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      Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum

      research-article
      1 , 2 , 3 , , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 9 , 12 , 13 , 7 , 8 , 9 , 14 , 15 , 10 , 9 , 16 , 15 , 12 , 14 , 17 , 1 , 18 , 3 , 19 , 9 , 6 , 9 , 15 , 19 , 19 , 14 , 15 , 16 , 20 , 7 , 15 , 21 , 10 , 7 , 4 , 5 , 1 , 2 , 7 , 8 , 9 ,
      BMC Genomics
      BioMed Central
      Parasitoid wasp, Aphid host, Aphidius ervi, Lysiphlebus fabarum, GC content, de novo genome assembly, DNA methylation loss, Chemosensory genes, Venom proteins, Toll and Imd pathways

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          Abstract

          Background

          Parasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biological control. Their success depends on adapting to develop inside aphids and overcoming both host aphid defenses and their protective endosymbionts.

          Results

          We present the de novo genome assemblies, detailed annotation, and comparative analysis of two closely related parasitoid wasps that target pest aphids: Aphidius ervi and Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae) . The genomes are small (139 and 141 Mbp) and the most AT-rich reported thus far for any arthropod (GC content: 25.8 and 23.8%). This nucleotide bias is accompanied by skewed codon usage and is stronger in genes with adult-biased expression. AT-richness may be the consequence of reduced genome size, a near absence of DNA methylation, and energy efficiency. We identify missing desaturase genes, whose absence may underlie mimicry in the cuticular hydrocarbon profile of L. fabarum. We highlight key gene groups including those underlying venom composition, chemosensory perception, and sex determination, as well as potential losses in immune pathway genes.

          Conclusions

          These findings are of fundamental interest for insect evolution and biological control applications. They provide a strong foundation for further functional studies into coevolution between parasitoids and their hosts. Both genomes are available at https://bipaa.genouest.org.

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          Most cited references144

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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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            • Record: found
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            • Article: not found

            A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data.

            Heng Li (2011)
            Most existing methods for DNA sequence analysis rely on accurate sequences or genotypes. However, in applications of the next-generation sequencing (NGS), accurate genotypes may not be easily obtained (e.g. multi-sample low-coverage sequencing or somatic mutation discovery). These applications press for the development of new methods for analyzing sequence data with uncertainty. We present a statistical framework for calling SNPs, discovering somatic mutations, inferring population genetical parameters and performing association tests directly based on sequencing data without explicit genotyping or linkage-based imputation. On real data, we demonstrate that our method achieves comparable accuracy to alternative methods for estimating site allele count, for inferring allele frequency spectrum and for association mapping. We also highlight the necessity of using symmetric datasets for finding somatic mutations and confirm that for discovering rare events, mismapping is frequently the leading source of errors. http://samtools.sourceforge.net. hengli@broadinstitute.org.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              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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                Author and article information

                Contributors
                alicebdennis@gmail.com
                gadauj@uni-muenster.de
                Journal
                BMC Genomics
                BMC Genomics
                BMC Genomics
                BioMed Central (London )
                1471-2164
                29 May 2020
                29 May 2020
                2020
                : 21
                : 376
                Affiliations
                [1 ]GRID grid.418656.8, ISNI 0000 0001 1551 0562, Department of Aquatic Ecology, , Eawag, ; 8600 Dübendorf, Switzerland
                [2 ]GRID grid.5801.c, ISNI 0000 0001 2156 2780, Institute of Integrative Biology, , ETH Zürich, ; 8092 Zürich, Switzerland
                [3 ]GRID grid.11348.3f, ISNI 0000 0001 0942 1117, Institute of Biochemistry and Biology, , University of Potsdam, ; 14476 Potsdam, Germany
                [4 ]GRID grid.10999.38, ISNI 0000 0001 0036 2536, Instituto de Ciencias Biológicas, , Universidad de Talca, ; Talca, Chile
                [5 ]GRID grid.10999.38, ISNI 0000 0001 0036 2536, Centre for Molecular and Functional Ecology in Agroecosystems, , Universidad de Talca, ; Talca, Chile
                [6 ]GRID grid.10999.38, ISNI 0000 0001 0036 2536, Laboratorio de Control Biológico, Instituto de Ciencias Biológicas, , Universidad de Talca, ; Talca, Chile
                [7 ]GRID grid.462490.d, ISNI 0000 0004 0556 944X, IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, ; 35650 Le Rheu, France
                [8 ]GRID grid.420225.3, ISNI 0000 0001 2298 7270, Université de Rennes 1, INRIA, CNRS, IRISA, ; 35000 Rennes, France
                [9 ]GRID grid.5949.1, ISNI 0000 0001 2172 9288, Institute for Evolution and Biodiversity, , Universität Münster, ; Münster, Germany
                [10 ]GRID grid.9851.5, ISNI 0000 0001 2165 4204, Department of Ecology and Evolution, , Université de Lausanne, ; 1015 Lausanne, Switzerland
                [11 ]GRID grid.6190.e, ISNI 0000 0000 8580 3777, Institute of Zoology, , Universität zu Köln, ; 50674 Köln, Germany
                [12 ]GRID grid.4830.f, ISNI 0000 0004 0407 1981, Groningen Institute for Evolutionary Life Sciences, , University of Groningen, ; Groningen, The Netherlands
                [13 ]GRID grid.5399.6, ISNI 0000 0001 2176 4817, Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, PINT, PFNT, ; Marseille, France
                [14 ]GRID grid.47840.3f, ISNI 0000 0001 2181 7878, Department of Environmental Science, Policy, & Management, , University of California, Berkeley, ; Berkeley, CA 94720 USA
                [15 ]GRID grid.4444.0, ISNI 0000 0001 2112 9282, Université Côte d’Azur, INRAE, CNRS, ISA, ; Sophia Antipolis, France
                [16 ]GRID grid.7367.5, ISNI 0000000119391302, Department of Sciences, , University of Basilicata, ; 85100 Potenza, Italy
                [17 ]GRID grid.256302.0, ISNI 0000 0001 0657 525X, Department of Biology, , Georgia Southern University, ; Statesboro, GA 30460 USA
                [18 ]GRID grid.5801.c, ISNI 0000 0001 2156 2780, Department of Environmental Systems Sciences, , D-USYS, ETH Zürich, ; Zürich, Switzerland
                [19 ]GRID grid.4444.0, ISNI 0000 0001 2112 9282, INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université Paris Diderot, Institute of Ecology and Environmental Sciences of Paris, iEES-Paris, ; F-78000 Versailles, France
                [20 ]GRID grid.255360.7, ISNI 0000 0001 1960 0522, Department of Biology, , Earlham College, ; Richmond, IN 47374 USA
                [21 ]GRID grid.418160.a, ISNI 0000 0004 0491 7131, Department of Entomology, , Max Planck Institute for Chemical Ecology, ; Jena, Germany
                Author information
                http://orcid.org/0000-0003-0948-9845
                Article
                6764
                10.1186/s12864-020-6764-0
                7257214
                32471448
                8006ab36-37fe-4591-9c71-28f49b918a76
                © 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
                : 16 January 2020
                : 30 April 2020
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100002850, Fondo Nacional de Desarrollo Científico y Tecnológico;
                Award ID: 1130483 and 1170943
                Funded by: FundRef http://dx.doi.org/10.13039/501100001665, Agence Nationale de la Recherche;
                Award ID: ANR-11-LABX-0028-01
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100001711, Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung;
                Award ID: PP00P3_123376
                Award ID: PP00P3_146341
                Award ID: PP00P3_170627
                Award Recipient :
                Funded by: Deutsches Forschungsgemeinschaft
                Award ID: GA 661/4-1
                Award Recipient :
                Funded by: Deutsche Forschungsgemeinschaft
                Award ID: 1554/3-1
                Award Recipient :
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2020

                Genetics
                parasitoid wasp,aphid host,aphidius ervi,lysiphlebus fabarum,gc content,de novo genome assembly,dna methylation loss,chemosensory genes,venom proteins,toll and imd pathways

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