Complete chloroplast genome sequence of medicinal plant <i>Potentilla lineata</i> Treviranus (Rosaceae) from Yunnan, China

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Abstract

Potentilla lineata Treviranus is a common medicinal plant distributed in the southwest of China. In this study, we sequenced the complete chloroplast genome sequence of P. lineata and investigated its phylogenetic relationship within Potentilla and related genera. The total length of the chloroplast genome is 156,985 bp. The genome exhibits a typical quadripartite structure containing a pair of IRs (inverted repeats) of 25,974 bp separated by a small single copy (SSC) region of 18,859 bp and a large single copy (LSC) region of 86,178 bp. The chloroplast genome contained 112 genes, including 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis indicates that Potentilla L. is a monophytic taxon that is sister to Potaninia Maxim. Potentilla lineata is closely related to P. centigrana Maxim in the present study. This study provides a reference for the phylogeny and species evolution of the genus Potentilla and related genera.

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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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MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

Fredrik Ronquist, Maxim Teslenko, Paul van der Mark … (2012)

Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.

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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 July 2021

Publication date (Electronic, collection): 2021

Volume: 6

Issue: 8

Pages: 2422-2424

Affiliations

[a ]College of Pharmacy, Dali University , Dali, China

[b ]Yunnan Key Laboratory of Screening and Research on Anti-pathogenic Plant Resources from Western Yunnan , Dali, China

Author notes

CONTACT Dequan Zhang zhangdeq2008@ 123456126.com College of Pharmacy, Dali University , Dali, Yunnan, 671003, China

Article

Publisher ID: 1951137

DOI: 10.1080/23802359.2021.1951137

PMC ID: 8291059

PubMed ID: 34350355

SO-VID: a118103b-d4b8-42b2-9cb1-7c5efe76f989

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This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Complete chloroplast genome sequence of medicinal plant Potentilla lineata Treviranus (Rosaceae) from Yunnan, China

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Genome Integrity

Most cited references 16

Trimmomatic: a flexible trimmer for Illumina sequence data

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

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

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