The overall phenomenon that the number of protein domains and their modularity increases as the genome expands has not been linked to a conclusive biological explanation yet. A rationale for the increase in interactions and functional subunits, however, may derive from the paradoxical absence of correlation between the number of genes encoded and organism complexity, the so-called G-value paradox [81] . There is indeed evidence that domains involved in the same functional pathway tend to converge in a single protein sequence, which would make pathways more controllable and reliable without the need for supplementary genes [73] . Additionally, the number of different arrangements found in higher eukaryotes is, given the vast scale of unique domains present, relatively limited. This in turn implies that evolutionary constraints have played an important role in selecting the right domain combinations and the right order from N-to C-terminus in multi-domain proteins [13, 82] . In fact, the ordering and co-occurrence of domains was demonstrated to hold enough evolutionary information to construct a tree of life similar to those based on canonical sequence data [70] . Furthermore, the increased use of alternative splicing and exon skipping in higher eukaryotes likely supplied a novel way of proteome diversification by restricting gene duplication and stimulating the formation of multi-domain proteins [83, 84] . In plants, however, the latter notion is not supported since both mono-and dicots show limited alternative splicing and a more extensive polyploidy [85] [86] [87] .