Figure 1.
Relationships among clonal lineages and distribution of recombination events in Verticillium dahliae.
The neighbor-joining tree was constructed in MEGA 5.10 [58] from 26,748 SNPs in 141 isolates of V. dahliae. Each clade or lineage had >99% bootstrap support out of the 1000 replicates. Clonal lineages (from top to bottom) 1A/1B, 2B334, 2A, 4B, 4A, 6 and 2B824 were named after their respective vegetative compatibility groups (VCGs) described previously. Lineage 2BR1 was not previously described. Recombinant lineages 2BR1 and 6 are indicated by arrows with an asterisk. Recombinant haplotypes are indicated by arrows, from isolates VEM481 (clade I), 395, V496 and V498 (clade II-1) and 320 (clade II-2). The number of unique recombination events associated with each hierarchy in the tree is shown on the right hand side (see also Table 3).
Table 1.
Sampling of Verticillium dahliae isolates genotyped from each vegetative compatibility group (VCG)a.
Table 2.
Identification of homologs of meiosis-specific genes in the sequenced genome of Verticillium dahliae isolate VdLs.17.
Figure 2.
Correlation of number of recombination events detected per contig with contig length in Verticillium dahliae (r = 0.91).
Table 3.
Recombination detected within and between clades of Verticillium dahliae shown in Figure 1 using the program RDP3 [59].
Figure 3.
A neighbor-net network of all lineages and recombinant haplotypes of Verticillium dahliae, based on 26,748 SNPs.
The prevalence of closed loops in the network is consistent with other analyses showing extensive recombination among clonal lineages (Figure 1; Table 3). The positions are shown for all lineages, plus individual haplotypes identified as recombinants (isolates VEM481, V496/V498, 395 and 320).
Table 4.
Nucleotide diversity within nonrecombining lineages of Verticillium dahliae based on 26,748 SNPs from genotyping by sequencing [52].
Figure 4.
Confounding effects of chromosome rearrangements on the estimation of the number and location of recombination events when aligning SNPs to a single, haploid reference genome.
In this example, recombination occurs between haplotypes ABCD and abcd. A. Pairings of two homologous chromosomes (blue and red) during meiosis in haploid genomes with the same organization as the reference genome. The four haplotypes of the gametes are shown after recombination between chromosomes by assortment (assuming no crossing over within chromosomes). Recombination is correctly inferred as occurring between AB and CD based on the presence of four gametic haplotypes. B. Mating between individuals with the same reciprocal translocation relative to the reference genome, but without recombination within or between the two chromosomes. No recombination is inferred: only two gametic haplotypes are present. C. Recombination between chromosomes in individuals with the same reciprocal translocation relative to the reference genome. When the gametic haplotypes are aligned to the reference genome, the gene order changes and three recombination events are inferred, two of which are incorrectly inferred as occurring within chromosomes of the reference genome (dashed arrows).