Diversity in essential and accessory chromosomes in the <i>Mycosphaerella</i> clade.

<p>Chromosomes of the outgroup species <i>Septoria passerinii</i> (S.p.), two isolates of <i>Mycosphaerella</i> S2, one isolate of <i>Mycosphaerella</i> S1, and three isolates of <i>M. graminicola</i> were visualized by pulsed-field gel electrophoresis (PFGE). <i>Mycosphaerella</i> S2 and S1 are found on wild grasses in Iran, the center of origin of <i>M. graminicola</i>, a major leaf pathogen of wheat <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002608#ppat.1002608-Stukenbrock1" target="_blank">[14]</a>. The size markers are <i>Hansenula wingei</i> chromosomes. The phylogenetic tree is based on a six-gene alignment.</p

Genomic characterization of chromosome 14 in the <i>Zymoseptoria tritici</i> reference isolate IPO323.

<p>Orange shades indicate the alignment breakpoints identified among isolates of <i>Z. tritici</i>. A) Repeat density (for repeats up to a period size of 50 bp). B) GC content is shown in sliding windows with a window length of 5 kb. C) Numbers of genes are reported for each 5 kb window.</p

Variability in accessory chromosomes among progeny of three crosses between <i>Zymoseptoria tritici</i> isolates.

<p>A) Progeny of a cross between isolates 3D7 and 1A5 (Cross 3). Chromosomal segments of core chromosomes 10 and 13 and accessory chromosomes 14–21 were assayed by PCR. The two top rows indicate the two parental genotypes. The green bars show the number of individual chromosomal segments among the 48 progeny. B), D) and F) Test for random segregation of chromosomal segments that are present in only one of the two parental isolates. The −log₁₀ transformed <i>p</i> values were corrected for non-independence and the horizontal bar represents the Bonferroni-corrected significance threshold (<i>p</i><0.0007). C) Chromosomal segment numbers among 48 progeny from a cross between isolates 1E4 and 1A5 (Cross 2). E) Chromosomal segment numbers among 48 progeny from a cross between isolates 9B8B and 9G4C (Cross 1).</p

Illumina resequencing and assembly statistics of <i>Zymoseptoria tritici</i> isolates from the Swiss population.

1<p>All samples were submitted under NCBI BioProject ID [PRJNA178194].</p

Breakage-fusion-bridge Cycles and Large Insertions Contribute to the Rapid Evolution of Accessory Chromosomes in a Fungal Pathogen

<div><p>Chromosomal rearrangements are a major driver of eukaryotic genome evolution, affecting speciation, pathogenicity and cancer progression. Changes in chromosome structure are often initiated by mis-repair of double-strand breaks in the DNA. Mis-repair is particularly likely when telomeres are lost or when dispersed repeats misalign during crossing-over. Fungi carry highly polymorphic chromosomal complements showing substantial variation in chromosome length and number. The mechanisms driving chromosome polymorphism in fungi are poorly understood. We aimed to identify mechanisms of chromosomal rearrangements in the fungal wheat pathogen <i>Zymoseptoria tritici</i>. We combined population genomic resequencing and chromosomal segment PCR assays with electrophoretic karyotyping and resequencing of parents and offspring from experimental crosses to show that this pathogen harbors a highly diverse complement of accessory chromosomes that exhibits strong global geographic differentiation in numbers and lengths of chromosomes. Homologous chromosomes carried highly differentiated gene contents due to numerous insertions and deletions. The largest accessory chromosome recently doubled in length through insertions totaling 380 kb. Based on comparative genomics, we identified the precise breakpoint locations of these insertions. Nondisjunction during meiosis led to chromosome losses in progeny of three different crosses. We showed that a new accessory chromosome emerged in two viable offspring through a fusion between sister chromatids. Such chromosome fusion is likely to initiate a breakage-fusion-bridge (BFB) cycle that can rapidly degenerate chromosomal structure. We suggest that the accessory chromosomes of <i>Z. tritici</i> originated mainly from ancient core chromosomes through a degeneration process that included BFB cycles, nondisjunction and mutational decay of duplicated sequences. The rapidly evolving accessory chromosome complement may serve as a cradle for adaptive evolution in this and other fungal pathogens.</p></div

DRYAD - All traits raw data_140912

Trait values of replicates of 14 isolates of each of nine Rhynchosporium commune populations. The eight quantitative traits studied were: growth rate at 12°C, growth rate at 18°C, growth rate at 22°C, fungicide resistance, melanization, spore size, spore number, and virulence

Initiation of a breakage-fusion-bridge cycle of <i>Zymoseptoria tritici</i> chromosome 17 during meiosis.

<p>A) Genome resequencing of two progeny (A2.2 and A66.2) from a cross between the parental isolates 1E4 and 1A5. Parent 1A5 carries accessory chromosome 17 (parent 1E4 is missing chromosome 17). Illumina sequencing reads were mapped to known coding regions of chromosome 17 on the reference genome IPO323. Black and white segments of the bars represent presence and absence, respectively, of particular coding sequences in 20 kb sections along chromosomes 17. B) Variation in read density along chromosome 17 of parental isolate 1A5 and progeny A2.2 and A66.2. C) Variation in read density among accessory chromosomes in the offspring A2.2 and A66.2. Illumina sequencing reads were mapped to coding sequences of the reference genome IPO323. Read density is reported as fold-difference between the offspring and the parental isolate 1A5. As a reference, the mean fold-difference on core chromosomes is reported as a horizontal line. Both offspring showed a near two-fold higher read density on chromosome 17 compared to other accessory chromosomes. D) Illumina sequencing of an excised chromosomal band at 0.9 Mb identified by PFGE in the offspring A2.2. Illumina sequencing reads were mapped to coding sequences of all chromosomes of the reference genome IPO323. E) Schematic illustration of the hypothesized non-allelic homologous recombination between inverted repeats that generated chromosome 17 in offspring A2.2 and A66.2. The resulting isodicentric chromosome can initiate a breakage-fusion-bridge cycle while the acentric chromosome will be lost during successive rounds of cell division.</p

Comparisons of synteny among different variants of accessory chromosome 14 in related species.

<p>Scaffolds from <i>de novo</i> assemblies of the <i>Z. tritici</i> isolates 1E4 (n = 17), 9G4C (n = 16), 3D1 (n = 11) and A26b (n = 7) aligning to chromosomes 14 of the reference isolate IPO323 (horizontal axis) are shown. Scaffolds from isolates of related species <i>Z. pseudotritici</i> (5.9.1; n = 9) and <i>Z. passerinii</i> (P63; n = 4) aligning to chromosomes 14 of the reference isolate IPO323 are shown below. Orange bars show conserved deletions shared among different isolates and species in comparison to the reference chromosome 14. The grey bar indicates a putative deletion in <i>Z. passerinii</i> not spanned by a scaffold. Scaffolds are differentiated by color.</p

Pulsed-field gel electrophoresis of accessory chromosomes in the parental isolates 1E4 and 1A5, as well as their progeny A2.2 and A66.2.

<p>The isolate IPO323 was added as a reference. Both progeny showed a new chromosomal band at 0.9 Mb that is absent in either parental isolate and other screened progeny. Sc represents chromosomes of <i>Saccharomyces cerevisiae</i> added as a size marker. A) Pulsed-field gel electrophoresis of medium-sized chromosomes (up to approx. 3 Mb) of parental isolates 1E4 and 1A5 and 7 progeny. Progeny A2.2 and A66.2 showed a new chromosomal band at 0.9 Mb indicated by an asterisk. B) Pulsed-field gel electrophoresis of accessory chromosomes of parental isolates 1E4 and 1A5 and progeny A2.2 and A66.2. Asterisks identify chromosome 17 variants identified by hybridization. C) Southern hybridization of a chromosome 17 specific probe on chromosomes separated by pulsed-field gel electrophoresis of parental isolates, progeny and the reference isolate IPO323 as in B).</p

Raw data Dryad

Growth rate data in mm/day for all temperatures, populations, isolates and replicates