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      Characterization of the complete chloroplast genome of Lonicera macranthoides

      research-article
      a , a , b , a , a
      Mitochondrial DNA. Part B, Resources
      Taylor & Francis
      Chloroplast genome, Lonicera macranthoides, Caprifoliaceae, Phylogenetic analysis

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          Abstract

          Lonicera macranthoides is an important Chinese traditional medicine plant which is endemic in southwest China. The complete chloroplast genome from L. macranthoides is determined in this study. The genome size was 154,897 bp, containing a large single copy (LSC) region of 88,692 bp and a small single copy (SSC) region of 18,623 bp, which were separated by a pair of 23,786 bp inverted repeat (IR) regions. The plastome contained 130 genes, including 81 protein-coding genes (77 PCG species), eight ribosomal RNA genes (4 rRNA species), 39 tRNA genes (29 tRNA species) and two pseudognes. The most of gene species occurred as a single copy, while 13 gene species occurred in double copies, including all rRNA species, six tRNA species and three PCG species, and two tRNA genes occur in treble copies. Finally, phylogenetic analysis demonstrated that L. macranthoides is closely related to L. japonica, and genus Lonicera shows a closer relationship with Triostrum for the current data.

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          The Sequence Alignment/Map format and SAMtools

          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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            Fast and accurate short read alignment with Burrows–Wheeler transform

            Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk
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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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                Author and article information

                Journal
                Mitochondrial DNA B Resour
                Mitochondrial DNA B Resour
                Mitochondrial DNA. Part B, Resources
                Taylor & Francis
                2380-2359
                28 September 2018
                2018
                : 3
                : 2
                : 1000-1001
                Affiliations
                [a ]Special Key Laboratory of Microbial Resources and Drug Development from Higher Education Institution of Guizhou Province, Research Center for Medicine and Biology, Zunyi Medical University , Zunyi, China;
                [b ]Department of Gastroenterology, Affiliated Hospital, Zunyi Medical University , Zunyi, China
                Author notes
                CONTACT Qian Wang qianwang07@ 123456126.com Special Key Laboratory of Microbial Resources and Drug Development from Higher Education Institution of Guizhou Province, Research Center for Medicine and Biology, Zunyi Medical University , Zunyi563003, China
                Article
                1507643
                10.1080/23802359.2018.1507643
                7799602
                33474395
                9dd1071d-669b-4845-81f0-dc95a567745d
                © 2018 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.

                History
                Page count
                Figures: 1, Pages: 2, Words: 1362
                Categories
                Research Article
                Mitogenome Announcement

                chloroplast genome,lonicera macranthoides,caprifoliaceae,phylogenetic analysis

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