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

Abstract

Abstract 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 (xylanmore » 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.« less

Authors:
; ORCiD logo; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1618762
Alternate Identifier(s):
OSTI ID: 1580869
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Published Article
Journal Name:
Biotechnology for Biofuels
Additional Journal Information:
Journal Name: Biotechnology for Biofuels Journal Volume: 12 Journal Issue: 1; Journal ID: ISSN 1754-6834
Publisher:
Springer Science + Business Media
Country of Publication:
Netherlands
Language:
English
Subject:
09 BIOMASS FUELS; Coniochaeta; Fungal genomics; Allopolyploidization; Lignocellulolytic enzymes; Lytic polysaccharide monoxygenases; Wheat straw

Citation Formats

Mondo, Stephen J., Jiménez, Diego Javier, Hector, Ronald E., Lipzen, Anna, Yan, Mi, LaButti, Kurt, Barry, Kerrie, van Elsas, Jan Dirk, Grigoriev, Igor V., and Nichols, Nancy N. Genome expansion by allopolyploidization in the fungal strain Coniochaeta 2T2.1 and its exceptional lignocellulolytic machinery. Netherlands: N. p., 2019. Web. doi:10.1186/s13068-019-1569-6.
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Mondo, Stephen J., Jiménez, Diego Javier, Hector, Ronald E., Lipzen, Anna, Yan, Mi, LaButti, Kurt, Barry, Kerrie, van Elsas, Jan Dirk, Grigoriev, Igor V., & Nichols, Nancy N. Genome expansion by allopolyploidization in the fungal strain Coniochaeta 2T2.1 and its exceptional lignocellulolytic machinery. Netherlands. https://doi.org/10.1186/s13068-019-1569-6
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Mondo, Stephen J., Jiménez, Diego Javier, Hector, Ronald E., Lipzen, Anna, Yan, Mi, LaButti, Kurt, Barry, Kerrie, van Elsas, Jan Dirk, Grigoriev, Igor V., and Nichols, Nancy N. Mon . "Genome expansion by allopolyploidization in the fungal strain Coniochaeta 2T2.1 and its exceptional lignocellulolytic machinery". Netherlands. https://doi.org/10.1186/s13068-019-1569-6.
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@article{osti_1618762,
title = {Genome expansion by allopolyploidization in the fungal strain Coniochaeta 2T2.1 and its exceptional lignocellulolytic machinery},
author = {Mondo, Stephen J. and Jiménez, Diego Javier and Hector, Ronald E. and Lipzen, Anna and Yan, Mi and LaButti, Kurt and Barry, Kerrie and van Elsas, Jan Dirk and Grigoriev, Igor V. and Nichols, Nancy N.},
abstractNote = {Abstract 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.},
doi = {10.1186/s13068-019-1569-6},
journal = {Biotechnology for Biofuels},
number = 1,
volume = 12,
place = {Netherlands},
year = {Mon Sep 23 00:00:00 EDT 2019},
month = {Mon Sep 23 00:00:00 EDT 2019}
}
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    Defining the eco-enzymological role of the fungal strain Coniochaeta sp. 2T2.1 in a tripartite lignocellulolytic microbial consortium
    journal, November 2019

    • Jiménez, Diego Javier; Wang, Yanfang; Chaib de Mares, Maryam
    • FEMS Microbiology Ecology, Vol. 96, Issue 1
    • DOI: 10.1093/femsec/fiz186
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