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

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 SSR 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

Simple sequence repeats in Puccinia graminis: abundance, cross-formae specialis and intra-species utility, and development of novel markers

We evaluated the abundance and nature of simple sequence repeats (SSRs) in the causal agent of stem rust of wheat, Puccinia graminis f. sp. tritici, in order to characterize and develop SSR markers. A strategy was tested in which publicly available genome datasets extracted from genome sequences of P. graminis f. sp. tritici were searched for abundance and mined for candidate novel SSR markers that could be applied to a wide range of Puccinia species. The genome analysis from 393 supercontigs yielded a total of 34,359 SSR repeat motifs. A majority of these (98 %) were mononucleotide, dinucleotide, and trinucleotide repeats. The AG/GA dinucleotide motifs were the most common, and a TTGTT motif was the longest of all SSRs. From a total of 500 primer pairs designed, 460 produced bands within the expected size range and 56 SSR markers were eventually developed. Most of these were tetranucleotide and pentanucleotide motifs with PIC values ranging from 0.40 to 0.91 with an average PIC value of 0.71. The cross amplification of these markers in 11 isolates representing five Puccinia species and six formae speciales of P. graminis was also investigated. The frequency of PCR amplifications was lower for the species P. coronata, P. striiformis and P. triticina, and consequently, no significant polymorphisms were detected. In contrast 10, 10, and 11 polymorphic SSR loci were identified in P. graminis f. sp. secalis, P. graminis f. sp. avenae, and the “Scabrum” rust, respectively. The SSR markers reported here will be useful to characterize and profile global diversity in the important pathogen P. graminis