Complete chloroplast genome of <i>Isoetes hypsophila</i> (Isoetaceae), the Endangered quillwort in China

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Abstract

Isoetes hypsophila Hand.-Mazz. is an Endangered quillwort living in plateau wetlands in China. In the present study, the complete chloroplast genome of I. hypsophila was assembled. It is a circular form of 146,362 bp in length, comprising a pair of inverted repeat (IR) regions of 13,691 bp, a large single copy (LSC) of 91,741 bp, and a small single copy (SSC) of 27,239 bp. After annotation, a total of 135 genes were predicted, which are 84 encode proteins 37 tRNA and 8 rRNA. The phylogenetic analysis indicated that I. hypsophila clustered with a clade of I. sinensis, I. taiwanensis and I. yunguiensis with strong support value. The chloroplast genome will contribute to further research and conservation of I. hypsophila.

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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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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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Bandage: interactive visualization of de novo genome assemblies

Ryan Wick, Mark B. Schultz, Justin Zobel … (2015)

Summary: Although de novo assembly graphs contain assembled contigs (nodes), the connections between those contigs (edges) are difficult for users to access. Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections. Users can zoom in to specific areas of the graph and interact with it by moving nodes, adding labels, changing colors and extracting sequences. BLAST searches can be performed within the Bandage graphical user interface and the hits are displayed as highlights in the graph. By displaying connections between contigs, Bandage presents new possibilities for analyzing de novo assemblies that are not possible through investigation of contigs alone. Availability and implementation: Source code and binaries are freely available at https://github.com/rrwick/Bandage. Bandage is implemented in C++ and supported on Linux, OS X and Windows. A full feature list and screenshots are available at http://rrwick.github.io/Bandage. Contact: rrwick@gmail.com Supplementary information : Supplementary data are available at Bioinformatics online.

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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): 13 September 2021

Publication date (Electronic, collection): 2021

Publication date PMC-release: 13 September 2021

Volume: 6

Issue: 10

Pages: 2908-2909

Affiliations

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

[b ]Key Laboratory of Plant Biology in Colleges of Heilongjiang Province, Life Science and Technology College, Harbin Normal University , Harbin, Heilongjiang, China

[c ]College of Life Science, Shanghai Normal University , Shanghai, China

[d ]Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences , Shanghai, China

Author notes

CONTACT Yuehong Yan yan.yh@ 123456126.com National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen , 518114, Shenzhen, Guangdong, China

Baodong Liu 99bd@ 123456163.com Life Science and Technology College, Harbin Normal University , Harbin, 150025, Heilongjiang, China

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Yufeng Gu https://orcid.org/0000-0002-4089-3937

Article

Publisher ID: 1960216

DOI: 10.1080/23802359.2021.1960216

PMC ID: 8439236

SO-VID: 7b3a708c-c8f3-4ff4-9390-7ce73633e285

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.

Complete chloroplast genome of Isoetes hypsophila (Isoetaceae), the Endangered quillwort in China

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Most cited references 11

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

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

Bandage: interactive visualization of de novo genome assemblies

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