The AGIPP team uses and develops bioinformatic approaches to study the co-evolution of plants with their parasites. By exploiting genomic and protein resources, we aim to characterise the evolution of genomes and gene repertoires in relation to plant-parasite interactions.
Biological Question
Using genomic, transcriptomic, and protein resources, we aim to elucidate the mechanisms underlying the co-evolution between plants and different types of parasites. The first are endogenous parasites, transposable elements (TEs), which are a major component of eukaryotic genomes and play a driving role in evolution by promoting phenomena such as mutation, exaptation, and recombination. These specific features are a source of genetic innovation, and studying these sequences and their diversity provides a better understanding of their influence on the evolution of plant genomes.
The second are obligate intracellular parasites, viruses, whose infection can be asymptomatic to lethal and cause major yield losses in crops of economic interest. By means of accidental integration events, these viruses find their way into the genome of their host, and analysis of these endogenous viral sequences (EVEs) enables us to specify the evolutionary history and host spectrum of the viruses and to study their impact on plant biology and the possible acquisition of antiviral immunity.
Finally, we are studying the relationships between plants and their bioaggressors (bacteria, insects, fungi, etc.), which use the plant's metabolism to ensure their growth. In particular, the characterization of horizontal gene transfer (HGT) events highlights the acquisition of important functions that can play a role in determining the host range of pests. The study of transferred genes allows us to discover adaptive strategies that are worth exploring in the context of climate change.
Models, tools and methods
We use bioinformatics approaches in the fields of genome annotation and evolutionary biology, mainly comparing sequences and three-dimensional structures.
We produce expert annotations of TEs and other repetitive elements in algal and plant genomes as part of national and international collaborations. In particular, this work enables masking genomes for gene prediction, characterizing new TE families, and studying their influence on genes, genomes, and the epigenome at the species level.
Concerning EVEs, we are particularly interested in the Caulimoviridae family, which is endogenously present in many vascular plant genomes, sometimes in large quantities. To automate the annotation of these elements, we have developed the CAULIFINDER tool. Using CAULIFINDER, we are studying the macroevolution of this viral family and trying to understand the impact of these endogenous sequences on their hosts, particularly on the regulation of gene expression and the acquisition of resistance in cultivated plants.
Finally, we contribute methodological development to improve the speed and efficiency of detecting candidate horizontally transferred genes. We use these approaches to characterize HGT events in plants and their pests.
Societal and economical impacts
Plant pests cause substantial yield losses in crop production, and phytosanitary control has ecological, biodiversity, and health implications. In the context of the agroecological transition, advances in the mechanisms underlying plant-parasite relationships allow the identification of new genes of interest that may play a crucial role in parasitism or plant resistance. This knowledge suggests ways of improving plant resilience and target genes for pest control.
Using genomic, transcriptomic, and protein resources, we aim to elucidate the mechanisms underlying the co-evolution between plants and different types of parasites. The first are endogenous parasites, transposable elements (TEs), which are a major component of eukaryotic genomes and play a driving role in evolution by promoting phenomena such as mutation, exaptation, and recombination. These specific features are a source of genetic innovation, and studying these sequences and their diversity provides a better understanding of their influence on the evolution of plant genomes.
The second are obligate intracellular parasites, viruses, whose infection can be asymptomatic to lethal and cause major yield losses in crops of economic interest. By means of accidental integration events, these viruses find their way into the genome of their host, and analysis of these endogenous viral sequences (EVEs) enables us to specify the evolutionary history and host spectrum of the viruses and to study their impact on plant biology and the possible acquisition of antiviral immunity.
Finally, we are studying the relationships between plants and their bioaggressors (bacteria, insects, fungi, etc.), which use the plant's metabolism to ensure their growth. In particular, the characterization of horizontal gene transfer (HGT) events highlights the acquisition of important functions that can play a role in determining the host range of pests. The study of transferred genes allows us to discover adaptive strategies that are worth exploring in the context of climate change.
Models, tools and methods
We use bioinformatics approaches in the fields of genome annotation and evolutionary biology, mainly comparing sequences and three-dimensional structures.
We produce expert annotations of TEs and other repetitive elements in algal and plant genomes as part of national and international collaborations. In particular, this work enables masking genomes for gene prediction, characterizing new TE families, and studying their influence on genes, genomes, and the epigenome at the species level.
Concerning EVEs, we are particularly interested in the Caulimoviridae family, which is endogenously present in many vascular plant genomes, sometimes in large quantities. To automate the annotation of these elements, we have developed the CAULIFINDER tool. Using CAULIFINDER, we are studying the macroevolution of this viral family and trying to understand the impact of these endogenous sequences on their hosts, particularly on the regulation of gene expression and the acquisition of resistance in cultivated plants.
Finally, we contribute methodological development to improve the speed and efficiency of detecting candidate horizontally transferred genes. We use these approaches to characterize HGT events in plants and their pests.
Societal and economical impacts
Plant pests cause substantial yield losses in crop production, and phytosanitary control has ecological, biodiversity, and health implications. In the context of the agroecological transition, advances in the mechanisms underlying plant-parasite relationships allow the identification of new genes of interest that may play a crucial role in parasitism or plant resistance. This knowledge suggests ways of improving plant resilience and target genes for pest control.
Leader:
Florian Maumus