A common whole-genome paleotetraploidization in Cucurbitales

Abstract

Cucurbitales are an important order of flowering plants known for encompassing edible plants of economic and medicinal value and numerous ornamental plants of horticultural value. By reanalyzing the genomes of two representative families (Cucurbitaceae and Begoniaceae) in Cucurbitales, we found that the previously identified Cucurbitaceae common paleotetraploidization that occurred shortly after the core-eudicot-common hexaploidization event is shared by Cucurbitales, including Begoniaceae. We built a multigenome alignment framework for Cucurbitales by identifying orthologs and paralogs and systematically redating key evolutionary events in Cucurbitales. Notably, characterizing the gene retention levels and genomic fractionation patterns between subgenomes generated from different polyploidizations in Cucurbitales suggested the autopolyploid nature of the Begoniaceae common tetraploidization and the allopolyploid nature of the Cucurbitales common tetraploidization and the Cucurbita-specific tetraploidization. Moreover, we constructed the ancestral Cucurbitales karyotype comprising 17 proto-chromosomes, confirming that the most recent common ancestor of Cucurbitaceae contained 15 proto-chromosomes and rejecting the previous hypothesis for an ancestral Cucurbitaceae karyotype with 12 proto-chromosomes. In addition, we found that the polyploidization and tandem duplication events promoted the expansion of gene families involved in the cucurbitacin biosynthesis pathway; however, gene loss and chromosomal rearrangements likely limited the expansion of these gene families.

Figure 1

Phylogenetic tree and examples of homologous gene dotplots in Cucurbitales. A, Phylogenetic relationships of the Cucurbitales plants and V. vinifera. B–G, Identified orthologous and paralogous regions between and within genomes of V. vinifera, C. melo, C. moschata, and B. loranthoides. Dark highlighted boxes represent the identified orthologous and paralogous regions, and the highlighted paralogous regions became lighter as the time of the WGD event gets older. The best BLAST-hits are plotted as red dots, and other hits are plotted as blue dots. The Ks median of collinear gene pairs in homologous regions is marked near to the boxes. The lengths of compared chromosome regions are shown in Mb. H, Species phylogenetic trees for the V. vinifera, C. melo, C. moschata, and B. loranthoides genomes. The red six-pointed star represents the ECH event, and the red, orange, and blue squares represent the CCT, BCT, and CST events, respectively. ECH, core-eudicot-common hexaploidization. I, Three ECH-produced paralogous genes in V. vinifera (V) are denoted V1, V2, and V3, each having four orthologous genes in the B. loranthoides (B) or C. moschata (O) genomes and two in the C. melo (E) genome.

Figure 2

Original and corrected Ks distribution among collinear genes of the studied genomes. A, Distribution of average synonymous substitution levels (Ks) between collinear gene pairs in intergenomic blocks and intragenomic blocks. The different colored peaks indicate the normal distribution of the Ks values of collinear gene pairs. The values in parentheses are the Ks peaks corresponding to the events. B, Correction to the Ks distribution and the time of occurrence of key evolutionary events. The values in parentheses are the times corresponding to the events. Vitis vinifera (Vvi), B. loranthoides (Blo), C. moschata (Cmo), C. argyrosperma (Car), C. melo (Cme), B. hispida (Bhi), C. sativus (Csa), and C. lanatus (Cla).

Figure 3

Genomic alignment of representative species in Cucurbitales. The chromosomes of V. vinifera constitute the innermost circle, and their collinear paralogous genes are linked by curved lines and correspondingly colored according to the previously inferred seven core-eudicot-common ancestor chromosomes. Cucumis melo is denoted by E, C. moschata is denoted by O, B. loranthoides is denoted by B, and V. vinifera is denoted by V. Each chromosomal region had 2, 4, and 4 orthologous regions in the C. melo, C. moschata, and B. loranthoides genomes, respectively; these regions are displayed as 33 circles, where each circle represents one subgenome. Short lines between two circles show collinear genes, which correspond to the colors of the encoded Ch#. The color scheme is shown at the bottom.

Figure 4

A specific polyploidization event in Begoniaceae generates intersubgenome retention level balance. A, Gene retention of B. loranthoides subgenomes along orthologous regions corresponding to the V. vinifera chromosome. Retention rates of genes in sliding windows of B. loranthoides homologous region group 1 (red line) and homologous region group 2 (black line), using V. vinifera as the reference. B, Retention rates of genes in sliding windows of B. loranthoides homologous region group 3 (blue line) and homologous region group 4 (green line) and C, difference in gene retention between sliding windows of B. loranthoides homologous groups 1 and 2 (blue line), where the red line is the difference between homologous groups 3 and 4. B, The retention pattern of B. loranthoides, using V. vinifera chromosome 1 as a reference, is consistent with that in the subfigure A. C, The gene loss rates of B. loranthoides with the V. vinifera genome as a reference. The x-axis indicates the number of consecutive lost genes, the y-axis indicates the number of lost fragments, and the red curve is the model fit of gene loss.

Figure 5

Inference of the ancestral karyotypes and chromosome evolutionary trajectory of major Cucurbitales species. A, Inference of the chromosomal karyotype of the Cucurbitales ancestor with the V. vinifera genome as a reference. Bhi, B. hispida and Blo, B. loranthoides. Highlighted boxes represent the identified orthologous regions between selected chromosomes among compared genomes. If the inferred proto-chromosomes in ACK-I involved rearrangement event before the CCT event, then the regions circled by the dotted lines. The identified chromosomal fusions of the 21 chromosomes of the AEK contain two EEJ fusions, two nested chromosome (NCF) fusions, and three nonreciprocal translocations to form ACK-I of 17 proto-chromosomes (H1–H17). B, Phylogeny and Cucurbitales ancestor karyotype reconstruction. Each polygon represents a polyploidization event. The chromosomal regions in each genome are colored based on the seven ancestral eudicot chromosomes.

Figure 6

Evolution and diversification of gene families involved in the CS pathway in Cucurbitales. A, Cucurbitacin synthesis pathway. B, Identification of the gene families involved in the CS pathway in the studied genomes. C, Phylogenetic tree of the genes in FPS family of the Cucurbitales and V. vinifera genomes. Genes from different species are marked with different colors. The dots on the three layers represent the gene tandem duplication, paralogous, and orthologous relationships (marked with a, b, and c, respectively), and the same color represents the same group of relationships within and between genomes. D, P450 gene amplification model related to gene duplication events in C. moschata. P450 genes are displayed in blue patches. Curved lines (gray) link the collinear gene pairs generated at the period from the divergence between V. vinifera and Cucurbitales to the CCT event. Curved lines (red and plum) link gene pairs generated at the period from now to the CST and from the CST to the CCT event, respectively. E, The chromosomal distributions of P450 genes in the selected genomes. The lines between gene pairs on the same chromosome represent homologous genes generated at the period from the divergence between V. vinifera and CCT event. The lines between gene pairs on the different chromosome represent homologous genes generated by the divergence between the species. The β1, β2, γ1, and γ2 represent the gene clusters. F, The CDS–UTR structures of a set of orthologous FPS genes in selected genomes. The genes with different colors present the different species, and the shadow in one species shows that they come from the different subgenomes generated by the polyploidization event.