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      Phylogenomic insights into the Fascicularia-Ochagavia group (Bromelioideae, Bromeliaceae)

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          Abstract

          Ochagavia (four species) and Fascicularia (one species) form a well-supported clade of the early-diverging Bromelioideae. The two genera are morphologically similar, but they can be easily discerned on the basis of generative characters. Besides the species distributed on the Chilean mainland, the group includes O. elegans, endemic to the Robinson Crusoe Island of the Juan Fernández Islands. In previous molecular phylogenetic studies, O. elegans formed a sister clade to the remainder of Fascicularia and Ochagavia. A phylogenomic approach, including nearly complete and, in five cases, full plastomes (c. 160 kbp) and the nuclear rDNA cistron (c. 6 kbp), and scanning electron microscope (SEM) images of pollen were used to analyse relationships in the Fascicularia-Ochagavia group. Plastome and nuclear trees were largely congruent and supported previous phylogenetic analyses of O. elegans being sister to the remainder of the group. A divergent phylogenetic position was suggested for O. carnea using different organellar trees. SEM analysis of pollen supported the division of Fascicularia and Ochagavia. Evolutionary and taxonomic implications of our results are discussed.

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          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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            Fast gapped-read alignment with Bowtie 2.

            As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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              Is Open Access

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

              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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                Author and article information

                Contributors
                Journal
                Botanical Journal of the Linnean Society
                Oxford University Press (OUP)
                0024-4074
                1095-8339
                April 2020
                March 27 2020
                December 21 2019
                April 2020
                March 27 2020
                December 21 2019
                : 192
                : 4
                : 642-655
                Affiliations
                [1 ]Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
                [2 ]Department of Botany, Faculty of Science, Charles University, Praha, Czech Republic
                [3 ]Institute of Botany, Czech Academy of Sciences, Průhonice, Czech Republic
                [4 ]Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
                [5 ]Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
                Article
                10.1093/botlinnean/boz085
                74469101-02cd-4786-823f-f69a498b3a1d
                © 2019

                https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model

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