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      The complete chloroplast genome sequence of Onosma paniculatum Bur. et Franch. (Boraginaceae), a medicinal plant in Yunnan and its adjacent regions

      a , a , b , c

      Mitochondrial DNA. Part B, Resources

      Taylor & Francis

      Onosma paniculatum, Boraginaceae, complete chloroplast genome, Illumina sequencing, phylogenetic analysis

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          Abstract

          Onosma paniculatum is a medicinal plant commonly used in Yunnan and its adjacent regions, China. In the present study, we sequenced the complete chloroplast (cp) genome sequence of O. paniculatum to investigate the phylogenetic relationship in the Tubiflorae. The total length of the chloroplast genome was 151,198 bp, with 37.4% overall GC content and exhibited typical quadripartite structure, a pair of IRs (inverted repeats) of 25,889 bp was separated by a small single copy (SSC) region of 17,274 bp and a large single copy (LSC) region of 82,146 bp. The cp genome was composed of 113 genes, including 79 protein coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic analysis indicated that Boraginaceae was closely related to Convolvulaceae and Solanaceae in Tubiflorae.

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          Most cited references 17

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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            MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

            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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              MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

              Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
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                Author and article information

                Journal
                Mitochondrial DNA B Resour
                Mitochondrial DNA B Resour
                Mitochondrial DNA. Part B, Resources
                Taylor & Francis
                2380-2359
                4 October 2019
                2019
                : 4
                : 2
                : 3330-3332
                Affiliations
                [a ]College of Pharmacy and Chemistry, Dali University , Dali, Yunnan, China;
                [b ]Institute of Materia Medica, Dali University , Dali, Yunnan, China;
                [c ]Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources , Yunnan, China
                Author notes
                CONTACT Dequan Zhang zhangdeq2008@ 123456126.com College of Pharmacy and Chemistry, Dali University , Dali671000, Yunnan, China
                Article
                1673230
                10.1080/23802359.2019.1673230
                7707209
                © 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

                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.

                Page count
                Figures: 1, Tables: 0, Pages: 3, Words: 1404
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                Research Article
                Mitogenome Announcement

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