Sequencing the nuclear genome for Amborella will root comparisons of monocot and eudicot genome sequences. (a,b) Sequence-based comparisons of the Amborella sequence (highlighted in yellow) with (a) Arabidopsis and (b) rice (Oryza) sequences for homologous genome segments (1, 1', 2 and 2') identify homologous genomic regions and genes (shown by colored arrows) that have undergone duplications and presumed gene loss in different segments. (c) From such comparisons investigators can identify the timings of segmental duplications and inversions, gene gains and losses, and whole-genome duplications (WGDs) in these three lineages. The large black circle indicates the monocot-eudicot split. The Amborella sequence resolves the timing of an inversion and a tandem duplication (versus loss of a duplicate) that distinguish homologous Arabidopsis and rice segments. Taken together, the map comparisons imply that the orientation of the green, blue and red genes in the Amborella sequence matches that in the common ancestor of monocots and eudicots. We can also infer that the purple gene was present in the common ancestor of monocots and eudicots. However, the homologous region would have to be sequenced in a gymnosperm to determine whether this gene was gained on the lineage leading to monocots and eudicots, or was present in the common ancestor of eudicots, monocots and Amborella and lost in the lineage leading to Amborella.
Soltis et al. Genome Biology 2008 9:402 doi:10.1186/gb-2008-9-3-402