PhD position in the IJPB team "Genomic Analysis of Plant-Parasite Interactions" AGIPP
Role of endogenous viral sequences in the regulation of plant genes and antiviral immunity
Scientific Background and PhD Objectives
Endogenous viral elements (EVEs) arise from the integration of viral genome fragments into the DNA of their hosts and constitute a unique archive of past interactions between viruses and organisms. In plants, most described EVEs belong to the Caulimoviridae family, the only family of reverse-transcribing viruses infecting plants. Although these viruses lack an integrase enzyme, they have left abundant traces in the genomes of vascular plants in the form of endogenous caulimovirid sequences (ECVs), which can occur in several thousand copies.
The study of ECVs has led to the identification of new Caulimoviridae lineages and the reconstruction of the evolutionary history of this viral family over hundreds of millions of years, revealing in particular a close co-evolution with vascular plants (tracheophytes). However, while their value as markers of viral evolution is well established, the functional impact of ECVs on the structure and functioning of plant genomes remains largely unexplored. Their potential roles in regulating gene expression, contributing to antiviral defense, and generating exploitable genomic diversity have yet to be fully investigated, and their possible contribution to the acquisition of adaptive traits warrants further study.
The main objective of this PhD project is therefore to characterize the role of ECVs in gene regulation and antiviral immunity in the Solanaceae family.
Role of ECVs in gene regulation
The first objective of the project is to investigate the potential of ECVs as sources of transcriptional regulation by identifying, validating, and experimentally testing their promoter sequences.
Comparative genomics approaches, based on the Caulifinder tool developed by the AGIPP team, will be used to systematically annotate and compare ECVs across Solanaceae genomes, with particular emphasis on model species such as tomato, potato, and eggplant. The project will focus on the potential contribution of ECVs to gene modification, the emergence of novel gene expression patterns, and the provision of functional viral promoters, which will be experimentally assessed through transient expression assays.
Role of ECVs in antiviral immunity
The second objective is to evaluate the contribution of ECVs to antiviral gene silencing by characterizing loci that produce small interfering RNAs (siRNAs) and assessing their functional impact through experimental infections using a synthetic viral genome derived from an endogenous caulimovirus of the genus Florendovirus. Analyses performed on tomato mutants defective in gene silencing pathways will allow direct testing of the hypothesis that ECVs mediate a form of acquired antiviral immunity.
Supervision
This PhD project is jointly funded by CIRAD and INRAE. It relies on a well-established collaboration between Pierre-Yves Teycheney, unité PVBMT, CIRAD and Nathalie Choisne & Florian Maumus "Genomic Analysis of Plant-Parasite Interactions" AGIPP team. Their complementary expertise in virology, genome analysis, and genome annotation has enabled them to succesfully investigate plant ECVs and the evolutionary history of the Caulimoviridae family. The project will also benefit from the support of the"Epigenetics, Reproduction and Transposable Elements" EPIREP team, led by Filipe Borges.
Required qualifications and skills
Applicants should hold a Master's degree (or an engineering degree equivalent to a Master's, i.e. five years of higher education) and have a strong background in molecular biology and bioinformatics, and at least one previous laboratory experience involving molecular cloning techniques. They should also possess a strong understanding of genome biology.
Références
> Vassilieff H, Serfraz S, Choisne N, Geering A, Lefeuvre P, Teycheney P. Y., Maumus F (2026) Endogenous viral elements trace the ancient origins and early evolution of the Caulimoviridae. PLoS Pathog 22(6): e1014340. https://doi.org/10.1371/journal.ppat.1014340
>Vassilieff H, Geering ADW, Choisne N, Teycheney P-Y, Maumus F (2023) Endogenous caulimovirids: fossils, zombies, and living in plant genomes. Biomolecules 13, 1069. https://doi.org/10.3390/biom13071069
> Valli AA, Gonzalo-Magro I, Sanchez DH (2023) Rearranged Endogenized Plant Pararetroviruses as Evidence of Heritable RNA-based Immunity. Mol Biol Evol, 40, doi: https://doi.org/10.1093/molbev/msac240
> Vassilieff H, Haddad S, Jamilloux V, Choisne N, Sharma V, Giraud D, Wan M, Serfraz S, Geering ADW, Teycheney P-Y, Maumus F (2022) CAULIFINDER: a pipeline for the automated detection and annotation of caulimovirid endogenous viral elements in plant genomes. Mobile DNA 13, 31. https://doi.org/ 10.1186/s13100-022-00288-w
> Lopez-Gomollon S, Muller SY, Baulcombe DC (2022) Interspecific hybridization in tomato influences endogenous viral sRNAs and alters gene expression. Genome Biol, 23, 120, doi:10.1186/s13059-022-02685-z.PMC9124383
> Diop S, Geering ADW, Alfama-Depauw F, Loarec M, Teycheney P-Y, Maumus F (2018) Tracheophyte genomes keep track of the deep evolution of the Caulimoviridae. Scientific Reports 8, 572. https://doi.org/10.1038/s41598-017-16399-x
> Serfraz S, Sharma V, Maumus F, Aubriot X, Geering ADW, Teycheney P.-Y. (2021). Insertion of badnaviral DNA in the late blight resistance gene (R1a) of eggplant (Solanum melongena). Front. Plant Sci. https://doi.org/10.3389/fpls.2021.683681.6
> Teycheney P.-Y, Geering ADW, Dasgupta I, Hull R, Kreuze JF, Lockhart B, Muller E, Olszewski N, Pappu N, Pooggin M, Richert-Pöggeler K, Schoelz JE, Seal S, Stavolone L, Umber M (2020). ICTV Virus Taxonomy Profile: Caulimoviridae. Journal of General Virology 101:1025–1026. https://doi.org/ 10.1099/jgv.0.001497
> Geering, AD, Maumus, F, Copetti, D, Choisne, N, Zwickl, DJ, Zytnicki M, McTaggart AR, Scalabrin S, Vezzulli S, Wing RA, Quesneville H, Teycheney PY (2014) Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution . Nat Commun, 5, 5269, doi:10.1038/ncomms6269
> Feschotte C, Gilbert C (2012) Endogenous viruses: insights into viral evolution and impact on host biology. Nat Rev Genet, 13, 283-296, doi:10.1038/nrg3199
Endogenous viral elements (EVEs) arise from the integration of viral genome fragments into the DNA of their hosts and constitute a unique archive of past interactions between viruses and organisms. In plants, most described EVEs belong to the Caulimoviridae family, the only family of reverse-transcribing viruses infecting plants. Although these viruses lack an integrase enzyme, they have left abundant traces in the genomes of vascular plants in the form of endogenous caulimovirid sequences (ECVs), which can occur in several thousand copies.
The study of ECVs has led to the identification of new Caulimoviridae lineages and the reconstruction of the evolutionary history of this viral family over hundreds of millions of years, revealing in particular a close co-evolution with vascular plants (tracheophytes). However, while their value as markers of viral evolution is well established, the functional impact of ECVs on the structure and functioning of plant genomes remains largely unexplored. Their potential roles in regulating gene expression, contributing to antiviral defense, and generating exploitable genomic diversity have yet to be fully investigated, and their possible contribution to the acquisition of adaptive traits warrants further study.
The main objective of this PhD project is therefore to characterize the role of ECVs in gene regulation and antiviral immunity in the Solanaceae family.
Role of ECVs in gene regulation
The first objective of the project is to investigate the potential of ECVs as sources of transcriptional regulation by identifying, validating, and experimentally testing their promoter sequences.
Comparative genomics approaches, based on the Caulifinder tool developed by the AGIPP team, will be used to systematically annotate and compare ECVs across Solanaceae genomes, with particular emphasis on model species such as tomato, potato, and eggplant. The project will focus on the potential contribution of ECVs to gene modification, the emergence of novel gene expression patterns, and the provision of functional viral promoters, which will be experimentally assessed through transient expression assays.
Role of ECVs in antiviral immunity
The second objective is to evaluate the contribution of ECVs to antiviral gene silencing by characterizing loci that produce small interfering RNAs (siRNAs) and assessing their functional impact through experimental infections using a synthetic viral genome derived from an endogenous caulimovirus of the genus Florendovirus. Analyses performed on tomato mutants defective in gene silencing pathways will allow direct testing of the hypothesis that ECVs mediate a form of acquired antiviral immunity.
Supervision
This PhD project is jointly funded by CIRAD and INRAE. It relies on a well-established collaboration between Pierre-Yves Teycheney, unité PVBMT, CIRAD and Nathalie Choisne & Florian Maumus "Genomic Analysis of Plant-Parasite Interactions" AGIPP team. Their complementary expertise in virology, genome analysis, and genome annotation has enabled them to succesfully investigate plant ECVs and the evolutionary history of the Caulimoviridae family. The project will also benefit from the support of the"Epigenetics, Reproduction and Transposable Elements" EPIREP team, led by Filipe Borges.
Required qualifications and skills
Applicants should hold a Master's degree (or an engineering degree equivalent to a Master's, i.e. five years of higher education) and have a strong background in molecular biology and bioinformatics, and at least one previous laboratory experience involving molecular cloning techniques. They should also possess a strong understanding of genome biology.
Références
> Vassilieff H, Serfraz S, Choisne N, Geering A, Lefeuvre P, Teycheney P. Y., Maumus F (2026) Endogenous viral elements trace the ancient origins and early evolution of the Caulimoviridae. PLoS Pathog 22(6): e1014340. https://doi.org/10.1371/journal.ppat.1014340
>Vassilieff H, Geering ADW, Choisne N, Teycheney P-Y, Maumus F (2023) Endogenous caulimovirids: fossils, zombies, and living in plant genomes. Biomolecules 13, 1069. https://doi.org/10.3390/biom13071069
> Valli AA, Gonzalo-Magro I, Sanchez DH (2023) Rearranged Endogenized Plant Pararetroviruses as Evidence of Heritable RNA-based Immunity. Mol Biol Evol, 40, doi: https://doi.org/10.1093/molbev/msac240
> Vassilieff H, Haddad S, Jamilloux V, Choisne N, Sharma V, Giraud D, Wan M, Serfraz S, Geering ADW, Teycheney P-Y, Maumus F (2022) CAULIFINDER: a pipeline for the automated detection and annotation of caulimovirid endogenous viral elements in plant genomes. Mobile DNA 13, 31. https://doi.org/ 10.1186/s13100-022-00288-w
> Lopez-Gomollon S, Muller SY, Baulcombe DC (2022) Interspecific hybridization in tomato influences endogenous viral sRNAs and alters gene expression. Genome Biol, 23, 120, doi:10.1186/s13059-022-02685-z.PMC9124383
> Diop S, Geering ADW, Alfama-Depauw F, Loarec M, Teycheney P-Y, Maumus F (2018) Tracheophyte genomes keep track of the deep evolution of the Caulimoviridae. Scientific Reports 8, 572. https://doi.org/10.1038/s41598-017-16399-x
> Serfraz S, Sharma V, Maumus F, Aubriot X, Geering ADW, Teycheney P.-Y. (2021). Insertion of badnaviral DNA in the late blight resistance gene (R1a) of eggplant (Solanum melongena). Front. Plant Sci. https://doi.org/10.3389/fpls.2021.683681.6
> Teycheney P.-Y, Geering ADW, Dasgupta I, Hull R, Kreuze JF, Lockhart B, Muller E, Olszewski N, Pappu N, Pooggin M, Richert-Pöggeler K, Schoelz JE, Seal S, Stavolone L, Umber M (2020). ICTV Virus Taxonomy Profile: Caulimoviridae. Journal of General Virology 101:1025–1026. https://doi.org/ 10.1099/jgv.0.001497
> Geering, AD, Maumus, F, Copetti, D, Choisne, N, Zwickl, DJ, Zytnicki M, McTaggart AR, Scalabrin S, Vezzulli S, Wing RA, Quesneville H, Teycheney PY (2014) Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution . Nat Commun, 5, 5269, doi:10.1038/ncomms6269
> Feschotte C, Gilbert C (2012) Endogenous viruses: insights into viral evolution and impact on host biology. Nat Rev Genet, 13, 283-296, doi:10.1038/nrg3199
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How to apply
Applicants are invited to submit the following documents
> A detailed curriculum vitae (CV)
> A cover letter outlining their motivation and relevant experience
> A letter of recommendation from their Master's (M2) internship supervisor
Application deadline : August 31, 2026
Contacts
Florian Maumus, contact
Pierre-Yves Teycheney, contact
Start date : 01/10/2026, for 3 years
Offer, file