Genome expansion by allopolyploidization in the fungal strain Coniochaeta 2T2.1 and its exceptional lignocellulolytic machinery

Authors: MONDO, STEPHEN - Department Of Energy Joint Genome; JIMENEZ, DIEGO JAVIER - Universidad De Los Andes; Hector, Ronald - Ron; LIPZEN, ANNA - Department Of Energy Joint Genome; YAN, MI - Department Of Energy Joint Genome; LABUTTI, KURT - Department Of Energy Joint Genome; BARRY, KERRIE - Department Of Energy Joint Genome; DIRK VAN ELSAS, JAN - University Of Groningen; GRIGORIEV, IGOR - Department Of Energy Joint Genome; Nichols, Nancy

Submitted to: Biotechnology for Biofuels and Bioproducts
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/12/2019
Publication Date: 9/23/2019
Citation: Mondo, S.J., Jimenez, D.J., Hector, R.E., Lipzen, A., Yan, M., Labutti, K., Barry, K., Dirk Van Elsas, J., Grigoriev, I.V., Nichols, N.N. 2019. Genome expansion by allopolyploidization in the fungal strain Coniochaeta 2T2.1 and its exceptional lignocellulolytic machinery. Biotechnology for Biofuels. 12:229. https://doi.org/10.1186/s13068-019-1569-6.
DOI: https://doi.org/10.1186/s13068-019-1569-6

Interpretive Summary: This study reports genome and gene expression features of the fungus, Coniochaeta sp. strain 2T2.1, which was isolated from microbial-degraded wheat straw. Interestingly, this fungus has a genome nearly twice the size of its closest relatives, likely due to recent hybridization with a closely-related strain. This phenomenon could increase fitness for plant cell wall deconstruction. Moreover, the results confirm that degradation of plant wall polymers such as arabinoxylan, xyloglucan, and cellulose are highly active processes in this strain. We have identified several highly expressed enzymes involved in degrading plant cell walls, which can be starting points for production, characterization and/or supplementation of enzyme cocktails used in converting agricultural residues to higher-value products.

Technical Abstract: Some species from the genus Coniochaeta exhibit great potential for bioabatement of furanic compounds and have been identified as an underexplored source of novel lignocellulolytic enzymes. However, there is a lack of information about its metabolic features. Here, we report the first in-depth genome/transcriptome survey of a Coniochaeta species (strain 2T2.1). Interestingly, we have detected a genome expansion event (74.53 Mbp) resulting in a duplication of ~97% of all gene models with ~92% of identity between the duplicated regions at the amino acid level. A self-synteny plot reveals that synteny is well conserved, with few genome rearrangements and gene losses between duplicates. Lack of gene loss despite high divergence, coupled with strong genome-wide signatures of purifying selection between copies indicates that this is likely a recent duplication, which arose through hybridization between two related Coniochaeta-like strains. Phylogenomic comparison analysis showed that 2T2.1 was closely related with the endophytes Coniochaeta sp. PMI546 and Lecythophora sp. AK0013. Based on carbohydrate-active enzyme (CAZy) annotation, we observed that 2T2.1 contains powerful lignocellulolytic machinery, even after removing duplicated content. Moreover, the transcriptomic data showed an overexpression of different endoxylanases, xylan esterases, a-L-arabinofuranosidases, cellulases and lytic polysaccharide monoxygenases when the fungus was grown on wheat straw compared with glucose as the sole carbon source. The data presented in this study increase the eco-evolutionary understanding of this fungus and identifies discovery of novel proteins useful in second-generation biorefinery applications.