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      The complete plastid genome sequence of Chloranthus fortunei (A. Gray) Solms-Laub. in Chloranthaceae

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      Author(s): a , b , a
      Publication date (Electronic, pub):
      Publication date (Electronic, collection):
      Journal: Mitochondrial DNA. Part B, Resources
      Publisher: Taylor & Francis
      Keywords: Chloranthus fortunei, Chloranthus, Chloranthaceae, plastid genome

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          Abstract

          Chloranthus fortunei (A. Gray) Solms-Laub. is a perennial herb in a basal angiosperm family Chloranthaceae. Here, we reported the complete plastid genome of C. fortunei using Illumina short-read data. The total genome size was 157,063 bp in length, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The gene content and order were consistent with previously reported Chloranthus plastid genomes. The overall GC content of the C. fortunei plastid genome was 39.0%. In the phylogenetic result, genus Chloranthus was monophyletic and divided into two subclades: C. japonicus+ C. angustifolius+ C. fortunei, and C. henryi+ C. spicatus+ C. erectus. Our phylogenetic result was consistent with previous phylogenetic studies, and was supported by a previously proposed infrageneric classification of the genus Chloranthus.

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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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            jModelTest 2: more models, new heuristics and parallel computing.

            Diego Darriba, Guillermo Taboada, Ramón Doallo … (2012)
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              RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.

              Alexandros Stamatakis (2006)
              RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical optimizations, a modification of the search algorithm, and the use of the GTR+CAT approximation as replacement for GTR+Gamma yield a program that is between 2.7 and 52 times faster than the previous version of RAxML. A large-scale performance comparison with GARLI, PHYML, IQPNNI and MrBayes on real data containing 1000 up to 6722 taxa shows that RAxML requires at least 5.6 times less main memory and yields better trees in similar times than the best competing program (GARLI) on datasets up to 2500 taxa. On datasets > or =4000 taxa it also runs 2-3 times faster than GARLI. RAxML has been parallelized with MPI to conduct parallel multiple bootstraps and inferences on distinct starting trees. The program has been used to compute ML trees on two of the largest alignments to date containing 25,057 (1463 bp) and 2182 (51,089 bp) taxa, respectively. icwww.epfl.ch/~stamatak
              Article 0 comments Cited 1506 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): 25 October 2022
                Publication date (Electronic, collection): 2022
                Publication date PMC-release: 25 October 2022
                Volume: 7
                Issue: 10
                Pages: 1829-1833
                Affiliations
                [a ]Department of Biological Sciences, Kangwon National University , Chuncheon, South Korea
                [b ]Plant Resources Division, National Institute of Biological Resources , Incheon, South Korea
                Author notes
                [*]

                Present address: Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, Seoul, South Korea

                CONTACT Ki-Oug Yoo yooko@ 123456kangwon.ac.kr Department of Biological Sciences, Kangwon National University , Chuncheon, Gangwon-do, South Korea
                Author information
                https://orcid.org/0000-0002-0172-0021
                https://orcid.org/0000-0002-2676-6878
                Article
                Publisher ID: 2132840
                DOI: 10.1080/23802359.2022.2132840
                PMC ID: 9621198
                PubMed ID: 36325282
                SO-VID: d12eaf49-d2ef-417b-952e-01650dc60a95
                Copyright © © 2022 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: 3, Tables: 0, Pages: 5, Words: 2660
                Categories
                Subject: Research Article
                Subject: Plastome Announcement

                Keywords: chloranthus fortunei,chloranthus,chloranthaceae,plastid genome
                Data availability:
                Keywords: chloranthus fortunei, chloranthus, chloranthaceae, plastid genome

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