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      • Record: found
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      The complete chloroplast genome sequence of a Chinese endemic plant Dendrobium hancockii Rolfe (Orchidaceae)

      research-article
      Author(s): a , b , a , b , a , b , a , b , a , b
      Publication date (Electronic, pub):
      Publication date (Electronic, collection):
      Journal: Mitochondrial DNA. Part B, Resources
      Publisher: Taylor & Francis
      Keywords: Dendrobium hancockii, chloroplast genome, phylogeny, sect. Dendrobium

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          Abstract

          Dendrobium hancockii Rolfe is a rare and endangered species endemic to China, with great medicinal value. Here, the first complete chloroplast genome sequence of D. hancockii was reported and characterized. The cpDNA exhibited the typical quadripartite structure of four parts: a long single-copy region, a short single-copy region and two inverted repeats. It encodes 106 genes, consisting of 72 unique protein-coding genes, 30 unique tRNA gene, and 4 unique rRNA genes. The phylogenetic analysis indicated that D. hancockii is basal-most species for the sect. Dendrobium.

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          RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

          Alexandros Stamatakis (2014)
          Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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            A rapid DNA isolation procedure for small quantities of fresh leaf tissue.

            JJ Doyle, JL Doyle, J. Doyle J. … (1987)
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              Automatic annotation of organellar genomes with DOGMA.

              Stacia K. Wyman, Robert K Jansen, Jeffrey Boore (2004)
              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.
              Article 0 comments Cited 857 times – based on 0 reviews     Review now
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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): 8 November 2019
                Publication date (Electronic, collection): 2019
                Volume: 4
                Issue: 2
                Pages: 3860-3861
                Affiliations
                [a ]College of Life Sciences, Nanjing Normal University , Nanjing, China;
                [b ]Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobium, Nanjing Normal Uniwersity , Nanjing, China
                Author notes
                [*]

                These authors contributed equally to this work.

                CONTACT Xiaoyu Ding dingxy@ 123456263.net College of Life Sciences, Nanjing Normal University , Jiangsu, Nanjing210046, China
                Article
                Publisher ID: 1687036
                DOI: 10.1080/23802359.2019.1687036
                PMC ID: 7707706
                SO-VID: 264e6653-86df-449a-8775-96ca3a539b96
                Copyright © © 2019 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 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: 992
                Categories
                Subject: Research Article
                Subject: Mitogenome Announcement

                Keywords: dendrobium hancockii,chloroplast genome,phylogeny,sect. dendrobium
                Data availability:
                Keywords: dendrobium hancockii, chloroplast genome, phylogeny, sect. dendrobium

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