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      Functional genomics and microbiome profiling of the Asian longhorned beetle ( Anoplophora glabripennis) reveal insights into the digestive physiology and nutritional ecology of wood feeding beetles

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          Abstract

          Background

          Wood-feeding beetles harbor an ecologically rich and taxonomically diverse assemblage of gut microbes that appear to promote survival in woody tissue, which is devoid of nitrogen and essential nutrients. Nevertheless, the contributions of these apparent symbionts to digestive physiology and nutritional ecology remain uncharacterized in most beetle lineages.

          Results

          Through parallel transcriptome profiling of beetle- and microbial- derived mRNAs, we demonstrate that the midgut microbiome of the Asian longhorned beetle ( Anoplophora glabripennis), a member of the beetle family Cerambycidae, is enriched in biosynthetic pathways for the synthesis of essential amino acids, vitamins, and sterols. Consequently, the midgut microbiome of A. glabripennis can provide essential nutrients that the beetle cannot obtain from its woody diet or synthesize itself. The beetle gut microbiota also produce their own suite of transcripts that can enhance lignin degradation, degrade hemicellulose, and ferment xylose and wood sugars. An abundance of cellulases from several glycoside hydrolase families are expressed endogenously by A. glabripennis, as well as transcripts that allow the beetle to convert microbe-synthesized essential amino acids into non-essential amino acids . A. glabripennis and its gut microbes likely collaborate to digest carbohydrates and convert released sugars and amino acid intermediates into essential nutrients otherwise lacking from their woody host plants.

          Conclusions

          The nutritional provisioning capabilities of the A. glabripennis gut microbiome may contribute to the beetles’ unusually broad host range. The presence of some of the same microbes in the guts of other Cerambycidae and other wood-feeding beetles suggests that partnerships with microbes may be a facilitator of evolutionary radiations in beetles, as in certain other groups of insects, allowing access to novel food sources through enhanced nutritional provisioning.

          Electronic supplementary material

          The online version of this article (doi:10.1186/1471-2164-15-1096) contains supplementary material, which is available to authorized users.

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          Most cited references63

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          Gene Ontology: tool for the unification of biology

          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            Profile hidden Markov models.

            S. Eddy (1998)
            The recent literature on profile hidden Markov model (profile HMM) methods and software is reviewed. Profile HMMs turn a multiple sequence alignment into a position-specific scoring system suitable for searching databases for remotely homologous sequences. Profile HMM analyses complement standard pairwise comparison methods for large-scale sequence analysis. Several software implementations and two large libraries of profile HMMs of common protein domains are available. HMM methods performed comparably to threading methods in the CASP2 structure prediction exercise.
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              The Pfam protein families database.

              Pfam is a large collection of protein families and domains. Over the past 2 years the number of families in Pfam has doubled and now stands at 6190 (version 10.0). Methodology improvements for searching the Pfam collection locally as well as via the web are described. Other recent innovations include modelling of discontinuous domains allowing Pfam domain definitions to be closer to those found in structure databases. Pfam is available on the web in the UK (http://www.sanger.ac.uk/Software/Pfam/), the USA (http://pfam.wustl.edu/), France (http://pfam.jouy.inra.fr/) and Sweden (http://Pfam.cgb.ki.se/).
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                Author and article information

                Contributors
                erin.scully@ars.usda.gov
                scott.geib@ars.usda.gov
                jec16@psu.edu
                mxt3@psu.edu
                dmckenna@memphis.edu
                kxh25@psu.edu
                Journal
                BMC Genomics
                BMC Genomics
                BMC Genomics
                BioMed Central (London )
                1471-2164
                12 December 2014
                2014
                : 15
                : 1
                : 1096
                Affiliations
                [ ]Intercollege Program in Genetics at the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Kragujevac, PA 16802 USA
                [ ]Department of Agronomy and Horticulture, University of Nebraska (UNL)-East Campus and USDA-ARS Grain, Forage, and Bioenergy Research Unit, Lincoln, NE 68583 USA
                [ ]Tropical Crop and Commodity Protection Research Unit, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, HI 96720 USA
                [ ]The Schatz Center for Tree Molecular Genetics, Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, Kragujevac, PA 16802 USA
                [ ]Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Kragujevac, PA 16802 USA
                [ ]Department of Biological Sciences, University of Memphis, Memphis, TN 38152 USA
                [ ]Department of Entomology and Center for Chemical Ecology, The Pennsylvania State University, 501 ASI Building, University Park, Kragujevac, PA 16802 USA
                Article
                6803
                10.1186/1471-2164-15-1096
                4299006
                25495900
                acc1f3dc-6aaa-48c6-94d1-3b2761b6d4de
                © Scully et al.; licensee BioMed Central Ltd. 2014

                This article is published under license to BioMed Central Ltd. 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 credited. 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.

                History
                : 5 August 2014
                : 24 November 2014
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2014

                Genetics
                metatranscriptome,cerambycidae,fusarium solani,nutrient-provisioning,amino acids,nitrogen recycling,xylose fermentation

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