A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres

Abstract

Background: Pyrenophora teres f. teres is a necrotrophic fungal pathogen and the cause of one of barley's most important diseases, net form of net blotch. Here we report the first genome assembly for this species based solely on short Solexa sequencing reads of isolate 0-1. The assembly was validated by comparison to BAC sequences, ESTs, orthologous genes and by PCR, and complemented by cytogenetic karyotyping and the first genome-wide genetic map for P. teres f. teres.

Results: The total assembly was 41.95 Mbp and contains 11,799 gene models of 50 amino acids or more. Comparison against two sequenced BACs showed that complex regions with a high GC content assembled effectively. Electrophoretic karyotyping showed distinct chromosomal polymorphisms between isolates 0-1 and 15A, and cytological karyotyping confirmed the presence of at least nine chromosomes. The genetic map spans 2477.7 cM and is composed of 243 markers in 25 linkage groups, and incorporates simple sequence repeat markers developed from the assembly. Among predicted genes, non-ribosomal peptide synthetases and efflux pumps in particular appear to have undergone a P. teres f. teres-specific expansion of non-orthologous gene families.

Conclusions: This study demonstrates that paired-end Solexa sequencing can successfully capture coding regions of a filamentous fungal genome. The assembly contains a plethora of predicted genes that have been implicated in a necrotrophic lifestyle and pathogenicity and presents a significant resource for examining the bases for P. teres f. teres pathogenicity.

Figure 1

Comparison of the P. teres f. teres Solexa assembly with Sanger-sequenced BACs using CIRCOS [69]. BACs 8F17 and 1H13 are represented in blue. Percent GC is shown in the middle track with regions >40% shown in green and regions <40% shown in red. The inner track shows assembly scaffold BLASTN hits to the BACs.

Figure 2

CHEF (clamped homogenous electric fields) separations of P. teres f. teres chromosomes. (a) Electro-karyotypes of isolate 0-1 with nine chromosomal bands indicated. (b) Chromosome level polymorphisms between isolates 0-1 and 15A.

Figure 3

Visualization of P. teres f. teres chromosomes using the germ tube burst method (GTBM). (a) Nuclei at interphase. (b) Nuclei at early metaphase. (c) Condensed metaphase chromosomes with nine larger chromosomes indicated. Scale bars = 2 μm.

Figure 4

Expanded P. teres f. teres gene clusters. The number of non-orthologous and paralogous genes in each class of genes (as defined by OrthoMCL [25]) is shown at the end of each chart slice and the number of clusters greater than 1 is given in the key.

Figure 5

Genetic linkage map of P. teres f. teres. Linkage groups are drawn with genetic distance in cM on the scale bar to the left and are ordered according to their genetic length. AFLP markers are indicated by the MseI (M) and EcoRI (E) primer combination (Additional file 6), followed by the size of the marker. SSR markers were developed from three sources: ESTs, STMSs and the genome assembly, prefixed PtESTSSR_, hSPT2_, and PttGS_, respectively. The mating type locus (MAT) is depicted in bold on linkage group 4.

Figure 6

Genetic linkage map of P. teres f. teres continued from Figure 5. Linkage groups are drawn with genetic distance in cM on the scale bar to the left and are ordered according to their genetic length.