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      Complete chloroplast genome of ornamental orchids Eulophia flava

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      Author(s): , , , ,
      Publication date (Electronic, pub):
      Publication date (Electronic, collection):
      Journal: Mitochondrial DNA. Part B, Resources
      Publisher: Taylor & Francis
      Keywords: Eulophia flava, ornamental orchids, chloroplast genome, phylogenomic tree

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          Abstract

          Eulophia flava (Lindl.) Hook.f. (Orchidaceae) is a high value ornamental plant especially for cutting flowers in China. In this paper, we reported and characterized the complete chloroplast genome sequence of E. flava by assembling from short reads generated by Illumina sequencing. Total chloroplast genome size was 148,903 bp, including inverted repeats (IRs) of 26,651 bp, separated by a large single copy (LSC) and a small single copy (SSC) of 84,465 and 13,132 bp, respectively. A total of 119 genes, including 36 tRNA, 8 rRNA, and 75 protein-coding genes, were identified. The GC content of E. flava is 36.8%. Phylogenetic analysis using the maximum-likelihood algorithm showed that E. flava is sister to a clade with one species in the genus Eulophia.

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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.
          Article 0 comments Cited 9171 times – based on 0 reviews     Review now
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            A rapid DNA isolation procedure for small quantities of fresh leaf tissue

            J. L. DOYLE, JJ, Doyle, JJ Doyle … (1987)
            Article 0 comments Cited 1087 times – based on 0 reviews     Review now
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              SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

              Ruibang Luo, Binghang Liu, Yinlong Xie … (2012)
              Background There is a rapidly increasing amount of de novo genome assembly using next-generation sequencing (NGS) short reads; however, several big challenges remain to be overcome in order for this to be efficient and accurate. SOAPdenovo has been successfully applied to assemble many published genomes, but it still needs improvement in continuity, accuracy and coverage, especially in repeat regions. Findings To overcome these challenges, we have developed its successor, SOAPdenovo2, which has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome. Conclusions Benchmark using the Assemblathon1 and GAGE datasets showed that SOAPdenovo2 greatly surpasses its predecessor SOAPdenovo and is competitive to other assemblers on both assembly length and accuracy. We also provide an updated assembly version of the 2008 Asian (YH) genome using SOAPdenovo2. Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp, respectively, which is 3-fold and 50-fold longer than the first published version. The genome coverage increased from 81.16% to 93.91%, and memory consumption was ~2/3 lower during the point of largest memory consumption.
              Article 0 comments Cited 868 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): 13 September 2019
                Publication date (Electronic, collection): 2019
                Volume: 4
                Issue: 2
                Pages: 2997-2998
                Affiliations
                Life Science and Technology School, Lingnan Normal University , Zhanjiang, China
                Author notes
                [*]

                These authors contributed equally to this work.

                CONTACT Ying Zhang Zhangyingred@ 123456lingnan.edu.cn Life Science and Technology School, Lingnan Normal University , Zhanjiang, GuangDong, PR, China
                Article
                Publisher ID: 1664946
                DOI: 10.1080/23802359.2019.1664946
                PMC ID: 7706861
                SO-VID: b1c0a255-475c-4fbd-9bf9-020ced733b7f
                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: 1077
                Categories
                Subject: Research Article
                Subject: Mitogenome Announcement

                Keywords: eulophia flava,ornamental orchids,chloroplast genome,phylogenomic tree
                Data availability:
                Keywords: eulophia flava, ornamental orchids, chloroplast genome, phylogenomic tree

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