ERC funded INRIA PhD Studentship (2010-2013)

Equipe INRIA Bamboo[i]

UMR203 INRA - INSA de Lyon, Biologie Fonctionnelle, Insectes et Interactions (BF2I)[ii]


Characterization of the transcriptional regulation networks in the trophic symbiosis

between the pea aphid Acyrthosiphon pisum and the bacteria Buchnera aphidicola.


Background. The pea aphid is a major pest of plants, mostly legumes (family Fabaceae), in temperate regions especially through the transmission of plant pathogenic viruses. Its important negative economic impact on agriculture is linked in particular to its successful reproductive rate (by parthenogenesis) in the spring/summer months. Recently the pea aphid genome sequencing and annotation by the International Aphid Genomics Consortium (IAGC), of which the UMR BF2I is a member, has been published1. The genome and its annotation are collected into the AphidBase[iii] database developed for the IAGC by the UMR BiO3P at INRA in Rennes. Our team has contributed in particular to the annotation of pea aphid genes involved in metabolism and transport. These annotations have been stored in an ad hoc BioCyc database AcypiCyc[iv] that we have implemented to study the pea aphid metabolic network and that of its symbiotic bacteria Buchnera aphidicola. In the last year, in collaboration with NimbleGen, we have also developed a microarray containing c.a. 24000 genes of the pea aphid. The availability of these genomics data and tools allows the development of novel functional genomics research approaches leading to a better understanding of this insect biology and thus to novel control strategies. In particular, our team is interested in the characterization of the regulatory networks underlying the trophic intracellular symbiosis between A. pisum and Buchnera aphidicola (for a recent review about prokaryotes-animal symbiosis see Moya et al.2).


Thesis project. The research project is centred on the study and characterization of transcriptional regulation in the pea aphids in response to nutritional stress and in the context of its interaction with its symbiotic bacteria Buchnera aphidicola, which synthesizes the essential aminoacids lacking in concentration in its food source, the plant phloem sap. The thesis research will be centred on the integration of experimental transcriptome type data with in silico characterization of the regulatory networks. In a first phase, the transcriptional response to a diet lacking specific aminoacids will be compared to that obtained feeding the aphids on a complete artificial diet (Ap33). A time course data analysis using R[v] (Bioconductor Project tools[vi]) and the AcypiCyc database will be performed. This work will be completed by bioinformatics analyses for the characterization of transcription factors to allow a first reconstruction of the transcriptional regulation network of the pea aphid. Furthermore, this reconstruction will be enriched by the analysis of small RNA expression (by RNAseq) in response to nutritional stress. This PhD project is an integral part of a broader systems biology research project (SISYPHE: Species Identity and SYmbiosis Formally and Experimentally explored) and it will include the collaboration with other bioinformatics scientists specialized in network analysis. The data generated in this thesis could be used as a benchmark for the validation of novel algorithms developed by the SISYPHE project team.





1.     The International Aphid Genomics Consortium. Genome Sequence of the Pea Aphid Acyrthosiphon pisum. PLoS Biol. 8, e1000313 (2010).

2.     Moya, A., Pereto, J., Gil, R. & Latorre, A. Learning how to live together: genomic insights into prokaryote-animal symbioses. Nat. Rev. Genet. 9, 218-229 (2008).

3.     Febvay, G., Rahbˇ, Y., Rynkiewicz, M., Guillaud, J. & Bonnot, G. Fate of dietary sucrose and neosynthesis of amino acids in the pea aphid, Acyrthosiphon pisum, reared on different diets. J. Exp. Biol. 202, 2639-2652 (1999).



Candidate profile


This project is open to students interested by genomics approaches, with a particular interest in metabolic networks and transcription regulation. Previous experience in data analysis and/or modelling is highly valued. The recruited candidate will work in the BF2I laboratory with a direct link with INRIA researchers from the Bamboo team working in the LBBE laboratory at the Universitˇ Claude Bernard Lyon 1.



This INRIA thesis is part of the Marie-France Sagot project SISYPHE (Species Identity and SYmbiosis Formally and Experimentally explored) and it is funded for 3 years by the European Reseach Council (ERC) Advanced Grant scheme. The approximate gross salary will be of 1750 Ū/month.


How to apply:

Interested candidates are invited to submit their application, including a cover letter, a full Curriculum Vitae, a brief description of their prior research experience, together with the names and addresses of one or more referee(s) by Tuesday, June 15th, 2010.


For supplementary information and for the application please contact:


Stefano Colella [vii]

INRA - Chargˇ de Recherche (CR2)

UMR203 BF2I, ˇquipe – Ē Symbiose : Gˇnomique Fonctionnelle des Interactions Trophiques Č

Tˇl : +33 (0)4 72 43 84 76 ; E-mail :   


Marie-France Sagot

INRIA – Directeur de Recherche (DR1)

Equipe INRIA Bamboo

Tˇl : +33 (0) 4 72 43 13 88; E-mail :