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      Complete chloroplast genome sequence of an ornamental grass Muhlenbergia capillaries (Poaceae: Chloridoideae)

      research-article
      Mitochondrial DNA. Part B, Resources
      Taylor & Francis
      Chloridoideae, chloroplast genome, relationship

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          Abstract

          Muhlenbergia capillaris (Lam.) Trin. is an ornamental grass belonging to the genus Muhlenbergia Schreb. in the family Poaceae. To better understand its phylogenetic relationship with respect to the other species in the tribe Chloridoideae, the first complete chloroplast genome of Muhlenbergia was determined. The complete chloroplast genome of Muhlenbergia capillaris is 134,907 bp in length, consisting of one large single-copy (LSC) region of 80,175 bp, one small single-copy (SSC) region of 12,706 bp, and a pair of inverted repeat (IR) regions of 21,013 bp. The overall GC content of the genome is 38.1%. Further, maximum likelihood phylogenetic analysis with TVM + F+R3 model was conducted using 28 complete plastomes of the Poaceae, which support close relationships among species of Muhlenbergia, Hilaria Kunth, Distichlis Raf., and Bouteloua Lag., followed by those of Tragus Haller.

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

          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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            GetOrganelle: a simple and fast pipeline for de novo assembly of a complete circular chloroplast genome using genome skimming data

            Background: Chloroplast genes and genomes are the most important genomic data for plant phylogeny and DNA barcoding. Since the rapid development of high throughput sequencing technologies, it is cheap to get the low coverage data of whole genome, which is enough to assemble a complete chloroplast genome. To date, there are many assembly processes/pipelines described to assemble a complete chloroplast genome. In this study, we reported a simple and fast procedure to assemble a circular chloroplast genome using GetOrganelle pipeline. Findings: The GetOrganelle pipeline consists of four steps: 1) recruiting plastid-like reads; 2) de novo assembly using SPAdes; 3) filtering plastid-like contigs; and 4) visualizing and editing de novo assembly graph. Of them, the first three steps can be fulfilled automatically just using a combined command; and the fourth step is to visualize and evaluate the assemblies. Of 57 tested species with public datasets, we directly reassembled the circular chloroplast genome in 47 species. The eight non-circular species having break points, which may be caused by mononucleotide or dinonucleotide repeats, or small reads pool. In addition, we successfully assembled the circular chloroplast genome for the other 903 species of angiosperms using this pipeline, representing 41 families and 358 genera. Conclusion: The GetOrganelle pipeline is an effective way for land plants to assemble the circular chloroplast genome, without needs for reference-guided scaffolding, gap filling nor start-end point closing. This pipeline can be also applied to assemble mitochondrial genomes and nuclear Ribosomal DNAs using genome skimming data.
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              Preservation of Plant Samples for DNA Restriction Endonuclease Analysis

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                Author and article information

                Journal
                Mitochondrial DNA B Resour
                Mitochondrial DNA B Resour
                Mitochondrial DNA. Part B, Resources
                Taylor & Francis
                2380-2359
                13 May 2020
                2020
                : 5
                : 3
                : 2074-2075
                Affiliations
                Yunnan Forestry Technological College , Kunming, Yunnan, China
                Author notes
                CONTACT Qi Wang wangqi3858@ 123456126.com Yunnan Forestry Technological College , Kunming, Yunnan, China
                Article
                1764403
                10.1080/23802359.2020.1764403
                7781977
                bbe46f26-8256-498a-88e3-1a5ddcf65422
                © 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

                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.

                History
                Page count
                Figures: 1, Tables: 0, Pages: 2, Words: 900
                Categories
                Research Article
                Mitogenome Announcement

                chloridoideae,chloroplast genome,relationship
                chloridoideae, chloroplast genome, relationship

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