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      Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest

      research-article
      1 , , 2 , 3 , 1 , 4 , 5 , 6 , 7 , 4 , 4 , 4 , 8 , 3 , 9 , 4 , 10 , 4 , 11 , 3 , 4 , 12 , 13 , 5 , 14 , 9 , 15 , 5 , 4 , 16 , 17 , 18 , 19 , 4 , 17 , 4 , 20 , 21 , 22 , 23 , 24 , 5 , 7 , 4 , 5 , 1 , 25 , 4 , 26 , 6 , 27 , 3 , 10 , 1 , 28 , 29 , 30 , 15 , 6 , 4 , 12 , 31 ,
      BMC Genomics
      BioMed Central
      Brown marmorated stink bug genome, Pentatomid genomics, polyphagy, chemoreceptors, odorant binding proteins, opsins, cathepsins, xenobiotic detoxification, invasive species

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          Abstract

          Background

          Halyomorpha halys (Stål), the brown marmorated stink bug, is a highly invasive insect species due in part to its exceptionally high levels of polyphagy. This species is also a nuisance due to overwintering in human-made structures. It has caused significant agricultural losses in recent years along the Atlantic seaboard of North America and in continental Europe. Genomic resources will assist with determining the molecular basis for this species’ feeding and habitat traits, defining potential targets for pest management strategies.

          Results

          Analysis of the 1.15-Gb draft genome assembly has identified a wide variety of genetic elements underpinning the biological characteristics of this formidable pest species, encompassing the roles of sensory functions, digestion, immunity, detoxification and development, all of which likely support H. halys’ capacity for invasiveness. Many of the genes identified herein have potential for biomolecular pesticide applications.

          Conclusions

          Availability of the H. halys genome sequence will be useful for the development of environmentally friendly biomolecular pesticides to be applied in concert with more traditional, synthetic chemical-based controls.

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          Most cited references152

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          The genome of the model beetle and pest Tribolium castaneum.

          Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development. Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.
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            A new generation of homology search tools based on probabilistic inference.

            Many theoretical advances have been made in applying probabilistic inference methods to improve the power of sequence homology searches, yet the BLAST suite of programs is still the workhorse for most of the field. The main reason for this is practical: BLAST's programs are about 100-fold faster than the fastest competing implementations of probabilistic inference methods. I describe recent work on the HMMER software suite for protein sequence analysis, which implements probabilistic inference using profile hidden Markov models. Our aim in HMMER3 is to achieve BLAST's speed while further improving the power of probabilistic inference based methods. HMMER3 implements a new probabilistic model of local sequence alignment and a new heuristic acceleration algorithm. Combined with efficient vector-parallel implementations on modern processors, these improvements synergize. HMMER3 uses more powerful log-odds likelihood scores (scores summed over alignment uncertainty, rather than scoring a single optimal alignment); it calculates accurate expectation values (E-values) for those scores without simulation using a generalization of Karlin/Altschul theory; it computes posterior distributions over the ensemble of possible alignments and returns posterior probabilities (confidences) in each aligned residue; and it does all this at an overall speed comparable to BLAST. The HMMER project aims to usher in a new generation of more powerful homology search tools based on probabilistic inference methods.
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              JBrowse: a dynamic web platform for genome visualization and analysis

              Background JBrowse is a fast and full-featured genome browser built with JavaScript and HTML5. It is easily embedded into websites or apps but can also be served as a standalone web page. Results Overall improvements to speed and scalability are accompanied by specific enhancements that support complex interactive queries on large track sets. Analysis functions can readily be added using the plugin framework; most visual aspects of tracks can also be customized, along with clicks, mouseovers, menus, and popup boxes. JBrowse can also be used to browse local annotation files offline and to generate high-resolution figures for publication. Conclusions JBrowse is a mature web application suitable for genome visualization and analysis.
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                Author and article information

                Contributors
                michael.sparks2@usda.gov
                dawn.gundersen-rindal@usda.gov
                Journal
                BMC Genomics
                BMC Genomics
                BMC Genomics
                BioMed Central (London )
                1471-2164
                14 March 2020
                14 March 2020
                2020
                : 21
                : 227
                Affiliations
                [1 ]ISNI 0000 0004 0404 0958, GRID grid.463419.d, USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, ; Beltsville, MD 20705 USA
                [2 ]ISNI 0000 0004 0404 0958, GRID grid.463419.d, USDA-ARS San Joaquin Valley Agricultural Sciences Center, ; Parlier, CA 93648 USA
                [3 ]ISNI 0000 0001 2179 9593, GRID grid.24827.3b, Department of Biological Sciences, , University of Cincinnati, ; Cincinnati, OH 45221 USA
                [4 ]ISNI 0000 0001 2160 926X, GRID grid.39382.33, Department of Human and Molecular Genetics, , Human Genome Sequencing Center, Baylor College of Medicine, ; Houston, TX 77030 USA
                [5 ]ISNI 0000 0001 0941 7177, GRID grid.164295.d, Department of Entomology, , University of Maryland, ; College Park, MD 20742 USA
                [6 ]ISNI 0000 0004 1936 9174, GRID grid.16416.34, Department of Biology, , University of Rochester, ; Rochester, NY 14627 USA
                [7 ]ISNI 0000 0001 2113 2895, GRID grid.483014.a, USDA-ARS National Agricultural Library, ; Beltsville, MD 20705 USA
                [8 ]ISNI 0000 0001 2342 9668, GRID grid.14476.30, A.N. Belozersky Institute of Physico-Chemical Biology, , Moscow State University, ; Moscow, 119911 Russia
                [9 ]ISNI 0000 0001 1456 7807, GRID grid.254444.7, Department of Biological Sciences, , Wayne State University, ; Detroit, MI 48201 USA
                [10 ]ISNI 0000 0001 0694 4940, GRID grid.438526.e, Department of Biochemistry, , Virginia Tech, ; Blacksburg, VA 24061 USA
                [11 ]ISNI 0000 0001 0790 959X, GRID grid.411377.7, Department of Biology, , Indiana University, ; Bloomington, IN 47405 USA
                [12 ]ISNI 0000 0001 2223 3006, GRID grid.419765.8, Department of Genetic Medicine and Development, , University of Geneva Medical School and Swiss Institute of Bioinformatics, ; 1211 Geneva, Switzerland
                [13 ]ISNI 0000 0004 0635 685X, GRID grid.4834.b, Present address: Institute of Molecular Biology and Biotechnology, , Foundation for Research and Technology-Hellas, ; 73100 Heraklion, Crete Greece
                [14 ]ISNI 0000 0004 4687 2082, GRID grid.264756.4, Department of Entomology, , Texas A&M University, ; College Station, TX 77843 USA
                [15 ]ISNI 0000 0001 2112 1969, GRID grid.4391.f, Center for Genome Research and Biocomputing, , Oregon State University, ; Corvallis, OR 97331 USA
                [16 ]ISNI 0000 0004 0555 3608, GRID grid.454320.4, Center for Data-Intensive Biomedicine and Biotechnology, , Skolkovo Institute of Science and Technology, ; Skolkovo, 143025 Russia
                [17 ]ISNI 0000 0001 2297 5165, GRID grid.94365.3d, National Center for Biotechnology Information, National Library of Medicine, , National Institutes of Health, ; Bethesda, MD 20894 USA
                [18 ]GRID grid.418070.a, URGI, INRA, Université Paris-Saclay, ; 78026 Versailles, France
                [19 ]ISNI 0000 0001 2231 4551, GRID grid.184769.5, Environmental Genomics and Systems Biology Division, , Lawrence Berkeley National Laboratory, ; Berkeley, CA 94720 USA
                [20 ]ISNI 0000 0004 0386 9246, GRID grid.267301.1, Department of Microbiology, Immunology and Biochemistry, , University of Tennessee Health Science Center, ; Memphis, TN 38163 USA
                [21 ]USDA-ARS Center for Grain and Animal Health Research, Manhattan, KS 66502 USA
                [22 ]ISNI 0000 0000 8580 3777, GRID grid.6190.e, Developmental Biology, , Institute for Zoology: University of Cologne, ; 50674 Cologne, Germany
                [23 ]ISNI 0000 0000 8809 1613, GRID grid.7372.1, School of Life Sciences, , University of Warwick, ; Gibbet Hill Campus, Coventry, CV4 7AL United Kingdom
                [24 ]ISNI 0000 0004 0541 873X, GRID grid.460200.0, EMBRAPA Genetic Resources and Biotechnology, ; Brasília, DF 70770-901 Brazil
                [25 ]ISNI 0000 0004 1936 7689, GRID grid.59062.38, Larner College of Medicine, , The University of Vermont, ; Burlington, VT 05452 USA
                [26 ]ISNI 0000 0004 1936 9684, GRID grid.27860.3b, Present address: Earth BioGenome Project, , University of California, Davis, ; Davis, CA 95616 USA
                [27 ]Department of Entomology, University of Illinois, Urbana-Champaign, IL 61801 USA
                [28 ]Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
                [29 ]ISNI 0000 0000 9025 8099, GRID grid.239573.9, Division of Biomedical Informatics, and Division of Developmental Biology, , Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, ; Cincinnati, OH 45229 USA
                [30 ]ISNI 0000 0001 2179 9593, GRID grid.24827.3b, Department of Pediatrics, College of Medicine, , University of Cincinnati, ; Cincinnati, OH 45267 USA
                [31 ]USDA-ARS European Biological Control Laboratory, 34980 Montferrier-sur-Lez, France
                Author information
                http://orcid.org/0000-0001-6251-8559
                Article
                6510
                10.1186/s12864-020-6510-7
                7071726
                32171258
                af76114d-90de-4f87-bb33-fa51c95e2d50
                © The Author(s). 2020

                Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                History
                : 29 September 2019
                : 20 January 2020
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100000051, National Human Genome Research Institute;
                Award ID: U54 HG003273
                Funded by: FundRef http://dx.doi.org/10.13039/100000009, Foundation for the National Institutes of Health;
                Award ID: R01GM113230
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100001711, Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung;
                Award ID: PP00P3_170664
                Award ID: 31003A_143936
                Funded by: FundRef http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: IOS1456233
                Award ID: DEB1257053
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2020

                Genetics
                brown marmorated stink bug genome,pentatomid genomics,polyphagy,chemoreceptors,odorant binding proteins,opsins,cathepsins,xenobiotic detoxification,invasive species

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