Sequencing and annotation of the Ophiostoma ulmigenome

Abstract

BackgroundThe ascomycete fungus Ophiostoma ulmi was responsible for the initial pandemic of the massively destructive Dutch elm disease in Europe and North America in early 1910. Dutch elm disease has ravaged the elm tree population globally and is a major threat to the remaining elm population. O. ulmi is also associated with valuable biomaterials applications. It was recently discovered that proteins from O. ulmi can be used for efficient transformation of amylose in the production of bioplastics.ResultsWe have sequenced the 31.5 Mb genome of O.ulmi using Illumina next generation sequencing. Applying both de novo and comparative genome annotation methods, we predict a total of 8639 gene models. The quality of the predicted genes was validated using a variety of data sources consisting of EST data, mRNA-seq data and orthologs from related fungal species. Sequence-based computational methods were used to identify candidate virulence-related genes. Metabolic pathways were reconstructed and highlight specific enzymes that may play a role in virulence.ConclusionsThis genome sequence will be a useful resource for further research aimed at understanding the molecular mechanisms of pathogenicity by O. ulmi. It will also facilitate the identification of enzymes necessary for industrial biotransformation applications.

Quorum-Sensing Mechanisms Mediated by Farnesol in Ophiostoma piceae: Effect on Secretion of Sterol Esterase

“…Genes homologous to those regulated by QS mechanisms in C. albicans, coding for transcriptional repressor (tup1) and adenylate cyclase (cyr1) (16,23), were searched in the publicly available genomes of O. piceae (29) and Ophiostoma ulmi (30). Once the genes with highest homology were identified, a BLAST search against the NCBI database was carried out for both genes.…”

Breeding and scientific advances in the fight against Dutch elm disease: Will they allow the use of elms in forest restoration?

“…Later studies explained the genetic diversity of DED fungi populations, mainly in Europe and North America, and reported (i) higher diversification of DED fungi populations in Europe than in North America; (ii) coexistence of O. ulmi and O. novo-ulmi during the initial stages of the second pandemic and the presence of rare but transient hybrids between the two species in Europe (Brasier et al 1998); (iii) rapid replacement of O. ulmi by O. novo-ulmi at each location; and (iv) rapid emergence of hybrids between the two subspecies of O. novo-ulmi, the European and North American races Temple et al 2006;Solla et al 2008;Brasier and Kirk 2010). The genomes of O. ulmi and O. novo-ulmi were subsequently sequenced and annotated (Forgetta et al 2013;Khoshraftar et al 2013;Comeau et al 2015), adding to information gathered earlier using traditional molecular methods. Insertional mutagenesis, analysis of genetic crosses and inspection of Ophiostoma spp.…”

Genomics of the Dutch elm disease pathosystem: are we there yet?

“…This approach was used by Khoshraftar and colleagues to get a first glimpse of the transcriptome of O. ulmi W9 yeast cultures. Approximately 80% of the gene models identified ab initio were represented by at least one transcript in the O. ulmi W9 RNA-Seq dataset (Khoshraftar et al 2013), which represents a ca 3.5-fold improvement over previous EST data for O. novo-ulmi H327 (Hintz et al 2011). The above-mentioned studies, however, were exploratory and did not include biological replicates.…”

“…On the other hand, none of the 8640 nuclear genes predicted by automated gene-calling algorithms was annotated. Conversely, the genome of O. ulmi W9 (Khoshraftar et al 2013) was not sequenced with the same depth and, as a consequence, could only be scaffolded and not completely assembled. The authors of this work, however, were able to provide an initial annotation of the O. ulmi W9 genome based on transcriptional data obtained by large-scale RNA sequencing (RNA-Seq).…”

“…In 2013, the genomic sequences of O. novo-ulmi subsp. novo-ulmi (Forgetta et al 2013) and O. ulmi (Khoshraftar et al 2013) were released within weeks of each other. The two genomes are very similar in size and gene number, with 31.8 Mb and 8640 nuclear genes predicted in O. novo-ulmi H327, compared to 31.5 Mb and 8639 predicted genes in O. ulmi W9 (Tab.…”