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      The complete chloroplast genome of Cerasus dictyoneura, an ornamental plant of China

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      Author(s): a , b , b , a , b
      Publication date (Electronic, pub):
      Publication date (Electronic, collection):
      Journal: Mitochondrial DNA. Part B, Resources
      Publisher: Taylor & Francis
      Keywords: Cerasus dictyoneura, chloroplast genome, Illumina sequencing, phylogenetic analysis

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          Abstract

          The complete cp genome of Cerasus dictyoneura was 158,084 bp in length, consisting of a LSC of 86,275 bp and a SSC of 19,039 bp, which were separated by a pair of 26,385 bp IRs. The genome contained 131 genes, including 86 proteincoding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content is 36.7%, while the corresponding values of the LSC, SSC, and IR regions are 34.6, 29.5, and 42.6%, respectively. Furthermore, phylogenetic analysis based on 16 complete cp genome sequences indicated that C. dictyoneura is within Eurosids I.

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          MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

          Sudhir Kumar, Glen Stecher, Koichiro Tamura (2016)
          We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
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            NOVOPlasty: de novo assembly of organelle genomes from whole genome data

            Nicolas Dierckxsens, Patrick Mardulyn, Guillaume Smits (2016)
            Abstract The evolution in next-generation sequencing (NGS) technology has led to the development of many different assembly algorithms, but few of them focus on assembling the organelle genomes. These genomes are used in phylogenetic studies, food identification and are the most deposited eukaryotic genomes in GenBank. Producing organelle genome assembly from whole genome sequencing (WGS) data would be the most accurate and least laborious approach, but a tool specifically designed for this task is lacking. We developed a seed-and-extend algorithm that assembles organelle genomes from whole genome sequencing (WGS) data, starting from a related or distant single seed sequence. The algorithm has been tested on several new (Gonioctena intermedia and Avicennia marina) and public (Arabidopsis thaliana and Oryza sativa) whole genome Illumina data sets where it outperforms known assemblers in assembly accuracy and coverage. In our benchmark, NOVOPlasty assembled all tested circular genomes in less than 30 min with a maximum memory requirement of 16 GB and an accuracy over 99.99%. In conclusion, NOVOPlasty is the sole de novo assembler that provides a fast and straightforward extraction of the extranuclear genomes from WGS data in one circular high quality contig. The software is open source and can be downloaded at https://github.com/ndierckx/NOVOPlasty.
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              A rapid DNA isolation procedure for small quantities of fresh leaf tissue.

              JJ Doyle, JL Doyle, J. Doyle J. … (1987)
              Article 0 comments Cited 1092 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): 7 October 2019
                Publication date (Electronic, collection): 2019
                Volume: 4
                Issue: 2
                Pages: 3383-3385
                Affiliations
                [a ]State Key Laboratory of Seeding Bioengineering, Ningxia Forestry Institute , Yinchuan, Ningxia, China;
                [b ]School of Agriculture, Ningxia University , Yinchuan, Ningxia, China
                Author notes
                CONTACT Ying Tian tianying_1982@ 123456126.com State Key Laboratory of Seeding Bioengineering, Ningxia Forestry Institute , 1350 Qinghe south Road, Yinchuan 750004, Ningxia, China
                Article
                Publisher ID: 1673236
                DOI: 10.1080/23802359.2019.1673236
                PMC ID: 7707308
                PubMed ID: 33366004
                SO-VID: 3eb61d5d-3d34-4dcd-890b-c7013112a92f
                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: 3, Words: 953
                Categories
                Subject: Research Article
                Subject: Mitogenome Announcement

                Keywords: cerasus dictyoneura,chloroplast genome,illumina sequencing,phylogenetic analysis
                Data availability:
                Keywords: cerasus dictyoneura, chloroplast genome, illumina sequencing, phylogenetic analysis

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