Coniochaeta pulveracea is a soft-rot-causing ascomycete able to degrade lignocellulosic biomass. The first draft genome sequence of strain CAB 683 reported here has an estimated size of 30 Mb assembled into 852 scaffolds and 10,035 predicted protein-coding genes.


Coniochaeta pulveracea (Ehrh.) Munk (1948) is a dimorphic ascomycete belonging to the family Coniochaetaceae (order Coniochaetales), inhabiting both living and decaying trees (1). Fungi causing soft-rot decay such as C. pulveracea, are efficient at degrading the polysaccharide constituents of woody material, mainly through the release of extracellular glycosidases from their cell wall-penetrating hyphae (2). Furthermore, soft-rot ascomycetes show various degrees of lignin degradation (3); however, unlike the white-rot-causing basidiomycetes, they do not possess the ligninolytic class II peroxidases, lignin (LiP) and manganese (MnP) peroxidase (4). As LiP and MnP play an essential role in white-rot-mediated lignin degradation (5), soft-rot fungi seemingly possess an alternative enzymatic system to degrade lignin. Reports that representatives from the genus Coniochaeta are capable of rapidly degrading lignocellulose into fermentable monosaccharides (6, 7) have highlighted the biotechnological potential of these fungi for lignocellulosic biomass-based industries, including the bioethanol industry. This led to bioprospecting for Coniochaeta strains and the isolation of C. pulveracea CAB 683 from a decaying Acacia tree in the Northern Cape of South Africa, whereafter it was confirmed that this strain is able to release glucose and cellobiose from a complex cellulosic substrate (8). The first genome sequence of C. pulveracea is reported here, providing a valuable resource to improve our understanding of the molecular mechanisms involved during soft-rot-mediated lignocellulose degradation.
The strain C. pulveracea CAB 683 was cultivated in yeast extract-peptone-dextrose (YPD) broth at 30°C. Total genomic DNA was extracted using a cetyltrimethylammonium bromide (CTAB) protocol (9). The DNA sample was sheared to obtain an average fragment size of 500 bp using an M220 focused Ultrasonicator (Covaris, Woburn, MA), whereafter a single dual-indexed sequencing library was prepared using the NEBNext Ultra DNA library prep kit. Size selection was performed using Agencourt AMPure XP beads. The library was then sequenced on an Illumina MiSeq platform generating 13.9 million paired-end reads with an average length of 250 bp. The quality of the raw sequencing reads was assessed with FastQC v.0.11.5 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) followed by Illumina adaptor trimming and read quality filtering (Phred score cutoff, 30) using Trim Galore v.0.4.3 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The quality-filtered reads were assembled de novo using SPAdes v.3.11 (10). The assembly comprises 852 scaffolds, a total length of 30 Mbp, and an N50 of 288,347 bp. Assembly completeness was assessed with a genome single-copy ortholog analysis using BUSCO v.3.0 (11) with a Sordariomyceta data set (3,725 genes), and a genome completeness of 94.9% was reported.
Genome annotation was performed with the Funannotate pipeline v.1.4.1 (http://www.github.com/nextgenusfs/funannotate), which includes repeat masking, training of ab initio gene predictors with C. pulveracea CAB 683 RNA-seq data, gene prediction, and assigning of functional annotation to protein-coding gene models. The Funannotate pipeline yielded a total of 10,035 gene predictions, which were subsequently investigated for genes encoding carbohydrate-active enzymes using a hidden Markov model (HMM)-based search of dbCAN HMM v.6.0 (12). The investigation identified 225 glycoside hydrolases, 64 glycosyl transferases, 6 polysaccharide lyases, 52 carbohydrate esterases, 22 carbohydrate-binding modules, and 64 enzymes with auxiliary activities of which 24 are lytic polysaccharide monooxygenases (AA9 and AA11 families). Assessing the genome of C. pulveracea CAB 683 for genes potentially involved in the degradation of lignin revealed 11 lignin oxidases (8 laccases, 2 cellobiose dehydrogenases, and 1 versatile peroxidase) and 6 lignin-degrading auxiliary enzymes (1 aryl alcohol oxidase, 1 glucose oxidase, 3 vanillyl alcohol oxidases, and 1 benzoquinone reductase).

Data availability.

This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number QVQW00000000. The version described in this paper is version QVQW01000000. The BioProject number of the sequenced strain is PRJNA473398. The genomic raw sequencing reads are available in the Sequence Read Archive (SRA) database under accession number SRR7704703. Raw sequences of the unpublished RNA-seq data are available in the SRA database under accession numbers SRR8182960, SRR8182961, SRR8182962, SRR8182963, SRR8182964, and SRR8182965.


We would like to acknowledge The Centre for Proteomic and Genomic Research (CPGR) for their contribution to the Illumina NGS.
This work was financially supported by the South African National Research Foundation (NRF) (grant number 93694).


Weber E. 2002. The Lecythophora-Coniochaeta complex I. Morphological studies on Lecythophora species isolated from Picea abies. Nova Hedw 74:159–185.
Hale MD, Eaton RA. 1985. The ultrastructure of soft rot fungi. II. cavity-forming hyphae in wood cell walls. Mycologia 77:594–605.
Liers C, Ullrich R, Steffen KT, Hatakka A, Hofrichter M. 2006. Mineralization of 14 C-labelled synthetic lignin and extracellular enzyme activities of the wood-colonizing ascomycetes Xylaria hypoxylon and Xylaria polymorpha. Appl Microbiol Biotechnol 69:573–579.
Shary S, Ralph SA, Hammel KE. 2007. New insights into the ligninolytic capability of a wood decay ascomycete. Appl Environ Microbiol 73:6691–6694.
Tuor U, Winterhalter K, Fiechter A. 1995. Enzymes of white-rot fungi involved in lignin degradation and ecological determinants for wood decay. J Biotechnol 41:1–17.
López MJ, Vargas-García MC, Suárez-Estrella F, Nichols NN, Dien BS, Moreno J. 2007. Lignocellulose-degrading enzymes produced by the ascomycete Coniochaeta ligniaria and related species: application for a lignocellulosic substrate treatment. Enzyme Microb Technol 40:794–800.
Bugos RC, Sutherland JB, Adler JH. 1988. Phenolic compound utilization by the soft rot fungus Lecythophora hoffmannii. Appl Environ Microbiol 54:1882–1885.
van Heerden A, van Zyl WH, Cruywagen CW, Mouton M, Botha A. 2011. The lignicolous fungus Coniochaeta pulveracea and its interactions with syntrophic yeasts from the woody phylloplane. Microb Ecol 62:609–619.
Nguyen NH, Landeros F, Garibay-Orijel R, Hansen K, Vellinga EC. 2013. The Helvella lacunose species complex in western North America: cryptic species, misapplied names and parasites. Mycologia 105:1275–1286.
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its application to single-cell sequencing. J Comput Biol 19:455–477.
Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210–3212.
Yin Y, Mao X, Yang JC, Chen X, Mao F, Xu Y. 2012. dbCAN: a Web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 40:W445–W451.

Information & Contributors


Published In

cover image Microbiology Resource Announcements
Microbiology Resource Announcements
Volume 8Number 13 January 2019
eLocator: 10.1128/mra.01429-18
Editor: Antonis Rokas, Vanderbilt University


Received: 16 October 2018
Accepted: 17 November 2018
Published online: 3 January 2019



Cornelius Johannes Borstlap https://orcid.org/0000-0002-6339-0873
Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa


Antonis Rokas
Vanderbilt University


Address correspondence to Heinrich Volschenk, [email protected].

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