Figure 1: Carrot chromosome 1 multidimensional topography and tandem repeat evolution.

(a) The integrated linkage map for carrot is shown to the far left (the vertical bar to the left indicates genetic distance in cM). Lines connect a subset of markers to the pseudomolecule. Next, from left to right, are shown the cM/Mb ratio, predicted genes (percent of nucleotides/200-kb window), transcriptomes (percent of nucleotides/200-kb window), class I and class II repetitive sequences (percent of nucleotides/200-kb window), noncoding RNAs (percent of nucleotides/200-kb window), and SNPs (number of SNPs/100-kb window). Genes and TEs are more abundant in the distal and pericentromeric regions of the chromosomes, respectively. DNA pseudomolecules are shown in orange to the right. Gray horizontal lines indicate gaps between superscaffolds. Horizontal blue and red lines labeled on the right indicate the locations of BAC probes hybridized to pachytene chromosome 1 (see b); a horizontal yellow line indicates the location of the telomeric repeats. To the far right is a digitally straightened representation of carrot chromosome 1 probed with oligonucleotide probes to the telomeric repeats (Telo; blue) and the CL80 and Cent-Dc repeats (red) and with probes corresponding to BAC 68M03 (red) specific to chromosome 1 and BACs 20G08 and 20P12 (green) flanking the CL80 repeat. (b) FISH mapping of oligonucleotide probes to telomeric repeats (Telo; yellow) and the CL80 repeat (red) and probes corresponding to BAC clones specific to the termini of the short (1S; green) and long (1L; red) arms of carrot chromosome 1. (c–e) FISH mapping of the CL80 (red) and Cent-Dc (K11; green) repeats on the pachytene complements of DH1 (c), D. guttatus (d), and Daucus littoralis (e). Cent-Dc did not generate any detectable signals in D. guttatus or D. littoralis. Scale bars, 5 μm.