The Kingdom Fungi constitutes the largest group of eukaryotic organisms on earth, and has been estimated to comprise between 2.2 and 3.8 million species.¹ Among these are thousands of species of scientifically, ecologically and commercially important mushrooms, molds, yeasts, and plant parasitic rusts and smuts, as well as the widely studied model organisms Saccharomyces cerevisiae,  Schizosaccharomyces pombe, Neurospora crassa and Penicillium chrysogenum.  Humans have enjoyed a love-hate-relationship with fungi for centuries, as they produce deadly toxins, life-threatening human illnesses, and devastating diseases of crops and livestock. Nevertheless, they allow us to bake bread, brew beer, and indulge in a plethora of cultured and fermented foods and beverages. In addition, fungi have given us many life-saving antibiotics, immunosuppressants and other chemotherapeutic agents. They have allowed us to characterize evolutionary relationships and ecosystem dynamics; understand cell cycle regulation, chromatin structure and gene regulation; identify biomarkers; produce recombinant proteins and energy, and can be used in bioremediation.

The Proximo^™ Genome Scaffolding Platform is fast becoming an indispensable tool in the study of fungi. Like their animal and plant cousins, fungal genomes contain challenging elements, such as repeats, duplications and structural elements that complicate both sequencing and assembly. Based on proximity ligation (Hi-C) technology, Proximo has enabled the untangling some of these sticky genomic knots, and shows promise in taming genomes across this diverse and neglected kingdom of life.

Learn how Hi-C was used:

• in combination with ChIP-seq and high-throughput sequencing to identify and characterize the centromeres in each of the ten species of the plant pathogenic fungal genus Verticillium.
• in combination with PacBio data, to assemble the unusually large (>1 Gb) and repetitive genome of the pandemic biotype of Austropuccinia psidii (myrtle rust).
• to eludicate how the devastating wheat stem rust pathogen, Puccinia graminis f. sp. tritici, mobilizes its RNAi machinery to quickly and aggressively overcome plant resistance.
• to assemble complete haplotypes for both haploid genomes of two strains of the deadly wheat stem rust Ug99, found to arise through somatic hybridization.
• to generate high-quality genomes of six strains of the cyclosporin-producing insect pathogen, Tolypocladium inflatum; thereby gaining valuable insights in secondary metabolite and toxin production.
• in combination with RNA-Seq to understand the genetic basis for symbiosis between the filamentous fungus Epichloë festucae and grasses.
• to discover a new hybrid yeast, later dubbed Pichia apotheca.  This novel hybrid species, which gives beer a very unique flavor, has since been used by home-brewers to ply their craft.
• by researchers from the Institut Pasteur and the University of Washington to resolve centromeres and rDNA clusters in the yeast genome.