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      Fern genomes elucidate land plant evolution and cyanobacterial symbioses

      research-article
      1 , 2 , , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 1 , 11 , 12 , 13 , 14 , 12 , 11 , 15 , 14 , 16 , 1 , 17 , 18 , 19 , 6 , 4 , 5 , 13 , 1 , 20 , 21 , 22 , 23 , 24 , 6 , 14 , 4 , 5 , 25 , 6 , 21 , 22 , 6 , 12 , 3 , 6 , 26 , 9
      Nature Plants
      Nature Publishing Group UK
      Plant symbiosis, Natural variation in plants, Phylogenetics, Comparative genomics, Genome evolution

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          Abstract

          Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns—one at the base of ‘core leptosporangiates’ and one specific to Azolla. One fern-specific gene that we identified, recently shown to confer high insect resistance, seems to have been derived from bacteria through horizontal gene transfer. Azolla coexists in a unique symbiosis with N 2-fixing cyanobacteria, and we demonstrate a clear pattern of cospeciation between the two partners. Furthermore, the Azolla genome lacks genes that are common to arbuscular mycorrhizal and root nodule symbioses, and we identify several putative transporter genes specific to Azolla–cyanobacterial symbiosis. These genomic resources will help in exploring the biotechnological potential of Azolla and address fundamental questions in the evolution of plant life.

          Abstract

          The genomes of two fern species, Azolla filiculoides and Salvinia cucullata, are reported and provide insights into fern-specific whole-genome duplications, fern-specific insect-resistant gene evolution and fern–cyanobacterial symbiosis.

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          Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

          We present an in silico approach for the reconstruction of complete mitochondrial genomes of non-model organisms directly from next-generation sequencing (NGS) data—mitochondrial baiting and iterative mapping (MITObim). The method is straightforward even if only (i) distantly related mitochondrial genomes or (ii) mitochondrial barcode sequences are available as starting-reference sequences or seeds, respectively. We demonstrate the efficiency of the approach in case studies using real NGS data sets of the two monogenean ectoparasites species Gyrodactylus thymalli and Gyrodactylus derjavinoides including their respective teleost hosts European grayling (Thymallus thymallus) and Rainbow trout (Oncorhynchus mykiss). MITObim appeared superior to existing tools in terms of accuracy, runtime and memory requirements and fully automatically recovered mitochondrial genomes exceeding 99.5% accuracy from total genomic DNA derived NGS data sets in <24 h using a standard desktop computer. The approach overcomes the limitations of traditional strategies for obtaining mitochondrial genomes for species with little or no mitochondrial sequence information at hand and represents a fast and highly efficient in silico alternative to laborious conventional strategies relying on initial long-range PCR. We furthermore demonstrate the applicability of MITObim for metagenomic/pooled data sets using simulated data. MITObim is an easy to use tool even for biologists with modest bioinformatics experience. The software is made available as open source pipeline under the MIT license at https://github.com/chrishah/MITObim.
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            tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence

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              LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

              Background Transposable elements are abundant in eukaryotic genomes and it is believed that they have a significant impact on the evolution of gene and chromosome structure. While there are several completed eukaryotic genome projects, there are only few high quality genome wide annotations of transposable elements. Therefore, there is a considerable demand for computational identification of transposable elements. LTR retrotransposons, an important subclass of transposable elements, are well suited for computational identification, as they contain long terminal repeats (LTRs). Results We have developed a software tool LTRharvest for the de novo detection of full length LTR retrotransposons in large sequence sets. LTRharvest efficiently delivers high quality annotations based on known LTR transposon features like length, distance, and sequence motifs. A quality validation of LTRharvest against a gold standard annotation for Saccharomyces cerevisae and Drosophila melanogaster shows a sensitivity of up to 90% and 97% and specificity of 100% and 72%, respectively. This is comparable or slightly better than annotations for previous software tools. The main advantage of LTRharvest over previous tools is (a) its ability to efficiently handle large datasets from finished or unfinished genome projects, (b) its flexibility in incorporating known sequence features into the prediction, and (c) its availability as an open source software. Conclusion LTRharvest is an efficient software tool delivering high quality annotation of LTR retrotransposons. It can, for example, process the largest human chromosome in approx. 8 minutes on a Linux PC with 4 GB of memory. Its flexibility and small space and run-time requirements makes LTRharvest a very competitive candidate for future LTR retrotransposon annotation projects. Moreover, the structured design and implementation and the availability as open source provides an excellent base for incorporating novel concepts to further improve prediction of LTR retrotransposons.
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                Author and article information

                Contributors
                fl329@cornell.edu
                Journal
                Nat Plants
                Nat Plants
                Nature Plants
                Nature Publishing Group UK (London )
                2055-0278
                2 July 2018
                2 July 2018
                2018
                : 4
                : 7
                : 460-472
                Affiliations
                [1 ]ISNI 000000041936877X, GRID grid.5386.8, Boyce Thompson Institute, ; Ithaca, NY USA
                [2 ]ISNI 000000041936877X, GRID grid.5386.8, Plant Biology Section, , Cornell University, ; Ithaca, NY USA
                [3 ]ISNI 0000000120346234, GRID grid.5477.1, Molecular Plant Physiology Department, , Utrecht University, ; Utrecht, the Netherlands
                [4 ]ISNI 0000 0001 2069 7798, GRID grid.5342.0, Bioinformatics Institute Ghent and Department of Plant Biotechnology and Bioinformatics, , Ghent University, ; Ghent, Belgium
                [5 ]ISNI 0000000104788040, GRID grid.11486.3a, VIB Center for Plant Systems Biology, ; Ghent, Belgium
                [6 ]ISNI 0000 0001 2034 1839, GRID grid.21155.32, BGI-Shenzhen, Beishan Industrial Zone, ; Shenzhen, China
                [7 ]ISNI 0000 0004 1936 8200, GRID grid.55602.34, Department of Biochemistry and Molecular Biology, , Dalhousie University, ; Halifax, Nova Scotia Canada
                [8 ]Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Castanet Tolosan, France
                [9 ]ISNI 0000 0004 1936 7961, GRID grid.26009.3d, Department of Biology, , Duke University, ; Durham, NC USA
                [10 ]ISNI 0000 0001 2176 9917, GRID grid.411327.2, Department of Plant Biochemistry, Cluster of Excellence on Plant Sciences, , Heinrich Heine University Düsseldorf, ; Dusseldorf, Germany
                [11 ]ISNI 0000 0001 2168 186X, GRID grid.134563.6, Department of Ecology and Evolutionary Biology, , University of Arizona, ; Tucson, AZ USA
                [12 ]ISNI 0000 0001 2292 8158, GRID grid.253559.d, Department of Biological Science, , California State University, ; Fullerton, CA USA
                [13 ]ISNI 0000 0004 1936 7910, GRID grid.1012.2, ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, , The University of Western Australia, ; Crawley, Western Australia Australia
                [14 ]ISNI 0000 0001 2097 4281, GRID grid.29857.31, Department of Biology, Huck Institutes of the Life Sciences, , Pennsylvania State University, ; University Park, PA USA
                [15 ]ISNI 0000 0001 0944 9128, GRID grid.7491.b, Faculty of Biology, , Bielefeld University, ; Bielefeld, Germany
                [16 ]ISNI 0000 0001 2176 9917, GRID grid.411327.2, Institute for Molecular Evolution, , Heinrich Heine University Düsseldorf, ; Dusseldorf, Germany
                [17 ]GRID grid.410768.c, Taiwan Forestry Research Institute, ; Taipei, Taiwan
                [18 ]ISNI 0000 0001 0660 6765, GRID grid.419498.9, Max Planck Genome Centre Cologne, , Max Planck Institute for Plant Breeding, ; Cologne, Germany
                [19 ]ISNI 0000 0001 2151 536X, GRID grid.26999.3d, Institute for Sustainable Agro-ecosystem Services, , University of Tokyo, ; Tokyo, Japan
                [20 ]ISNI 0000000120346234, GRID grid.5477.1, Geolab, Faculty of Geosciences, , Utrecht University, ; Utrecht, the Netherlands
                [21 ]ISNI 0000 0004 1936 9756, GRID grid.10253.35, Faculty of Biology, , University of Marburg, ; Marburg, Germany
                [22 ]ISNI 0000 0001 2185 8768, GRID grid.53857.3c, Department of Biology, , Utah State University, ; Logan, UT USA
                [23 ]ISNI 0000 0001 2181 7878, GRID grid.47840.3f, University Herbarium and Department of Integrative Biology, , University of California, ; Berkeley, CA USA
                [24 ]ISNI 0000 0000 9831 5270, GRID grid.266621.7, Department of Biology, , University of Louisiana, ; Lafayette, LA USA
                [25 ]ISNI 0000 0001 2107 2298, GRID grid.49697.35, Department of Biochemistry, Genetics and Microbiology, , University of Pretoria, ; Pretoria, South Africa
                [26 ]GRID grid.17089.37, Department of Biological Sciences, Department of Medicine, , University of Alberta, ; Edmonton, Alberta Canada
                Author information
                http://orcid.org/0000-0002-0076-0152
                http://orcid.org/0000-0003-3507-5195
                http://orcid.org/0000-0002-3388-3757
                http://orcid.org/0000-0001-5300-1216
                http://orcid.org/0000-0001-7173-1319
                http://orcid.org/0000-0002-5309-0527
                http://orcid.org/0000-0002-2038-8474
                http://orcid.org/0000-0003-3256-2940
                http://orcid.org/0000-0002-5341-136X
                http://orcid.org/0000-0002-0225-873X
                http://orcid.org/0000-0002-1629-9786
                http://orcid.org/0000-0002-6605-1770
                http://orcid.org/0000-0003-4327-3730
                http://orcid.org/0000-0002-8578-3387
                http://orcid.org/0000-0001-9668-2525
                http://orcid.org/0000-0001-6108-5560
                Article
                188
                10.1038/s41477-018-0188-8
                6786969
                29967517
                11ffb6aa-3ccf-45f4-bf62-cb2351851ded
                © The Author(s) 2018

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 9 February 2018
                : 24 May 2018
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                © The Author(s) 2018

                plant symbiosis,natural variation in plants,phylogenetics,comparative genomics,genome evolution

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