Figure 1.
Grapevine chromosome groups based on NBS-R gene-to-gene similarities.
Relationships (indicated by joining lines) between grapevine chromosomes based on the 93rd percentile of the distribution of among-clusters BLAST bit scores generated by a pairwise BLAST-P protein sequence comparison. Va (green) and Vc (red) define two genomes based on the chromosome groups indicated. Chromosomes that were also associated with Va or Vc genomes based on the identity scores are highlighted by an asterisk. NBS-R gene clusters (CL) are indicated within gray circles with the number of NBS-R genes in brackets.
Figure 2.
Phylogenetic analysis of grapevine NBS-R genes.
The most abundant NBS-R gene classes were distributed among the different clades as follows: clades B, C, D, I and J included 80, 84, 88, 55, and 73% of CC-type genes, respectively; clade A included 70% of TIR-type genes; clades E, K, and M included 55, 60, and 59% of NBS-LRR genes, respectively; clades F, G, and H included 90, 63, and 67% of NBS-tr genes, respectively. Clades were assigned to Va (green) and Vc (red) genomes based only on clustered genes (Table 1 and Table S5). Asterisks mark clustered genes considered as exceptions to the genome assignment of a specific clade. Bootstrap values for clades A to M are expressed as percentages. The analysis included seven outgroup NBS-R genes of Pinus monticola [24].
Table 1.
Presence of clustered and single (in brackets) NBS-R genes in putative Va and Vc component genomes.
Figure 3.
Triplicate state of Vitis chromosomes.
The formation of triplets is based on the homology among groups of genes located on specific chromosome fragments and homologous DNA segments present on other chromosomes [5], [6], [22]. Assignment of chromosomes to either Va (green) or Vc (red) genomes was based on cluster i) similarity and ii) identity scores. Grey lines represent chromosomes not assigned to the two genomes; they could represent a third genome (Vb), for which we lack direct proof. Roman numbers indicate chromosomes, while Arabic numbers represent the length of the chromosomes in megabase pairs. Exceptions to the assignment of chromosomes are represented by chromosome IV and XIV, which could not be definitively assigned to one of the putative genomes.
Figure 4.
NBS-R genes showing features of residual helitron activity.
The CTAG tetranucleotide and of the inverted repeat forming a stem and loop structure (underlined) are shown. The numbers of nucleotides between the two gene regions are also indicated.
Table 2.
Estimated time of transposition of NBS-R genes.
Table 3.
Estimated time of homogeneous NBS-R cluster formation.
Figure 5.
Hypothesized time of events for the evolution of the Vitis genome.
The evolution of this genome is proposed to have followed two steps leading to hexaploidisation starting from a paleotetraploid state. In the text, a second scenario is discussed in light of the cytological data for the Rosa canina. The same two steps can be hypothesised, with Va and Vc genomes first coexisting in the same nucleus but not exchanging genetic material, and later fusing to generate the hexaploid state. In such a case, polyploidization probably occurred at an intermediate time between 100 and 60 mya.