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      Large-scale gene discovery in the pea aphid Acyrthosiphon pisum (Hemiptera)

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          Abstract

          A large-scale sequencing analysis of the Hemiptera Acyrthosiphon pisumexpressed sequence tags corresponding to about 12,000 unique transcripts is described, along with an in silico profiling analysis that identifies 135 aphid tissue-specific transcripts.

          Abstract

          Aphids are the leading pests in agricultural crops. A large-scale sequencing of 40,904 ESTs from the pea aphid Acyrthosiphon pisum was carried out to define a catalog of 12,082 unique transcripts. A strong AT bias was found, indicating a compositional shift between Drosophila melanogaster and A. pisum. An in silico profiling analysis characterized 135 transcripts specific to pea-aphid tissues (relating to bacteriocytes and parthenogenetic embryos). This project is the first to address the genetics of the Hemiptera and of a hemimetabolous insect.

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          Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis.

          L Duret, D Mouchiroud (1999)
          We measured the expression pattern and analyzed codon usage in 8,133, 1,550, and 2,917 genes, respectively, from Caenorhabditis elegans, Drosophila melanogaster, and Arabidopsis thaliana. In those three species, we observed a clear correlation between codon usage and gene expression levels and showed that this correlation is not due to a mutational bias. This provides direct evidence for selection on silent sites in those three distantly related multicellular eukaryotes. Surprisingly, there is a strong negative correlation between codon usage and protein length. This effect is not due to a smaller size of highly expressed proteins. Thus, for a same-expression pattern, the selective pressure on codon usage appears to be lower in genes encoding long rather than short proteins. This puzzling observation is not predicted by any of the current models of selection on codon usage and thus raises the question of how translation efficiency affects fitness in multicellular organisms.
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            Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy.

            H Akashi (1994)
            I present evidence that natural selection biases synonymous codon usage to enhance the accuracy of protein synthesis in Drosophila melanogaster. Since the fitness cost of a translational misincorporation will depend on how the amino acid substitution affects protein function, selection for translational accuracy predicts an association between codon usage in DNA and functional constraint at the protein level. The frequency of preferred codons is significantly higher at codons conserved for amino acids than at nonconserved codons in 38 genes compared between D. melanogaster and Drosophila virilis or Drosophila pseudoobscura (Z = 5.93, P < 10(-6)). Preferred codon usage is also significantly higher in putative zinc-finger and homeodomain regions than in the rest of 28 D. melanogaster transcription factor encoding genes (Z = 8.38, P < 10(-6)). Mutational alternatives (within-gene differences in mutation rates, amino acid changes altering codon preference states, and doublet mutations at adjacent bases) do not appear to explain this association between synonymous codon usage and amino acid constraint.
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              Insect diversity in the fossil record.

              C. C. Labandeira, J Sepkoski (1993)
              Insects possess a surprisingly extensive fossil record. Compilation of the geochronologic ranges of insect families demonstrates that their diversity exceeds that of preserved vertebrate tetrapods through 91 percent of their evolutionary history. The great diversity of insects was achieved not by high origination rates but rather by low extinction rates comparable to the low rates of slowly evolving marine invertebrate groups. The great radiation of modern insects began 245 million years ago and was not accelerated by the expansion of angiosperms during the Cretaceous period. The basic trophic machinery of insects was in place nearly 100 million years before angiosperms appeared in the fossil record.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Biol
                Title: Genome Biology
                Publisher: BioMed Central (London )
                ISSN (Print): 1465-6906
                ISSN (Electronic): 1465-6914
                Publication date (Print): 2006
                Publication date (Electronic): 10 March 2006
                Volume: 7
                Issue: 3
                Page: R21
                Affiliations
                [1 ]INRA Rennes, UMR INRA-Agrocampus BiO3P, BP 35327, F-35653 Le Rheu Cedex, France
                [2 ]INRA, URGI - Genoplante Info, Infobiogen, 523 place des Terrasses, F-91000 Evry, France
                [3 ]Biochemistry Department, University of Otago, PO Box 56, Dunedin, New Zealand
                [4 ]GENOSCOPE and CNRS UMR 8030, Centre National de Séquençage, 2 rue Gaston Crémieux, F-91000 Evry Cedex, France
                [5 ]USDA, Agricultural Research Service, US Horticultural Research Laboratory, 2001 South Rock Road, Fort Pierce, FL 34945, USA
                [6 ]Department of Entomology, Kansas State University, Manhattan, KS 66506, USA
                [7 ]Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBIBE), Universitat de Valencia, Apartado de Correos 2085, 46071 Valencia, Spain
                [8 ]Environmental Molecular Biology Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan
                [9 ]INRA Lyon, UMR INRA-INSA BF2I, INSA Bâtiment Louis-Pasteur, 20 avenue A. Einstein, 69621 Villeurbanne cedex, France
                [10 ]Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
                [11 ]Current address: Instituto Valenciano de Investigaciones Agrarias (IVIA), Proteccion Vegetal y Biotecnologia, Lab Entomologia, 46113 Moncada, Valencia, Spain
                Article
                Publisher ID: gb-2006-7-3-r21
                DOI: 10.1186/gb-2006-7-3-r21
                PMC ID: 1557754
                PubMed ID: 16542494
                SO-VID: 11ba00b0-40bf-45b3-9861-15ce45de2517
                Copyright © Copyright © 2006 Sabater-Muñoz et al.; licensee BioMed Central Ltd.
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 22 November 2005
                Date revision received : 23 January 2006
                Date accepted : 16 February 2006
                Categories
                Subject: Method

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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