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      The organellar genomes of Silvetia siliquosa (Fucales, Phaeophyceae) and comparative analyses of the brown algae

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          Abstract

          The brown alga Silvetia siliquosa (Tseng et Chang) Serrão, Cho, Boo & Brawly is endemic to the Yellow-Bohai Sea and southwestern Korea. It is increasingly endangered due to habitat loss and excessive collection. Here, we sequenced the mitochondrial (mt) and chloroplast (cp) genomes of S. siliquosa. De novo assembly showed that the mt-genome was 36,036 bp in length, including 38 protein-coding genes (PCGs), 26 tRNAs, and 3 rRNAs, and the cp-genome was 124,991 bp in length, containing 139 PCGs, 28 tRNAs, and 6 rRNAs. Gene composition, gene number, and gene order of the mt-genome and cp-genome were very similar to those of other species in Fucales. Phylogenetic analysis revealed a close genetic relationship between S. siliquosa and F. vesiculosus, which diverged approximately 8 Mya (5.7–11.0 Mya), corresponding to the Late Miocene (5.3–11.6 Ma). The synonymous substitution rate of mitochondrial genes of phaeophycean species was 1.4 times higher than that of chloroplast genes, but the cp-genomes were more structurally variable than the mt-genomes, with numerous gene losses and rearrangements among the different orders in Phaeophyceae. This study reports the mt- and cp-genomes of the endangered S. siliquosa and improves our understanding of its phylogenetic position in Phaeophyceae and of organellar genomic evolution in brown algae.

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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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            PAML 4: phylogenetic analysis by maximum likelihood.

            PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (d(N) and d(S)) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations. This note discusses some of the major applications of the package, which includes example data sets to demonstrate their use. The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at -- (http://abacus.gene.ucl.ac.uk/software/paml.html).
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              Clustal W and Clustal X version 2.0.

              The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems. The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/
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                Author and article information

                Contributors
                Role: Writing – original draft
                Role: InvestigationRole: Resources
                Role: Software
                Role: Writing – review & editing
                Role: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS One
                plos
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                16 June 2022
                2022
                : 17
                : 6
                : e0269631
                Affiliations
                [1 ] CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
                [2 ] Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
                [3 ] University of Chinese Academy of Sciences, Beijing, China
                [4 ] Faculty of Biological Science and Institute for Environmental Science, Wonkwang University, Iksan, Korea
                Saint Mary’s University, CANADA
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                https://orcid.org/0000-0001-5179-5956
                Article
                PONE-D-21-32930
                10.1371/journal.pone.0269631
                9202911
                28e197d8-2a59-4fcd-8f47-e79e098e5f6c
                © 2022 Liang et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 14 October 2021
                : 24 May 2022
                Page count
                Figures: 6, Tables: 2, Pages: 17
                Funding
                Funded by: Strategic Priority Research Program of Chinese Academy of Sciences
                Award ID: XDB42030203, XDB42040106, XDA19060102
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 31971395, 41761144057
                Award Recipient :
                This research was supported by the Strategic Priority Research Program of Chinese Academy of Sciences (XDB42030203, XDB42040106, XDA19060102) (received by DD) and the National Natural Science Foundation of China (Nos. 31971395, 41761144057) (received by Z-MH).
                Categories
                Research Article
                Biology and Life Sciences
                Organisms
                Eukaryota
                Plants
                Algae
                Biology and Life Sciences
                Genetics
                Genomics
                Biology and Life Sciences
                Biochemistry
                Bioenergetics
                Energy-Producing Organelles
                Mitochondria
                Biology and Life Sciences
                Cell Biology
                Cellular Structures and Organelles
                Energy-Producing Organelles
                Mitochondria
                Biology and Life Sciences
                Cell Biology
                Cellular Structures and Organelles
                Chloroplasts
                Biology and Life Sciences
                Cell Biology
                Plant Cell Biology
                Chloroplasts
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                Engineering and Technology
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                Biology and Life Sciences
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                Biology and Life Sciences
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                Biology and Life Sciences
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                Custom metadata
                The datasets analysed during the current study are available in the National Center for Biotechnology Information, and the GenBank accession numbers of the mt-genome and cp-genome of S. siliquosa are MW485980 and MW485976, respectively. The raw reads of Silvetia siliquosa organelle genomes have been deposited in the NCBI Sequence Read Archive under the BioProject number PRJNA824893, Sequence Read Archive accession number of mitochondrial and chloroplast genomes are SAMN27488512 and SAMN27488513, respectively.

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