The complete chloroplast genome of desert spiny semi-shrub  Alhagi sparsifolia  (Fabaceae) from Central Asia

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Abstract

Alhagi sparsifolia is a sand-resistant subshrub and food resource for camels in the desert and semi-desert areas of Central Asia. In China, this is the olny Alhagi species and it is restricted in the Northwestern region. Its complete chloroplast genome was sequenced using the Illumina Hiseq X-Ten platform. The genome lacks an inverted repeat (IR) region, containing 74 protein-coding genes, 30 tRNAs genes, and four rRNAs. The overall GC content is 43.6%. Based on the chloroplast genome sequence, a maximum-likelihood (ML) tree was constructed along with its 15 taxa, indicating that A. sparsifolia belong to the tribe Hedysareae, which nested in IRLC group of the subfamily Papilionoideae (Fabaceae).

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Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger, Marc Lohse, Bjoern Usadel (2014)

Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.

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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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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen, Heiko Schmidt, Arndt von Haeseler … (2014)

Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.

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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): 30 July 2020

Publication date (Electronic, collection): 2020

Volume: 5

Issue: 3

Pages: 3098-3099

Affiliations

[a ]Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou, China

[b ]Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Nanning Normal University , Nanning, PR China

Author notes

CONTACT Lei Duan duanlei@ 123456scbg.ac.cn ;

Hong-Feng Chen h.f.chen@ 123456scbg.ac.cn Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou510650, China

Article

Publisher ID: 1797558

DOI: 10.1080/23802359.2020.1797558

PMC ID: 7782650

PubMed ID: 33458072

SO-VID: f54be076-65e1-4a89-bea8-676c83e91e74

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 complete chloroplast genome of desert spiny semi-shrub Alhagi sparsifolia (Fabaceae) from Central Asia

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Most cited references 15

Trimmomatic: a flexible trimmer for Illumina sequence data

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

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

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