Table 1.
Estimation of genome size and sequencing of selected Fabeae species.
Fig 1.
Genome size evolution and repeat composition of Fabeae species.
(A) Phylogenetic tree of the 23 investigated species with their genome sizes shown by the colours of the terminal branches. Colour gradients within the tree branches indicate inferred genome size changes and species names are represented by the codes given in Table 1. All nodes except those labelled with "x" were highly supported with posterior probabilities >0.95 (see S1 Fig for details). (B) Graphical representation of the genomic abundances of major types of repetitive sequences. The area of the rectangles are proportional to the total length of individual repeats per monoploid genome size (1Cx) (see S2 Table). For LTR-retrotransposons, the colour of the rectangle indicates the estimated ratio of solo-LTRs to full-length elements (data given in Table 3). Repeat abbreviations: Chrom, Chromovirus; Max., Maximus/SIRE; DNA, DNA (class II) transposons; SAT, satellite repeats. Copia includes all Ty1/copia lineages except Maximus/SIRE and Angela; LTR, unclassified LTR-retrotransposons, Other 0.01 includes remaining repeats with abundance exceeding 0.01% of the genome.
Table 2.
Correlation of repeat amounts with genome size variation in Fabeae and contribution of individual repeats to the genome size differences between species.
Fig 2.
Phylogenetic distribution, abundance and sequence similarity between the thirty largest clusters representing satellite repeats (A) and Ogre retrotransposons (B) from the comparative clustering analysis.
Bar plots at the top show cluster sizes (total length of all reads in Mbp) and rectangle areas below display the relative proportions of reads from individual species within each cluster. Previously described families of satellite repeats are marked with their names on panel A. The colours of the rectangles indicate the average pairwise similarities of read sequences.
Fig 3.
Southern blot detection of selected Ogre and Angela sequences in the genomes of Fabeae species.
The blots were prepared from equal amounts of genomic DNA of each species digested with SspI and hybridized to probes corresponding to sequence variants of Ogre derived from Vicia sylvatica (A), Lathyrus latifolius (B) and Vicia pannonica (C). These variants are evident as narrow parallel paths on a graph representation [31] of cluster CL7 (E) where reads from these species are highlighted by blue, red and green colours, respectively (reads of all other species are in grey). For the Angela element cluster CL177, reads of all species (grey dots) generated a narrow linear graph due to their high sequence similarities (F). The corresponding probe detected several conserved bands (arrows) on the Southern blot (D).
Fig 4.
Sequence conservation of repeats between Fabeae species.
The ratio Hs/Ho was calculated for each read within individual groups of repeats, where Hs was the frequency of similarity hits to reads from the same species and Ho was the frequency of hits to reads from all other species. The histograms show the distribution of Hs/Ho ratios for different repeats, with numbers of reads plotted along the y-axis. The Hs/Ho ratios are close to 1 (0 on the log scale) for highly conserved sequences whereas larger values correspond to sequence divergence, resulting in higher frequencies of hits within than between species (for example, a value of 2 on the x-axis corresponds to reads producing 100-fold more intra-specific than inter-specific hits).
Table 3.
Estimated ratios of solo-LTRs to complete elements (Rsf).