Abstract

During the last decade, technological improvements led to the development of large sets of plant genomic resources permitting the emergence of high-resolution comparative genomic studies. In an attempt to unravel the structure and evolution of the plant ancestor genome we have re-assed the synteny and duplications of Angiosperm genomes to identify and characterize shared duplications. We combined the data on the intra-genomic duplications with those on the colinear blocks and found duplicated segments that have been conserved at orthologous positions since the divergence of plants. By conducting detailed analysis of the length, composition, and divergence time of the conserved duplications, we identified common and lineage-specific patterns of conservation between the different genomes that allowed us to propose a model in which the plant genomes have evolved from a common ancestor with a basic number of five/seven chromosomes (90 MYA ) through whole genome duplications (i.e. paleopolyploidization) and translocations followed by lineage specific segmental duplications, chromosome fusions and translocations (Abrouk et al. 2010; Murat et al. 2010; Salse et al. 2011).

Based on these data an ‘inner circle’ comprising 5/7 ancestral chromosomes with 10000 protogenes was defined providing a new reference for the plant chromosomes and new insights into their ancestral relationships that have led to arrange their chromosomes into concentric ‘crop circles’ of synteny blocks (Abrouk et al. 2010). The established plant ancestor genome structure in term of chromosome structure and gene content offered the opportunity to study the impact of evolutionary shuffling events such as polyploidizations on (i) genome structure (i.e. mechanism driving the diploidization process), (ii) genome function (i.e. polyploidization resistant vs sensitive genes), (iii) genome expression (i.e. role of epigenetics on neo/sub-functionalization process), (iv) trait elaboration (i.e. conserved vs lineage specific traits), that will be discussed in details (Quraishi et al 2011ab).