Polyploid evolution in Oryza officinalis complex of the genus Oryza

Area of Science:

• Plant evolutionary biology
• Genomics
• Phylogenetics

Background:

• Polyploidization is a key driver of plant evolution, but its mechanisms and spatio-temporal dynamics are not fully understood.
• The Oryza officinalis complex, with diverse ploidy levels and a pantropical distribution, offers a model to study polyploid evolution.
• The C-genome is central to the polyploidization history of this complex.

Purpose of the Study:

• To trace the evolutionary history of the C-genome within the Oryza officinalis complex.
• To elucidate genomic relationships, polyploid formation times, and diploidization processes.
• To investigate the geographic spread and origins of polyploid species.

Main Methods:

• Phylogenetic analyses
• Molecular-clock dating
• Fluorescent in situ hybridization (FISH) using genome-specific probes

Main Results:

• The C-genome diverged from the B-genome around 4.8 million years ago (Mya).
• Speciation of C-genome diploids occurred between 1.8-0.9 Mya, followed by tetraploid formation (CCDD and BBCC) between 0.9-0.3 Mya.
• Inter-genomic translocations and genomic modifications were observed in polyploid species, with distinct FISH patterns among CCDD species.

Conclusions:

• The C-genome underwent distinct evolutionary trajectories post-polyploidization, including inter-genomic exchange and genomic invasion.
• Polyploid species spread across continents through long-distance dispersal, not vicariance.
• An extinct Asian BB diploid species is identified as the likely direct donor to sympatric tetraploids.