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

Autor: Anna Lipzen, Nancy N. Nichols, Jan Dirk van Elsas, Diego Javier Jiménez, Kurt LaButti, Mi Yan, Igor V. Grigoriev, Kerrie Barry, Stephen J. Mondo, Ronald E. Hector
Přispěvatelé: Van Elsas lab
Jazyk: angličtina
Rok vydání: 2019
Předmět:
Allopolyploidization
CAZy
Coniochaeta
In silico
lcsh:Biotechnology
Cellulase
Management
Monitoring
Policy and Law
Biology
Applied Microbiology and Biotechnology
Genome
SEQUENCE
lcsh:Fuel
BIOMASS
Industrial Biotechnology
03 medical and health sciences
chemistry.chemical_compound
lcsh:TP315-360
lcsh:TP248.13-248.65
Gene duplication
Genetics
Lignocellulolytic enzymes
VEGETATIVE COMPATIBILITY
PHYLOGENETIC ANALYSIS
Fungal genomics
TRANSCRIPTOME
Gene
030304 developmental biology
0303 health sciences
030306 microbiology
Renewable Energy
Sustainability and the Environment
Research
MICROBIAL CONSORTIA
Human Genome
GLYCOSIDE HYDROLASE FAMILY
Wheat straw
BETA-L-ARABINOFURANOSIDASE
Chemical Engineering
Reticulate evolution
Xyloglucan
General Energy
chemistry
LYTIC POLYSACCHARIDE MONOOXYGENASES
Lytic polysaccharide monoxygenases
biology.protein
ENZYMES
Biotechnology
Zdroj: Biotechnology for Biofuels, Vol 12, Iss 1, Pp 1-18 (2019)
Biotechnology for biofuels, vol 12, iss 1
Biotechnology for Biofuels, 12(1):229. BioMed Central Ltd.
Biotechnology for Biofuels
ISSN: 1754-6834
DOI: 10.1186/s13068-019-1569-6
Popis: Background Particular species of the genus Coniochaeta (Sordariomycetes) exhibit great potential for bioabatement of furanic compounds and have been identified as an underexplored source of novel lignocellulolytic enzymes, especially Coniochaeta ligniaria. However, there is a lack of information about their genomic features and metabolic capabilities. Here, we report the first in-depth genome/transcriptome survey of a Coniochaeta species (strain 2T2.1). Results The genome of Coniochaeta sp. strain 2T2.1 has a size of 74.53 Mbp and contains 24,735 protein-encoding genes. Interestingly, we detected a genome expansion event, resulting ~ 98% of the assembly being duplicated with 91.9% average nucleotide identity between the duplicated regions. The lack of gene loss, as well as the high divergence and 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 species (allopolyploidization). Phylogenomic analysis revealed that 2T2.1 is related Coniochaeta sp. PMI546 and Lecythophora sp. AK0013, which both occur endophytically. Based on carbohydrate-active enzyme (CAZy) annotation, we observed that even after in silico removal of its duplicated content, the 2T2.1 genome contains exceptional lignocellulolytic machinery. Moreover, transcriptomic data reveal the overexpression of proteins affiliated to CAZy families GH11, GH10 (endoxylanases), CE5, CE1 (xylan esterases), GH62, GH51 (α-l-arabinofuranosidases), GH12, GH7 (cellulases), and AA9 (lytic polysaccharide monoxygenases) when the fungus was grown on wheat straw compared with glucose as the sole carbon source. Conclusions We provide data that suggest that a recent hybridization between the genomes of related species may have given rise to Coniochaeta sp. 2T2.1. Moreover, our results reveal that the degradation of arabinoxylan, xyloglucan and cellulose are key metabolic processes in strain 2T2.1 growing on wheat straw. Different genes for key lignocellulolytic enzymes were identified, which can be starting points for production, characterization and/or supplementation of enzyme cocktails used in saccharification of agricultural residues. Our findings represent first steps that enable a better understanding of the reticulate evolution and “eco-enzymology” of lignocellulolytic Coniochaeta species.
Databáze: OpenAIRE
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