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      Complete chloroplast genome sequence and phylogenetic analysis of Chimonobambusa sichuanensis (Bambusoideae)

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      Publication date (Electronic, pub):
      Publication date (Electronic, collection):
      Journal: Mitochondrial DNA. Part B, Resources
      Publisher: Taylor & Francis
      Keywords: Poaceae, Chimonobambusa sichuanensis, phylogeny, chloroplast genome

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          Abstract

          Chimonobambusa sichuanensis is an ornamental shrubby bamboo endemic to southern China. In this study, the complete chloroplast genome (cpDNA) sequence of Chimonobambusa sichuanensis was first reported. The cpDNA is 139,594 bp in length, including a small single-copy (SSC) region of 12,820 bp and a large single-copy (LSC) region of 83,196 bp, which were separated by a pair of inverted repeat (IR) regions of 21,789 bp. The genome contains 140 genes, consisting of 93 protein-coding genes, seven ribosomal RNA (rRNA) genes, and 40 transfer RNA (tRNA) genes. The phylogenetic analysis showed that C. sichuanensis is highly clustered in the Phyllostachys clade, sister to C. tumidissinoda.

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

          Alexandros Stamatakis (2014)
          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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            MrBayes 3: Bayesian phylogenetic inference under mixed models.

            Fredrik Ronquist, John P. Huelsenbeck (2003)
            MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types-e.g. morphological, nucleotide, and protein-and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.
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              The complete chloroplast genome sequence of Acidosasa gigantea (Bambusoideae: Arundinarieae): an ornamental bamboo species endemic to China

              Xiao Zheng, Meng Yang, Yu-long Ding … (2020)
              Abstract We, at first, fully characterized the complete chloroplast genome of the woody bamboo Acidosasa gigantea using genome skimming and focused on comparative analyses among Acidosasa and Indosasa. This newly sequenced chloroplast genome (GenBank NO. MN917206) is a typical circular structure with 139,711 bp in length and comprises of an 83,295 bp large single-copy (LSC) region, a 12,824 bp small single-copy (SSC) region, and a pair of 21,796 bp inverted repeats (IRs). The GC content of A. gigantea is 38.9% and the sequences contained 132 unique genes were successfully annotated, including 39 tRNA genes, 8 rRNA genes, and 85 protein-coding genes. Phylogenetic analysis shows that A. gigantea is highly clustered in the Arundinaria clade (clade VI) of Arundinarieae, a sister of the clade of Acidosasa purpurea and was not clustered on the same branch as Indosasa sinica. Therefore, it is more accurate to classify A. gigantea into Acidosasa.
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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): 11 March 2021
                Publication date (Electronic, collection): 2021
                Volume: 6
                Issue: 3
                Pages: 824-825
                Affiliations
                Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University , Nanchang, PR China
                Author notes
                CONTACT Fen Yu yufen@ 123456jxau.edu.cn Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University , Nanchang330045, PR China
                Author information
                https://orcid.org/0000-0003-0946-8614
                https://orcid.org/0000-0001-7230-8520
                Article
                Publisher ID: 1884017
                DOI: 10.1080/23802359.2021.1884017
                PMC ID: 7954435
                SO-VID: 28b007d5-04c6-4b8a-bd80-221266682f2c
                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: 2, Words: 1012
                Categories
                Subject: Research Article
                Subject: Mitogenome Announcement

                Keywords: poaceae,chimonobambusa sichuanensis,phylogeny,chloroplast genome
                Data availability:
                Keywords: poaceae, chimonobambusa sichuanensis, phylogeny, chloroplast genome

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