Pan-angiosperm Syntenic Mappings Using Key Reconstructed Ancestral Genomes

Up to now, it has been impossible to identify true evolutionary orthologous genes and genomic regions between the monocots and the eudicots.  This is due to their evolutionary history being littered by independent polyploidy events followed by massive genomic restructuring which obfuscates proper identification and assignment of orthologous and homeologous syntenic relationships of genes, gene families, and genomic regions.  Here we used the OMG and MWM methods to reconstruct key pre-polyploid ancestral angiosperm genomes, which ‘reversed’ the scrambling effects from polyploidy and rearrangements that have occurred during the evolution of much of the extant plant lineages. Two key ancestral genomes were reconstructed: the Eudicot Pre-Gamma Ancestor (EPGA) and Poales Pre-Rho Ancestor (PPRA), which represent the ancestral genome of the eudicot lineage prior to its basal whole genome triplication (gamma event) and the grass lineage prior to its most recent whole genome duplication (rho event), respectively.  The EPGA was reconstructed using three rosid genomes with no subsequent polyploidy, grape, cacao, and peach, and a basal angiosperm with no lineage specific polyploidy events, Amborella; the PPRA was reconstructed using four grass genomes without subsequent polyploidy, sorghum, rice, Brachypodium, and foxtail millet. Using these ancestral genomes as transitive synteny ‘hubs’, it becomes straightforward to map orthology between the monocots and eudicots. We have generated pan-angiosperm syntenic gene sets across a wide spectrum of monocot and eudicot genomes, and to which any new plant genomes genes may be syntenically mapped.  The methods detailed here for in silico reconstruction of key pre-polyploid genomes are generally applicable to unravelling syntenic relationships for any clade of organisms with multiple shared and independent polyploidy events.