Characterization and phylogenetic analysis of the complete chloroplast genome of <i>Saussurea sagittifolia</i> (Asteraceae, Cardueae)

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Abstract

The species of Saussurea sagittifolia Y. S. Chen & S. R. Yi belongs to the family Asteraceae (Cardueae). The complete chloroplast genome of S. sagittifolia was assembled and annotated for the first time in this study. The complete chloroplast genome of S. sagittifolia was 152,535 bp, including a large single-copy (LSC) region of 83,511 bp, a small single-copy (SSC) region of 18,632 bp, and a pair of inverted repeats (IRs) of 25,196 bp. The overall GC content of the chloroplast genome was 37.7%. The chloroplast genome encoded 131 genes, including 87 protein-coding genes, 36 tRNA genes, and eight rRNA genes. Phylogenetic analysis based on complete chloroplast sequences revealed that it related closely to Saussurea medusa.

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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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SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

Anton Bankevich, Sergey Nurk, Dmitry Antipov … (2012)

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

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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 November 2023

Publication date (Electronic, collection): 2023

Publication date PMC-release: 17 November 2023

Volume: 8

Issue: 11

Pages: 1268-1272

Affiliations

[a ]Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Ministry of Education , Chengdu, China

[b ]College of Life Sciences, Sichuan Normal University , Chengdu, China

[c ]Nanba High School , Dazhou, China

[d ]Sichuan Environmental Monitoring Center , Chengdu, China

[e ]Museum of Natural History/School of Life Sciences, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, Key Laboratory of Conservation Biology on Endangered Wildlife of Sichuan Province, Sichuan University , Chengdu, China

[f ]Sustainable Development Research Center of Resources and Environment of Western Sichuan, Sichuan Normal University , Chengdu, China

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Supplemental data for this article can be accessed online at https://doi.org/10.1080/23802359.2023.2281704.

CONTACT Liang Dou 547738389@ 123456qq.com Museum of Natural History/School of Life Sciences, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, Key Laboratory of Conservation Biology on Endangered Wildlife of Sichuan Province, Sichuan University , Chengdu, China

Zhi-Xi Fu fuzx2017@ 123456sicnu.edu.cn Key Laboratory of Land Resources Evaluation and Monitoring in Southwest, Sichuan Normal University, Ministry of Education , Chengdu, China

Article

Publisher ID: 2281704

DOI: 10.1080/23802359.2023.2281704

PMC ID: 10769533

SO-VID: dfae6843-ffb3-43cb-be10-2479a1e39309

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. The terms on which this article has been published allow the posting of the Accepted Manuscript in a repository by the author(s) or with their consent.

Characterization and phylogenetic analysis of the complete chloroplast genome of Saussurea sagittifolia (Asteraceae, Cardueae)

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Most cited references 25

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

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

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