Characterization of the complete chloroplast genome of  Ligusticum sinense , as a Chinese herb to treat toothache in China

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Abstract

Ligusticum sinense is a popular herb in Chinese medicine. The circular double-stranded complete chloroplast genome of L. sinense was 146,342 bp in length, exhibiting a typical quadripartite structure. It contained a large single-copy region (LSC) of 91,788 bp, a small single-copy region (SSC) of 17,618 bp and two identical inverted repeat (IR) regions of 18,468 bp each. The overall nucleotide composition of chloroplast genome sequence is: A (30.8%), T (31.6%), C (19.2%), G (19.4%) and the total G + C content of 38.6%. The chloroplast genome contained 127 genes, including 83 protein-coding genes, 36 transfer RNA genes and 8 ribosomal RNA genes were annotated. The total of 15 genes duplicated in one of the IR, including 6 tRNA, 4 rRNA, and 5 protein-coding genes. The ML phylogenetic tree indicated that L. sinense is closely related to L. tenuissimum in the phylogenetic relationship.

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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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MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

Sudhir Kumar, Glen Stecher, Michael KaWah Li … (2018)

The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.

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Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

Matthew Kearse, Richard Moir, Amy Wilson … (2012)

Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com

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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): 17 August 2020

Publication date (Electronic, collection): 2020

Volume: 5

Issue: 3

Pages: 3174-3175

Affiliations

[a ]Central South University Xiangya School of Stomatology , Changsha, Hunan, China

[b ]Traditional Chinese Medicine Department, The Second People’s Hospital of Datong , Datong, Shanxi, China

[c ]Department of Pain Management, The Third Medical Centre, Chinese PLA General Hospital , Beijing, China

[d ]The Molecular Pathology Lab, The Second People’s Hospital of Datong , Datong, Shanxi, China

Author notes

CONTACT Xin Zhao zhaoxin09018@ 123456163.com The Molecular Pathology Lab, The Second People’s Hospital of Datong , Datong, Shanxi, China;

Li-Kang Wang wlk0306@ 123456126.com Department of Pain Management, The Third Medical Centre, Chinese PLA General Hospital , Beijing, China

Article

Publisher ID: 1808103

DOI: 10.1080/23802359.2020.1808103

PMC ID: 7782014

PubMed ID: 33458101

SO-VID: eb0e1d5c-8e93-4dcc-8450-f41ab5f9cbe9

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.

Characterization of the complete chloroplast genome of Ligusticum sinense, as a Chinese herb to treat toothache in China

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Most cited references 8

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

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

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