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Open Access Research article

Bioinformatic prediction, deep sequencing of microRNAs and expression analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon pisum

Fabrice Legeai12, Guillaume Rizk3, Thomas Walsh4, Owain Edwards4, Karl Gordon5, Dominique Lavenier6, Nathalie Leterme1, Agnès Méreau7, Jacques Nicolas2, Denis Tagu1 and Stéphanie Jaubert-Possamai1*

Author Affiliations

1 INRA, UMR1099 BiO3P, Domaine de la Motte, F-35653 Le Rheu, France

2 INRIA Centre Rennes - Bretagne Atlantique, GenOuest, Campus de Beaulieu, 35042 Rennes, France

3 Université de Rennes I/IRISA Campus de Beaulieu, 35042 Rennes, France

4 CSIRO Entomology, GPO Box 1700, Canberra ACT 2601, Australia

5 CSIRO Entomology, Centre for Environment and Life Sciences (CELS), Floreat Park, WA, 6014, Australia

6 ENS Cachan/IRISA Campus de Beaulieu, 35042 Rennes, France

7 CNRS, Univ Rennes 1, UMR 6061, IFR 140, Rennes, France

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BMC Genomics 2010, 11:281  doi:10.1186/1471-2164-11-281

Published: 5 May 2010

Abstract

Background

Post-transcriptional regulation in eukaryotes can be operated through microRNA (miRNAs) mediated gene silencing. MiRNAs are small (18-25 nucleotides) non-coding RNAs that play crucial role in regulation of gene expression in eukaryotes. In insects, miRNAs have been shown to be involved in multiple mechanisms such as embryonic development, tissue differentiation, metamorphosis or circadian rhythm. Insect miRNAs have been identified in different species belonging to five orders: Coleoptera, Diptera, Hymenoptera, Lepidoptera and Orthoptera.

Results

We developed high throughput Solexa sequencing and bioinformatic analyses of the genome of the pea aphid Acyrthosiphon pisum in order to identify the first miRNAs from a hemipteran insect. By combining these methods we identified 149 miRNAs including 55 conserved and 94 new miRNAs. Moreover, we investigated the regulation of these miRNAs in different alternative morphs of the pea aphid by analysing the expression of miRNAs across the switch of reproduction mode. Pea aphid microRNA sequences have been posted to miRBase: http://microrna.sanger.ac.uk/sequences/ webcite

Conclusions

Our study has identified candidates as putative regulators involved in reproductive polyphenism in aphids and opens new avenues for further functional analyses.