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      The complete chloroplast genome sequence of Cosmos bipinnatus, the first of the genu s Cosmos

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      a , a , a , b , a
      Mitochondrial DNA. Part B, Resources
      Taylor & Francis
      Cosmos bipinnatus, chloroplast genome, phylogeny

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          Abstract

          Cosmos bipinnatus has been used widely in traditional medicines. Here, we sequenced and assembled the complete chloroplast genome of C. bipinnatus. This genome is 150,356 bp in size with a pair of inverted repeats (IRs) of 25,082 bp, a large single-copy (LSC) region of 83,003 bp, and a small single-copy region (SSC) of 18,397 bp. It contains 112 unique genes, including 80 protein-coding, 4 rRNA, and 28 tRNA genes. The phylogenomic analysis showed the C. bipinnatus and species belonging to the Madieae, Millerieae, Heliantheae, and Eupatorieae tribes were clustered together. The availability of chloroplast genome provided valuable information for future conservation, taxonomy, evolution, and differentiation studies of C. bipinnatus.

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          RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

          Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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            NOVOPlasty: de novo assembly of organelle genomes from whole genome data

            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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              CPGAVAS2, an integrated plastome sequence annotator and analyzer

              Abstract We previously developed a web server CPGAVAS for annotation, visualization and GenBank submission of plastome sequences. Here, we upgrade the server into CPGAVAS2 to address the following challenges: (i) inaccurate annotation in the reference sequence likely causing the propagation of errors; (ii) difficulty in the annotation of small exons of genes petB, petD and rps16 and trans-splicing gene rps12; (iii) lack of annotation for other genome features and their visualization, such as repeat elements; and (iv) lack of modules for diversity analysis of plastomes. In particular, CPGAVAS2 provides two reference datasets for plastome annotation. The first dataset contains 43 plastomes whose annotation have been validated or corrected by RNA-seq data. The second one contains 2544 plastomes curated with sequence alignment. Two new algorithms are also implemented to correctly annotate small exons and trans-splicing genes. Tandem and dispersed repeats are identified, whose results are displayed on a circular map together with the annotated genes. DNA-seq and RNA-seq data can be uploaded for identification of single-nucleotide polymorphism sites and RNA-editing sites. The results of two case studies show that CPGAVAS2 annotates better than several other servers. CPGAVAS2 will likely become an indispensible tool for plastome research and can be accessed from http://www.herbalgenomics.org/cpgavas2.
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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
                22 November 2019
                2019
                : 4
                : 2
                : 4204-4206
                Affiliations
                [a ]Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing, P. R. China;
                [b ]Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Sciences , Enshi, Hubei, P. R. China
                Author notes
                [*]

                These authors have contributed equally to this work.

                CONTACT Chang Liu cliu6688@ 123456yahoo.com Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing, 100193, P. R. China
                Author information
                https://orcid.org/0000-0003-3879-7302
                Article
                1693298
                10.1080/23802359.2019.1693298
                7707777
                5c3a433e-d095-4e3c-94dc-dbea5a39166e
                © 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.

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                Page count
                Figures: 1, Tables: 0, Pages: 3, Words: 1243
                Categories
                Research Article
                Mitogenome Announcement

                cosmos bipinnatus,chloroplast genome,phylogeny
                cosmos bipinnatus, chloroplast genome, phylogeny

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