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      The complete chloroplast genome of Vitex trifolia L. (Lamiaceae)

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          Abstract

          The three-leaved chaste tree ( Vitex trifolia) is a medicinal and ornamental plant widely distributed from East Africa to the Pacific but has no complete chloroplast genome sequence. We assembled and characterized the V. trifolia accession from the germplasm collection of the Institute of Crop Science, University of the Philippines Los Baños. The complete plastome sequence is 154,444-bp long with 131 coding genes comprising 87 mRNA genes, 36 tRNA genes, and 8 rRNA genes. A phylogenetic analysis of the assembled genome, together with nine other Lamiaceae species, identified V. rotundifolia as its closest relative with available complete cpDNA sequence. The clustering also supports the genotypic similarity of the species belonging to trifolia group of the genus Vitex.

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          Kazutaka Katoh, Daron Standley (2013)
          We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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            MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

            Sudhir Kumar, Glen Stecher, Michael KaWah Li … (2018)
            The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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              GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes

              Jian-Jun Jin, Wen-Bin Yu, Jun-Bo Yang … (2020)
              GetOrganelle is a state-of-the-art toolkit to accurately assemble organelle genomes from whole genome sequencing data. It recruits organelle-associated reads using a modified “baiting and iterative mapping” approach, conducts de novo assembly, filters and disentangles the assembly graph, and produces all possible configurations of circular organelle genomes. For 50 published plant datasets, we are able to reassemble the circular plastomes from 47 datasets using GetOrganelle. GetOrganelle assemblies are more accurate than published and/or NOVOPlasty-reassembled plastomes as assessed by mapping. We also assemble complete mitochondrial genomes using GetOrganelle. GetOrganelle is freely released under a GPL-3 license (https://github.com/Kinggerm/GetOrganelle).
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                Author and article information

                Journal
                Journal ID (nlm-ta): Mitochondrial DNA B Resour
                Journal ID (iso-abbrev): Mitochondrial DNA B Resour
                Title: Mitochondrial DNA. Part B, Resources
                Publisher: Taylor & Francis
                ISSN (Electronic): 2380-2359
                Publication date (Electronic, pub): 18 July 2022
                Publication date (Electronic, collection): 2022
                Publication date PMC-release: 18 July 2022
                Volume: 7
                Issue: 7
                Pages: 1316-1318
                Affiliations
                [a ]Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños , Laguna, Philippines
                [b ]Institute of Food Science, College of Agriculture and Food Science, University of the Philippines Los Baños , Laguna, Philippines
                [c ]Agricultural Systems Institute, College of Agriculture and Food Science, University of the Philippines Los Baños , Laguna, Philippines
                Author notes
                CONTACT Renerio P. Gentallan Jr. rpgentallan@ 123456up.edu.ph Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños , Laguna, Philippines
                Author information
                https://orcid.org/0000-0002-6436-7878
                Article
                Publisher ID: 2097027
                DOI: 10.1080/23802359.2022.2097027
                PMC ID: 9295813
                PubMed ID: 35866139
                SO-VID: 4e942bb8-cbbc-488e-8b69-dc4b70b9aa42
                Copyright © © 2022 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Page count
                Figures: 1, Tables: 0, Pages: 3, Words: 1854
                Categories
                Subject: Research Article
                Subject: Plastome Announcement

                Keywords: verbenaceae,viticoideae,cpdna,medicinal plant,three-leaved chaste tree
                Data availability:
                Keywords: verbenaceae, viticoideae, cpdna, medicinal plant, three-leaved chaste tree

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