The Aquilegia genome reveals a hybrid origin of core eudicots

Abstract

Background: Whole-genome duplications (WGDs) have dominated the evolutionary history of plants. One consequence of WGD is a dramatic restructuring of the genome as it undergoes diploidization, a process under which deletions and rearrangements of various sizes scramble the genetic material, leading to a repacking of the genome and eventual return to diploidy. Here, we investigate the history of WGD in the columbine genus Aquilegia, a basal eudicot, and use it to illuminate the origins of the core eudicots.

Results: Within-genome synteny confirms that columbines are ancient tetraploids, and comparison with the grape genome reveals that this tetraploidy appears to be shared with the core eudicots. Thus, the ancient gamma hexaploidy found in all core eudicots must have involved a two-step process: first, tetraploidy in the ancestry of all eudicots, then hexaploidy in the ancestry of core eudicots. Furthermore, the precise pattern of synteny sharing suggests that the latter involved allopolyploidization and that core eudicots thus have a hybrid origin.

Conclusions: Novel analyses of synteny sharing together with the well-preserved structure of the columbine genome reveal that the gamma hexaploidy at the root of core eudicots is likely a result of hybridization between a tetraploid and a diploid species.

Fig. 1

Intragenomic synteny blocks in the columbine genome. Pairs of synteny blocks are denoted as uniquely colored small rectangles. Larger rectangles of the same color outline large regions of synteny. Arrows under the synteny blocks show the orientation of the alignment between collinear genes. Gray dots highlight BLAST hits of a 329 bp centromeric repeat monomer [19, 27]

Fig. 2

Three scenarios for the relationship between columbine tetraploidy and core eudicot “gamma” hexaploidy. The gamma hexaploidy is a two-step process: a single round of WGD creates tetraploids (4n) whose unreduced gametes then fuse with diploid gametes (+2n). Scenario 1: gamma hexaploidy precedes the split between columbine and core eudicots, with the former undergoing an additional tetraploidy. Scenario 2: both gamma hexaploidy and columbine tetraploidy occur after the split between columbines and core eudicots. Scenario 3: columbine tetraploidy is derived from the ancient tetraploidy which was the first step of the process leading to gamma hexaploidy

Fig. 3

Synteny between the homologous regions of columbine and grape. The results for columbine chromosomes 1 and 2 and grape chromosomes 6, 8, and 13, shown here, reflect the overall synteny relationship of 3:2 between grape:columbine chromosomes (see Additional file 1: Figure S3 and Additional file 3: Table S2). This pattern argues against Scenario 1 but is consistent with either Scenario 2 or Scenario 3 in Fig. 2

Fig. 4

The distribution of the median Ks across syntenic regions. Synteny blocks are identified within columbine, between columbine and grape, and within grape. Note that only the putative WGD-derived blocks (median Ks = 1–2) are kept in columbine (Additional file 1: Figure S2)

Fig. 5

Gene order-based clustering expected under ancient tetraploidy common to all eudicots. Represented here by blue and purple rectangles, each member of the paralogous chromosome pair experiences intra-chromosomal rearrangements as a part of the diploidization process. Deletions (denoted as “-”) will create the gene order “1, 3, 5” on the blue chromosome while both deletions and an inversion will create the gene order “2, 1, 4” on the purple chromosome. These differential paralogous gene orders will be inherited by both columbine and grape. If we compare the gene order on the homologous chromosomes of columbine and grape at this particular region, we should see “blue” chromosomes of columbine and grape forming one cluster while “purple” chromosomes of columbine and grape forming another cluster. Note that we show here only the “allohexaploidy” model, which predicts that the third grape paralog added via hybridization is an outgroup in this clustering analysis. See Additional file 1: Figure S11 for the expected gene orders under the “autohexaploidy” model

Fig. 6

Tracing the genome reshuffling in columbine following tetraploidy. Grape chromosomes (bottom right) are colored by within-genome synteny. Seven distinct colors represent the haploid set of seven ancestral chromosomes before the eudicot-wide WGD. Each color is shared by three grape chromosomes reflecting the triplicate genome structure of core eudicots. The only exception is the “green” chromosome which is shared by four grape chromosomes due to a fission event [38]. Columbine chromosomes (bottom left) are colored by their synteny to grape chromosomes. Each color is generally shared by two chromosomes, reflecting columbine paleotetraploidy. As few as 7 fusions and a single fission are enough to explain the current structure of the columbine genome. Of these 7 fusions, 5 are between different chromosomes while 2 are between WGD-derived paralogous chromosomes. Columbine chromosomes 3 and 7 are examples of the latter (Fig. 1 and Additional file 1: Figure S4). Note that chromosome 5 of columbine and chromosome 7 of grape (*) both have the colors “orange” and “green” (cf. Fig. 7)

Fig. 7

Schematic of predicted synteny patterns in the case of shared ancestral fusion. Two ancestral chromosomes (orange and green rectangles, with genes depicted as numbers) undergo WGD. Paralogous chromosome pairs diverge as a part of the diploidization process. A fusion joins one version of the “orange” chromosome (“1, 3, 5”) with one version of the “green” chromosome (“7, 10, 8.”) If this took place in the common tetraploid ancestor of eudicots, the fused chromosomes in columbine and grape should also carry these versions on their “orange” and “green” portions. In the hypothetical example here, diploidization precedes the fusion event but may well happen afterwards with no effect on the predicted synteny patterns

Fig. 8

The shared history of chromosomes in columbine, grape, and cacao. Gene order-based clustering results (left panel) are summarized here for the chromosomes harboring the “orange” and “green” homologous portions. The former corresponds to 5, 7, 14 in grape and 1, 4, 5 in cacao. The latter corresponds to 3, 4 + 7 (products of a fission), 18 in grape, and 1, 2, 8 in cacao. In columbine, the “orange” portions are on chromosomes 2 and 5 while the “green” portions are on chromosomes 6 and 5, each pair of which being denoted as colum A and colum B, respectively. Both grape- and cacao-columbine pairing distinguish tetraploidy-derived regions (blue and purple rectangles) from hybridization-derived ones (light blue rectangles), defining the orthologous sets of regions across the three eudicot genomes (right panel). The conservation of gene order exclusively between the putatively orthologous regions of grape and cacao (black arrows, Additional file 1: Figure S10) further strengthens our columbine-based inference of orthology

Fig. 9

Synteny between columbine chromosome 4 and grape chromosomes 12 and 19. Much smaller grape chromosomes look like the compact versions of columbine chromosome 4. Note that this result is generated with the most relaxed parameter combination in Additional file 1: Figure S15, but holds true for a less relaxed combination of parameters as well (Additional file 1: Figure S16)