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      The complete chloroplast genome of Prunus japonica thunb.(Rosaceae), an ornamental and medicinal plant

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      Author(s): , , , ,
      Publication date (Electronic, pub):
      Publication date (Electronic, collection):
      Journal: Mitochondrial DNA. Part B, Resources
      Publisher: Taylor & Francis
      Keywords: : Prunus japonica, chloroplast genome, phylogenetic analysis

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          Abstract

          Prunus japonica is an ornamental and medicinal plant that is widely cultivated. The complete chloroplast genome of P. japonica was sequenced using Illumina Hiseq X Ten platform. The chloroplast genome was 158,080 bp in length, containing two short inverted repeat (IRa and IRb) regions of 26,385 bp, which was separated by a large single copy (LSC) region of 86,270 bp and a small single copy (SSC) region of 19,040 bp. The GC content of the whole chloroplast genome was 36.8%. The chloroplast DNA of P. japonica comprised 112 distinct genes, including 78 protein-coding genes, 4 ribosomal RNA genes and 30 transfer RNA genes. Phylogenetic analysis indicated that all species of Prunus formed a monophyletic group, P. japonica was closely related to P. hulimis.

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          Basic local alignment search tool.

          Stephen F Altschul, Warren Gish, Webb Miller … (1990)
          A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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            IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

            Lam-Tung Nguyen, Heiko Schmidt, Arndt von Haeseler … (2014)
            Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
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              SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

              Anton Bankevich, Sergey Nurk, Dmitry Antipov … (2012)
              The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.
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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 January 2021
                Publication date (Electronic, collection): 2021
                Volume: 6
                Issue: 1
                Pages: 112-114
                Affiliations
                National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences , Beijing, China
                Author notes
                CONTACT Jiahui Sun sunjh_2010@ 123456sina.com
                Qingjun Yuan yuanqingjun@ 123456icmm.ac.cn National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences , Beijing, China
                Author information
                https://orcid.org/0000-0002-4561-5258
                Article
                Publisher ID: 1848477
                DOI: 10.1080/23802359.2020.1848477
                PMC ID: 7819125
                PubMed ID: 33521281
                SO-VID: d92973e9-6d3f-4657-b542-f19f8f1b39e7
                Copyright © © 2021 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: 1193
                Categories
                Subject: Research Article
                Subject: Mitogenome Announcement

                Keywords: : prunus japonica,chloroplast genome,phylogenetic analysis
                Data availability:
                Keywords: : prunus japonica, chloroplast genome, phylogenetic analysis

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