Almost finished: the complete genome sequence of Mycosphaerella graminicola

Mycosphaerella graminicola is a haploid ascomycete causing septoria tritici blotch of wheat. An 8.9x shotgun sequence of bread wheat strain IPO323 was generated through the Community Sequencing Program of the U.S. Department of Energy’s Joint Genome Institute (JGI), and was finished at the Stanford Human Genome Center. The finished genome of M. graminicola contains 39.6 Mb. All available ESTs (37,747) were placed on the finished assembly to assess completeness. In addition, 1793 Diversity Array Technology markers were sequenced at JGI and aligned with the physical map. The genetic and physical maps showed near-perfect colinearity, demonstrating the high quality of both the genetic linkage map and the genome assembly. Fifteen scaffolds are complete and represent entire chromosomes with sizes from 548 kb to 6 Mb. In addition, six scaffolds (ranging from 21 kb to 2.4 Mb) contain a single telomere and could connect in any combination. Two additional scaffolds do not contain telomeres and only 17 gaps remain to be closed. Our sequence data suggest that isolate IPO323 contains 18-20 chromosomes, which represents the highest number of chromosomes reported among ascomycetes. This conclusion is corroborated by high-density genetic linkage maps and detailed pulsed-field gel analyses. The complete mitochondrial sequence is a circular genome of 43,947 bp. The machine annotation predicted 13,413 genes, of which 1126 have been annotated manually (http://www.jgi.doe.gov/Mgraminicola). Gene annotations generally indicate that M. graminicola has fewer genes per family than other plant-pathogenic filamentous fungi, which may reflect its initially extracellular biotrophic and subsequently necrotrophic lifestyle. This genome represents the first nearly finished genome of any filamentous plant pathogen and is of great importance for comparative genomics involving other Dothideales, such as the destructive banana Black Sigatoka pathogen Mycosphaerella fijiensis that currently is sequenced at the ~7.1x level. http://www.fgsc.net/asil2007/xxivprogram.pdf