Principle : Modern species are paleopolyploids deriving from diploid extinct ancestors.
Paleogenomics, the study of ancestral genome structure of modern species, allows the identification and characterization of mechanisms (i.e. duplications, translocations, and inversions) that have shaped the genome of present-day living species during their evolution. Two scientific approaches can be investigated to address this issue. The first consists in sequencing (at least partially) fossil DNA from recovered ancestral genome structures. The second approach, when fossil DNA is not available, can be performed through large-scale comparative analyses of modern species and then ancestor modeling in term of its paleo-chromosome structure and gene content. The ancestor modeling procedure consists in identifying the minimal genomic structure (gene content and order) considered to be ancestral, based on the synteny-based comparison of present-day genomes. Unlike mammals, paleogenomics is still little studied in plants, and more specifically in angiosperms that have undergone a large number of segmental or even global genome duplications (polyploidization) as well as local rearrangements (gene inversion, tandem duplication or conversion), making difficult to carry out robust comparative genomics studies in monocotyledons (mainly cereals) and eudicotyledons.
The development of bioinformatics, statistical and combinatorial mathematical tools has enabled us to characterize and validate syntenic and duplication relationships in plant genomes (Arabidopsis, soybean, poplar, papaya, vine, rice, maize, sorghum, barley, Triticeae, Brachypodium…) and made then possible to characterise ancestral duplication events (that are by sense common to the considered genomes), as well as duplication events specific to each of them. For the first time, the integration of duplication and syntenic relationships offers the opportunity to characterise seven paleoduplications present in the studied genomes. We have thus been able to model both the genome of extinct plant ancestors, as well as an evolutionary scenario that has shaped the genome of modern plant species.
Our research has established in the field of plant paleogenomics that:
- Monocotyledons arise from an ancestor structured with seven protochromosomes carrying 9138 protogenes, and the eudicotyledons come from an ancestor with seven protochromosomes carrying 9731 protogenes.
- Based on these ancestors, the evolutionary paleohistory of present-day plants involves four major events.
- Of these events, whole genome duplication (polyploidy) appears as a major force for the adaptation of plants to their environment.
Evolutionary scenario of the plant genomes (Salse et al. 2012) The present-day monocot (right) and eudicot (left) genomes (bottom) are represented with color codes to illustrate the evolution of segments from their founder ancestors with seven protochromosomes according to the time scale (left in mya). The WGD events that have shaped the structure of the modern plant genomes during their evolution are indicated as red dots.