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      Chloroplast genome structure and phylogenetic position of Calanthe sylvatica (Thou.) Lindl. (Orchidaceae)

      research-article
      a , b , a , a , b , a
      Mitochondrial DNA. Part B, Resources
      Taylor & Francis
      Calanthe sylvatica, Illumina sequencing, chloroplast genome, phylogenetic

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          Abstract

          Calanthe sylvatica plays an important role in horticulture and is undergoing the pressure of population decline. In this study, its complete chloroplast genome sequence was successfully obtained by the technology of Illumina sequencing. The whole chloroplast genome length was 158,828 bp with a typical quadripartite structure: one large single copy (LSC) region (87,277 bp), one small single copy (SSC) region (18,535 bp) and a pair of inverted repeats (IR) regions (26,508 bp). The GC content of this genome was 36.7%. The genome contained 118 genes consisting of 84 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic analysis indicated a close relationship between C. sylvatica and Calanthe triplicata.

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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            MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

            We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.
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              Automatic annotation of organellar genomes with DOGMA.

              The Dual Organellar GenoMe Annotator (DOGMA) automates the annotation of organellar (plant chloroplast and animal mitochondrial) genomes. It is a Web-based package that allows the use of BLAST searches against a custom database, and conservation of basepairing in the secondary structure of animal mitochondrial tRNAs to identify and annotate genes. DOGMA provides a graphical user interface for viewing and editing annotations. Annotations are stored on our password-protected server to enable repeated sessions of working on the same genome. Finished annotations can be extracted for direct submission to GenBank.
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                Author and article information

                Journal
                Mitochondrial DNA B Resour
                Mitochondrial DNA B Resour
                Mitochondrial DNA. Part B, Resources
                Taylor & Francis
                2380-2359
                18 July 2019
                2019
                : 4
                : 2
                : 2625-2626
                Affiliations
                [a ]Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Chenshan Botanical Garden , Shanghai, China;
                [b ]College of Life and Environmental Sciences, Shanghai Normal University , Shanghai, China
                Author notes
                CONTACT Kai Jiang jiangkai@ 123456csnbgsh.cn Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Chenshan Botanical Garden , Chenhua Road 3888, Shanghai201602, China
                Article
                1642157
                10.1080/23802359.2019.1642157
                7706738
                33365654
                84b593c7-5cbf-41fa-a21f-96e86657af7f
                © 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

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

                History
                Page count
                Figures: 1, Tables: 0, Pages: 2, Words: 914
                Categories
                Research Article
                Mitogenome Announcement

                calanthe sylvatica,illumina sequencing,chloroplast genome,phylogenetic

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