First fungal genome sequence from Africa: A preliminary analysis

Abstract

Some of the most significant breakthroughs in the biological sciences this century will emerge from the development of next generation sequencing technologies. The ease of availability of DNA sequence made possible through these new technologies has given researchers opportunities to study organisms in a manner that was not possible with Sanger sequencing. Scientists will, therefore, need to embrace genomics, as well as develop and nurture the human capacity to sequence genomes and utilise the 'tsunami' of data that emerge from genome sequencing. In response to these challenges, we sequenced the genome of Fusarium circinatum, a fungal pathogen of pine that causes pitch canker, a disease of great concern to the South African forestry industry. The sequencing work was conducted in South Africa, making F. circinatum the first eukaryotic organism for which the complete genome has been sequenced locally. Here we report on the process that was followed to sequence, assemble and perform a preliminary characterisation of the genome. Furthermore, details of the computer annotation and manual curation of this genome are presented. The F. circinatum genome was found to be nearly 44 million bases in size, which is similar to that of four other Fusarium genomes that have been sequenced elsewhere. The genome contains just over 15 000 open reading frames, which is less than that of the related species, Fusarium oxysporum, but more than that for Fusarium verticillioides. Amongst the various putative gene clusters identified in F. circinatum, those encoding the secondary metabolites fumosin and fusarin appeared to harbour evidence of gene translocation. It is anticipated that similar comparisons of other loci will provide insights into the genetic basis for pathogenicity of the pitch canker pathogen. Perhaps more importantly, this project has engaged a relatively large group of scientists including students in a significant genome project that is certain to provide a platform for growth in this important area of research in the future.

Exposure to a pine pathogen enhances growth and disease resistance in Pinus radiata seedlings

“…The effects of F. circinatum may also involve production of growthenhancing compounds in planta or in soil, as has been described for Fusarium oxysporum, which produces volatiles that enhance growth of diverse plant species (Bitas et al, 2011) and Fusarium fujikuroi, which stimulates growth of rice seedlings by synthesizing gibberellic acid (Tudzynski, 1999). Although F. circinatum apparently does not produce gibberellic acid (Malonek et al, 2005;Wingfield et al, 2012), scrutiny of the F. circinatum genome, which is now fully sequenced , may reveal the capacity to synthesize other plant growth promoting metabolites. The results of this study demonstrate that exposure of roots to F. circinatum can enhance resistance to shoot infections by the same fungus and promote survival following stem inoculation.…”

Comparative “Omics” of theFusarium fujikuroiSpecies Complex Highlights Differences in Genetic Potential and Metabolite Synthesis

“…The genome of F. graminearum , annotation version 3.2, was retrieved from http://www.helmholtz-muenchen.de/en/ibis/institute/groups/fungal-microbial-genomics/resources/index.html (Wong et al 2011). Brenda Wingfield, University of Pretoria, South Africa provided access to genome sequence of F. circinatum FSP 34 (Wingfield et al 2012). The genome of F. fujikuroi IMI58289 was retrieved from the PEDANT analysis (Wiemann et al 2013).…”

“…At the start of the current study, genome sequences of only eight Fusarium species were publicly available: the FFC species F. circinatum , F. fujikuroi and F. verticillioides , and the nonFFC species F. avenaceum, F. graminearum , F. oxysporum , F. pseudograminearum , and F. solani (Cuomo et al 2007; Coleman et al 2009; Ma et al 2010; Gardiner et al 2012; Wingfield et al 2012; Wiemann et al 2013; Lysøe et al 2014) . In silico analyses indicated that each of these fusaria has the genetic potential to produce 30–60 structurally distinct families of SMs.…”

MAT gene idiomorphs suggest a heterothallic sexual cycle in a predominantly asexual and important pine pathogen

“…To confirm the robustness of NJ analyses, a maximum parsimony analysis was also performed in PAUP 4.0 (Swofford, 2003), using a heuristic search and bootstrapping with 1000 replications. The protein sequences of the MAT genes of Fusarium circinatum (Wingfield et al 2012) were used as an out-group.…”