Discovery of single-nucleotide polymorphisms (SNPs) in the uncharacterized genome of the ascomycete Ophiognomonia clavigignenti-juglandacearum from 454 sequence data

• Published in: Molecular ecology resources Vol. 11; no. 4; pp. 693 - 702
• Main Authors: BRODERS, K. D., WOESTE, K. E., SanMIGUEL, P. J., WESTERMAN, R. P., BOLAND, G. J.
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01.07.2011; Wiley Subscription Services, Inc
• Subjects: Ascomycetes; Ascomycota - genetics; asexual fungi; butternut canker; Computational Biology; Genome, Fungal - genetics; Genomes; Genomics; high-throughput marker identification; High-Throughput Nucleotide Sequencing; next generation sequencing; non-model organism; Polymorphism; Polymorphism, Single Nucleotide; reference sequence; Sequence Alignment; single-nucleotide polymorphism
• ISSN: 1755-098X; 1755-0998
• DOI: 10.1111/j.1755-0998.2011.02998.x

The benefits from recent improvement in sequencing technologies, such as the Roche GS FLX (454) pyrosequencing, may be even more valuable in non‐model organisms, such as many plant pathogenic fungi of economic importance. One application of this new sequencing technology is the rapid generation of genomic information to identify putative single‐nucleotide polymorphisms (SNPs) to be used for population genetic, evolutionary, and phylogeographic studies on non‐model organisms. The focus of this research was to sequence, assemble, discover and validate SNPs in a fungal genome using 454 pyrosequencing when no reference sequence is available. Genomic DNA from eight isolates of Ophiognomonia clavigignenti‐juglandacearum was pooled in one region of a four‐region sequencing run on a Roche 454 GS FLX. This yielded 71 million total bases comprising 217 000 reads, 80% of which collapsed into 16 125 754 bases in 30 339 contigs upon assembly. By aligning reads from multiple isolates, we detected 298 SNPs using Roche’s GS Mapper. With no reference sequence available, however, it was difficult to distinguish true polymorphisms from sequencing error. Eagleview software was used to manually examine each contig that contained one or more putative SNPs, enabling us to discard all but 45 of the original 298 putative SNPs. Of those 45 SNPs, 13 were validated using standard Sanger sequencing. This research provides a valuable genetic resource for research into the genus Ophiognomonia, demonstrates a framework for the rapid and cost‐effective discovery of SNP markers in non‐model organisms and should prove especially useful in the case of asexual or clonal fungi with limited genetic variability.