Whole chloroplast genome sequence of a subtropical tree  Eriobotrya bengalensis  (Rosaceae)

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Abstract

Eriobotrya bengalensis (Roxb.) is a subtropical plant under the family Rosaceae with high economic and medicinal value. The whole chloroplast genome of E. bengalensis was sequenced to better understand its phylogenetic position relative to other Rosaceae species. The total length of the E. bengalensis chloroplast genome was 159,270 bp, which was composed of a large single-copy (LSC) region of 87,362 bp, a small single-copy (SSC) region of 19,184 bp, and a pair of inverted repeats (IRs) with a length of 26,362 bp separated by LSC and SSC. The total G + C content of the whole chloroplast genome was 36.7%. Phylogenetic analysis of maximum likelihood (TVM + F+R2) was completed using 15 complete chloroplast genomes of Rosaceae species. The results of phylogenetic analysis show that sisterhood exists in E. bengalensis with nine other species of Eriobotrya.

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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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Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs.

Jun-Bo Yang, De-Zhu Li, Hong-Tao Li (2014)

Chloroplast genomes supply indispensable information that helps improve the phylogenetic resolution and even as organelle-scale barcodes. Next-generation sequencing technologies have helped promote sequencing of complete chloroplast genomes, but compared with the number of angiosperms, relatively few chloroplast genomes have been sequenced. There are two major reasons for the paucity of completely sequenced chloroplast genomes: (i) massive amounts of fresh leaves are needed for chloroplast sequencing and (ii) there are considerable gaps in the sequenced chloroplast genomes of many plants because of the difficulty of isolating high-quality chloroplast DNA, preventing complete chloroplast genomes from being assembled. To overcome these obstacles, all known angiosperm chloroplast genomes available to date were analysed, and then we designed nine universal primer pairs corresponding to the highly conserved regions. Using these primers, angiosperm whole chloroplast genomes can be amplified using long-range PCR and sequenced using next-generation sequencing methods. The primers showed high universality, which was tested using 24 species representing major clades of angiosperms. To validate the functionality of the primers, eight species representing major groups of angiosperms, that is, early-diverging angiosperms, magnoliids, monocots, Saxifragales, fabids, malvids and asterids, were sequenced and assembled their complete chloroplast genomes. In our trials, only 100 mg of fresh leaves was used. The results show that the universal primer set provided an easy, effective and feasible approach for sequencing whole chloroplast genomes in angiosperms. The designed universal primer pairs provide a possibility to accelerate genome-scale data acquisition and will therefore magnify the phylogenetic resolution and species identification in angiosperms.

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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): 16 January 2020

Publication date (Electronic, collection): 2020

Volume: 5

Issue: 1

Pages: 697-698

Affiliations

[a ]South and Southeast Asia Joint R&D Center of Economic Forest Full Industry Chain, Southwest Forestry University , Kunming, China;

[b ]International Technologial Cooperation Base of High Effective Economic Forestry Cultirating, Southwest Forestry University , Kunming, China;

[c ]Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University , Kunming, China

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CONTACT Zhenghai Sun sunzhenghai1978@ 123456163.com South and Southeast Asia Joint R&D Center of Economic Forest Full Industry Chain, Southwest Forestry University , Kunming650224, China

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Publisher ID: 1714510

DOI: 10.1080/23802359.2020.1714510

PMC ID: 7748530

SO-VID: be1f2bbc-2313-4d90-8d9c-d380cfb2b8e2

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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.

Whole chloroplast genome sequence of a subtropical tree Eriobotrya bengalensis (Rosaceae)

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Most cited references 8

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

Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs.

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