertheless, the general model results are slightly superior to any of its particular cases.
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              A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region

              Background A useful DNA barcode requires sufficient sequence variation to distinguish between species and ease of application across a broad range of taxa. Discovery of a DNA barcode for land plants has been limited by intrinsically lower rates of sequence evolution in plant genomes than that observed in animals. This low rate has complicated the trade-off in finding a locus that is universal and readily sequenced and has sufficiently high sequence divergence at the species-level. Methodology/Principal Findings Here, a global plant DNA barcode system is evaluated by comparing universal application and degree of sequence divergence for nine putative barcode loci, including coding and non-coding regions, singly and in pairs across a phylogenetically diverse set of 48 genera (two species per genus). No single locus could discriminate among species in a pair in more than 79% of genera, whereas discrimination increased to nearly 88% when the non-coding trnH-psbA spacer was paired with one of three coding loci, including rbcL. In silico trials were conducted in which DNA sequences from GenBank were used to further evaluate the discriminatory power of a subset of these loci. These trials supported the earlier observation that trnH-psbA coupled with rbcL can correctly identify and discriminate among related species. Conclusions/Significance A combination of the non-coding trnH-psbA spacer region and a portion of the coding rbcL gene is recommended as a two-locus global land plant barcode that provides the necessary universality and species discrimination.
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                Author and article information

                Contributors
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: Writing – original draft
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: SoftwareRole: Writing – original draft
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: SoftwareRole: Writing – original draft
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: SoftwareRole: Writing – original draft
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: SoftwareRole: Writing – original draft
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: SoftwareRole: Writing – original draft
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: SoftwareRole: Writing – original draft
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: SoftwareRole: Writing – original draft
                Role: Data curationRole: Investigation
                Role: ConceptualizationRole: Funding acquisitionRole: Project administrationRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                9 April 2019
                2019
                : 14
                : 4
                : e0215176
                Affiliations
                [1 ] Regional Agriculture Research and Development Centre, Makandura, Gonawila, North Western Province, Sri Lanka
                [2 ] Postgraduate Institute of Science, University of Peradeniya, Peradeniya, Sri Lanka
                [3 ] Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, Peradeniya, Sri Lanka
                [4 ] Department of Plant, Soil and Microbial Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing, Michigan, United States of America
                Institute for Biological Research, SERBIA
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0002-5592-1742
                Article
                PONE-D-18-35357
                10.1371/journal.pone.0215176
                6456250
                30964918
                b8439d4a-9c3e-4e7e-94f1-9c894437c980
                © 2019 Kumari et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 9 January 2019
                : 27 March 2019
                Page count
                Figures: 7, Tables: 4, Pages: 22
                Funding
                The authors received no specific funding for this work.
                Categories
                Research Article
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Biology and Life Sciences
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Computer and Information Sciences
                Data Management
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Biology and Life Sciences
                Organisms
                Eukaryota
                Plants
                Fruits
                Biology and Life Sciences
                Plant Science
                Plant Anatomy
                Seeds
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Processes
                Speciation
                Species Delimitation
                People and places
                Geographical locations
                Asia
                Sri Lanka
                Research and Analysis Methods
                Database and Informatics Methods
                Bioinformatics
                Sequence Analysis
                Sequence Alignment
                Biology and Life Sciences
                Plant Science
                Plant Anatomy
                Leaves
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Artificial Gene Amplification and Extension
                Polymerase Chain Reaction
                Research and Analysis Methods
                Molecular Biology Techniques
                Artificial Gene Amplification and Extension
                Polymerase Chain Reaction
                Custom metadata
                All the sequence data have been submitted to the GenBank under the accession numbers: MK279335, MK279336, MK279337, MK279338, MK279339, MK279340, MK279341, MK279342, MK279343, MK279344, MK279345, MK279346, MK279347, MK279348, MK279349, MK279350, MK271063, MK271064, MK271065, MK271066, MK271067, MK271068, MK271069, MK271070. All the other relevant data are within the manuscript and Supporting Information files.

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