Figure 3. Genome-wide mapping of interchromosomal synteny breakpoints in C. tropicalis identifies a spatial cue for karyotype evolution.

(A) Scaled representation of the color-coded orthoblocks (relative to C. albicans chromosomes) and ICSBs (white lines) in C. tropicalis (Materials and methods). Orthoblocks are defined as stretches of the target genome (C. tropicalis) carrying more than two syntenic ORFs from the same chromosome of the reference genome (C. albicans). The centromeres are represented with black arrowheads. (B) Zoom in view of the C. tropicalis centromere-specific ICSBs on CEN2, CEN3, CEN5 and CENR showing the color-coded (relative to C. albicans chromosomes) ORFs flanking each centromere. C. tropicalis-specific unique ORFs proximal to CEN3 and CEN5 are shown in red. (C) A plot showing the chromosome-wise ICSB density, calculated as number of ICSBs per 100 kb of the C. tropicalis genome (y-axis), as a function of the linear distance from the centromere in nine bins. These bins are a) 0–100 kb on both sides of centromere (bin I), (b) 100–200 kb (bin II), (c) 200–300 kb (bin III), (d) 300–400 kb (bin IV), (e) 400–500 kb (bin V), (f) 500–600 kb (bin VI), (g) 600–700 kb (bin VII), (h) >700 kb to 200 kb from telomere ends (bin VIII), and i) 200 kb from the telomere ends (bin IX). Chr6 was excluded from this analysis, as it does not harbor any ICSB. (D) A violin plot comparing the distribution of lengths of orthoblocks (y-axis) at three different genomic zones: a) the centromere-proximal zone (CP), (b) the centromere-distal zone (CD), and c) telomere-proximal zone (TP). Orthoblocks, which span over more than one zone, were assigned to the zone with maximum overlap. The centromere-distal dataset was compared with the other two groups using the Mann-Whitney U test and the respective P values are mentioned. (E - F) Circos plots representing the convergence of centromere-proximal ORFs of C. tropicalis chromosomes near the centromeres (CEN4 and CEN7) of C. albicans. Chromosomes of C. tropicalis and C. albicans are marked with black and purple filled circles at the beginning of each chromosome, respectively.

Figure 3—figure supplement 1. Genome-wide synteny analysis between C. albicans and C. tropicalis suggests evidence of inter-centromere translocations in the last common ancestor.

(A) Synteny maps of C. tropicalis chromosomes (the lowermost line of each panel, marked by filled black circles numbered from 1 to R), with respect to C. albicans chromosomes (lines above the C. tropicalis chromosomes), in the order of Chr1 to ChrR (top to bottom) for all panels. Centromeres, black triangles. The ORFs (represented as beads) are color-coded: inverted, red and non-inverted, green. The more conserved the reciprocal best hits (RBH) are, the darker are the shades of red/green color. (B) Zoom in view of the synteny relationship between the centromere proximal ORFs of C. tropicalis Chr6 with C. albicans Chr7. (C) The zoom in view of RBH ORFs proximal to the centromeres of C. tropicalis as indicated in the figure, where each centromere is located at an ICSB. (D) A scaled representation of the color-coded orthoblocks (relative to C. tropicalis chromosomes) and ICSBs (white lines) in C. albicans (Materials and methods). Orthoblocks are defined as stretches of the target genome (C. albicans) carrying more than two syntenic ORFs from the same chromosome of the reference genome (C. tropicalis). The centromeres are represented with black arrowheads. (E) Circos plot showing the ICSBs (purple lines on the outer-most circle) on C. tropicalis chromosomes (marked with black filled circles). The centromere proximal ORFs (10 ORFs on both sides) present in C. tropicalis are connected to their homologs present on C. albicans chromosomes (marked by purple filled circles) by color-coded lines (based on their origin). The positions of centromeres are marked with black lines of the inner-most circle in each chromosome. The genomic locations in C. albicans chromosomes showing the convergence of ORFs from at least two centromere-proximal loci of C. tropicalis are marked with red (proximal to the C. albicans centromere) and purple (a non-centromere locus) triangles. Note that all centromeres of C. albicans are proximal to ORFs, homologs of which are proximal to centromeres of C. tropicalis. (F - G) Circos plots showing the convergence of centromere proximal ORFs of C. tropicalis chromosomes near the centromeres on C. albicans chromosomes 3 (CaChr3) and 7 (CaChr7), respectively. Chromosomes of C. tropicalis and C. albicans are marked with black and purple filled circles at the beginning of each chromosome, respectively.