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      • Record: found
      • Abstract: found
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      The complete mitochondrial genome of new species candidate of Rosa rugosa (Rosaceae)

      research-article
      Author(s): a , b , a , b , a , b , c , a , b
      Publication date (Electronic, pub):
      Publication date (Electronic, collection):
      Journal: Mitochondrial DNA. Part B, Resources
      Publisher: Taylor & Francis
      Keywords: Rosa angusta, mitochondrial genome, Rosa rugosa, Rosaceae, new species candidate

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          Abstract

          Completed mitochondrial genome of a new species candidate of Rosa rugosa, named as Rosa angusta, is 303,484 bp long. The overall GC content of this mitochondrial genome is 45.2%. It contains 52 genes covering 31 protein-coding genes, 17 tRNAs, and 3 rRNAs. In comparison to R. rugosa mitochondrial genome assembled from the public NGS raw reads, 124 SNPs and 769 INDELs were identified. Phylogenetic trees suggest that more Rosa mitochondrial genomes will be needed to understand phylogenetic relationship of the two Rosa species.

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          The Sequence Alignment/Map format and SAMtools

          Heng Li, Bob Handsaker, Alec Wysoker … (2009)
          Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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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.
              Article 0 comments Cited 9172 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): 29 September 2020
                Publication date (Electronic, collection): 2020
                Volume: 5
                Issue: 3
                Pages: 3435-3437
                Affiliations
                [a ]InfoBoss Inc ., Seoul, Republic of Korea
                [b ]InfoBoss Research Center , Seoul, Republic of Korea
                [c ]Baekdudaegan National Arboretum , Gyeongsangbuk-do, Korea
                Author notes
                [†]

                Present address:Garden Business Division in Sejong National Arboretum, Yeongmyeon-myeon, Sejong city, Republic of Korea.

                CONTACT Jongsun Park starflr@ 123456infoboss.co.kr InfoBoss Inc ., Seoul, Republic of Korea
                Author information
                https://orcid.org/0000-0003-0786-4701
                https://orcid.org/0000-0002-5349-9226
                https://orcid.org/0000-0002-6951-8102
                Article
                Publisher ID: 1821820
                DOI: 10.1080/23802359.2020.1821820
                PMC ID: 7782103
                PubMed ID: 33458196
                SO-VID: 57921fae-9304-4fd1-9b93-1ef1af5fc45a
                Copyright © © 2020 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: 1725
                Categories
                Subject: Research Article
                Subject: Mitogenome Announcement

                Keywords: rosa angusta,mitochondrial genome,rosa rugosa,rosaceae,new species candidate
                Data availability:
                Keywords: rosa angusta, mitochondrial genome, rosa rugosa, rosaceae, new species candidate

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