The Amborella genome: an evolutionary reference for plant biology

Abstract

The nuclear genome sequence of Amborella trichopoda, the sister species to all other extant angiosperms, will be an exceptional resource for plant genomics.

Figure 1

The position of Amborella in the angiosperm phylogenetic tree. Taxa for which whole-genome sequences have been published are indicated in parentheses. The node highlighted by a star on the tree identifies the 'ancestral angiosperm', or most recent common ancestor of all living angiosperms. An Amborella genome sequence will allow the ancestral genes and genomic features of living angiosperms to be identified and will provide the essential root for angiosperm comparative genomics. Based on [14,15].

Figure 2

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.

Figure 3

Synteny of the Amborella genome with other plant genomes. Illustrated here is a physical map of a 0.65 Mb region of the Amborella nuclear genome (highlighted in yellow) showing synteny with segments in each of the Arabidopsis, poplar, grapevine, and rice genomes. Two homologous segments are shown in each case: one above and one below the Amborella map. The physical map is based on high information content fingerprinting of an Amborella BAC library. Synteny was inferred over 5 Mb tracts of sequenced genomes on the basis of BAC-end sequences matching the reference genomes with TBLASTX bit scores of greater than 80. Red and green ovals depict BAC-end Amborella sequences with significant hits to known transposable elements and protein-coding genes, respectively.