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Info • Piromyces UH3-1 haplotypes
Group Name:
Piromyces UH3-1 haplotypes

Piromyces sp. UH3-1 (proposed name Piromyces indianae) is an obligate anaerobic fungus (phylum Chytridiomycota, class Neocallimastigomycetes). Anaerobic fungi are commonly found within the digestive tracts of ruminants and hindgut fermenters (large herbivores), where they provide nutrition to the host animal by digesting fiber-rich plant substrates. UH3-1 was isolated from the feces of a donkey (Equus africanus asinus) in Independence, Indiana in 2016. The species is monocentric, possessing a single oval zoosporangium, which develops dozens of zoospores in a life cycle similar to other members of Chytridiomycota. The zoosporangium also develops an extensively branched rhizoidal system devoid of nuclei that grows invasively into plant material. UH3-1, and other anaerobic fungi, are of particular interest as they secrete a wide array of fungal- and bacterially-sourced carbohydrate active enzymes (CAZymes) for hydrolysis of plant cell walls (Solomon et al, 2016, Haitjema et al, 2017). Secreted CAZymes are tailored to plant composition: UH3-1 growth and CAZyme activity is not hindered by the type of lignin present in the plant substrate, unlike many other fungi, suggesting that they are able to recognize and adapt well to varying plant cell wall structures (Hooker et al, 2018). The genome of UH3-1 will aid in the discovery of novel CAZymes that are better suited to specific components of lignocellulosic biomass including enzymes more robust to lignin composition. Furthermore, the genomes will enable future systems biology characterization of the genetic and epigenetic regulatory strategies these fungi use to adapt to substrate composition, ultimately paving the way for strain optimization and development.

Chromatin capture data (Hi-C) was generated by Phase genomics for the sequencing of the Piromyces sp. UH3-1 genome. The draft assembly of Piromyces sp. UH3-1 generated using PacBio (Piromy1), was then used along with PacBio read data to purify haplotypes using FALCON-Phase (Kronenberg et al., 2019). Phase Genomics' Hi-C genome scaffolding platform was then used to create chromosome-scale scaffolds (generated by Kyle Langford at Phase Genomics), followed by error correction using Juicebox (Neva et al., 2016, Suhas et al., 2014). The final scaffolds included 12 chromosomes for Piromyces sp. UH3-1 Phase 0 (spanning 83.4 Mbp) with a scaffold N50 of 7.3 Mbp, and 12 chromosomes (spanning 83.1 Mbp) for Piromyces sp. UH3-1 phase 1 with a scaffold N50 of 7.2 Mbp. While most of the assembly is contained within these 12 scaffolds, unplaced scaffolds were additionally included here for annotation using the JGI annotation pipeline.

References:

Haitjema, C. H. et al. A parts list for fungal cellulosomes revealed by comparative genomics. Nature Microbiology 2, 17087 (2017).

Hooker, C. A. et al. Hydrolysis of untreated lignocellulosic feedstock is independent of S-lignin composition in newly classified anaerobic fungal isolate, Piromyces sp. UH3-1. Biotechnology for Biofuels 11, 293 (2018).

Solomon, K. V. et al. Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes. Science 351, 1192–1195 (2016).

Kronenberg Z.N, Hall R.J, Hiendleder S, Smith T.P.L, Sullivan S.T, Williams J.L, Kingan S.B. "FALCON-Phase: Integrating PacBio and Hi-C data for phased diploid genomes." bioRxiv 327064; doi: https://doi.org/10.1101/327064.

Neva C. Durand*, James T. Robinson*, Muhammad S. Shamim, Ido Machol, Jill P. Mesirov, Eric S. Lander, and Erez Lieberman Aiden. “Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom.” Cell Systems, July 2016.

Suhas S.P. Rao*, Miriam H. Huntley*, Neva C. Durand, Elena K. Stamenova, Ivan D. Bochkov, James T. Robinson, Adrian L. Sanborn, Ido Machol, Arina D. Omer, Eric S. Lander, Erez Lieberman Aiden. “A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping.” Cell 159, 2014.