The complete chloroplast genome of an endangered species  Cymbidium mastersii  (Orchidaceae)

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Abstract

Cymbidium mastersii Griff. & Lindl. is an endangered orchid. In this study, we report the complete chloroplast (cp) genome sequence and the cp genome features of C. mastersii. The cp genome sequence of C. mastersii was 155,362 bp in length. It included one large single-copy region (LSC, 84,465 bp), one small single-copy region (SSC, 20,647 bp), and two inverted repeat regions (IRs, 25,125 bp). The cp genome encoded 130 genes, of which 107 were unique genes (80 protein-coding genes, 23 tRNAs, and 4 rRNAs). The maximum-likelihood phylogenetic analysis showed that C. mastersii was a sister of C. erythraeum and C. nanulum.

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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh, Daron Standley (2013)

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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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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Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

Christoph Hahn, Lutz Bachmann, Bastien Chevreux (2013)

We present an in silico approach for the reconstruction of complete mitochondrial genomes of non-model organisms directly from next-generation sequencing (NGS) data—mitochondrial baiting and iterative mapping (MITObim). The method is straightforward even if only (i) distantly related mitochondrial genomes or (ii) mitochondrial barcode sequences are available as starting-reference sequences or seeds, respectively. We demonstrate the efficiency of the approach in case studies using real NGS data sets of the two monogenean ectoparasites species Gyrodactylus thymalli and Gyrodactylus derjavinoides including their respective teleost hosts European grayling (Thymallus thymallus) and Rainbow trout (Oncorhynchus mykiss). MITObim appeared superior to existing tools in terms of accuracy, runtime and memory requirements and fully automatically recovered mitochondrial genomes exceeding 99.5% accuracy from total genomic DNA derived NGS data sets in <24 h using a standard desktop computer. The approach overcomes the limitations of traditional strategies for obtaining mitochondrial genomes for species with little or no mitochondrial sequence information at hand and represents a fast and highly efficient in silico alternative to laborious conventional strategies relying on initial long-range PCR. We furthermore demonstrate the applicability of MITObim for metagenomic/pooled data sets using simulated data. MITObim is an easy to use tool even for biologists with modest bioinformatics experience. The software is made available as open source pipeline under the MIT license at https://github.com/chrishah/MITObim.

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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): 19 September 2019

Publication date (Electronic, collection): 2019

Volume: 4

Issue: 2

Pages: 3068-3069

Affiliations

[a ]Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen , Shenzhen, China;

[b ]Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen , Shenzhen, China

Author notes

CONTACT Li-Qiang Li 5622520@ 123456qq.com Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen , Shenzhen, 518114, China

Article

Publisher ID: 1666047

DOI: 10.1080/23802359.2019.1666047

PMC ID: 7706812

PubMed ID: 33365859

SO-VID: 67fc4efc-312a-4c3b-be47-4d8da1bbc0ca

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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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Figures: 1, Tables: 0, Pages: 2, Words: 1288

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The complete chloroplast genome of an endangered species Cymbidium mastersii (Orchidaceae)

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Most cited references 18

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

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

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

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