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Announcement
26 February 2015

Draft Genome Sequence of Talaromyces cellulolyticus Strain Y-94, a Source of Lignocellulosic Biomass-Degrading Enzymes

ABSTRACT

Talaromyces cellulolyticus (formerly Acremonium cellulolyticus) is a promising fungus for cellulase production. Here, we present the draft genome sequence of T. cellulolyticus strain Y-94. The genome is 36.4 Mbp long and contains genes for several enzymes involved in the degradation of lignocellulosic biomass, including cellulases, hemicellulases, pectinases, and amylases.

GENOME ANNOUNCEMENT

Talaromyces cellulolyticus strain Y-94 (CBS 136886, FERM BP-5826), which was isolated in Japan (1), is one of several promising filamentous fungi for the industrial production of cellulase and hemicellulase to hydrolyze lignocellulosic biomass (25). The taxonomic classification of this organism has been revised from the genus Acremonium to Talaromyces (6). Recently, a transformation system with a uracil auxotrophic strain has been developed, and some glycoside hydrolase (GH) family enzymes and transcription factors have been analyzed (711).
We present here the draft genome sequence of T. cellulolyticus Y-94. 454/Roche (FLX Titanium) and Illumina Genome Analyzer II sequencers were used in this study. T. cellulolyticus Y-94 genomic DNA was sheared into 3-kb paired-end fragments to generate a library according to the Roche paired-end library preparation method manual. A 454 Titanium draft library with 699 Mb of total reads and an average read length of 391 bases, which provided 19-fold coverage of the genome, was generated. Reads were assembled using the gsAssembler (454 Life Sciences, Roche Applied Science, Branford, CT, USA), and 60 scaffolds were obtained. The genome size of T. cellulolyticus predicted by the total scaffold length was 36.4 Mbp. Illumina Genome Analyzer II sequencing was done to account for 454/Roche sequencing errors. T. cellulolyticus genomic DNA was sheared into 0.3-kb fragments for paired-end library construction. An Illumina draft library with 2,686 Mb of total reads and a read length of 75 bases was generated. Reads were mapped onto the 454 assembly using Mapping and Assembly with Quality (Maq) and used to correct 454 sequencing errors. In total, 10,980 open reading frames (ORFs) were predicted using AUGUSTUS (12) trained on Aspergillus nidulans FGSC A4 gene models.
We screened the draft sequence for GH family genes. At least 249 ORFs were annotated as GH family proteins, including 133 potentially secreted proteins (based on a SignalP version 4.1 analysis and our secretome data). The number of GH family genes of T. cellulolyticus was similar to that of A. nidulans (247 genes), less than that of Aspergillus oryzae (285 genes), and greater than that of Trichoderma reesei (200 genes) (13). Based on the CAZy database (14), carbohydrate-active enzymes related to the hydrolysis of lignocellulosic biomass were identified: 22 cellulases (12 GH5s [including hemicellulases such as mannanase], 1 GH6, 2 GH7s, 4 GH12s, 1 GH61, and 2 GH45s); 37 hemicellulases (22 GH43s, 1 GH10, 7 GH11s, 1 GH74, 1 GH62, 1 GH53, 1 GH54, 2 GH67s, and 1 GH26); 38 pectinases (16 GH28s, 12 GH78s, 4 PL1s, 2 PL4s, 2 CE8s, and 2 CE12s); and 8 amylases (5 GH13s and 3 GH15s). These results support the ability of T. cellulolyticus to degrade various types of biomass (1, 3, 10, 15). The genome sequence data will provide suggestions for improvements in cellulase and hemicellulase production in T. cellulolyticus.

Nucleotide sequence accession numbers.

The nucleotide sequence of T. cellulolyticus strain Y-94 has been deposited at DDBJ/EMBL/GenBank as follows: 1,723 contigs under accession numbers BBPS01000001 to BBPS01001723 and 60 scaffolds under accession numbers DF933797 to DF933856. The version described in this study is the first version.

ACKNOWLEDGMENTS

This work was funded by a research grant from the National Institute of Advanced Industrial Science and Technology.
We thank Tamotsu Hoshino, Kazuhiko Ishikawa, Kenichi Nakayama, and Katsuji Murakami (National Institute of Advanced Industrial Science and Technology) for helpful discussions.

REFERENCES

1.
Yamanobe T, Mitsuishi Y, Takasaki Y. 1987. Isolation of a cellulolytic enzyme producing microorganism, culture conditions and some properties of the enzymes. Agric Biol Chem 51:65–74.
2.
Gusakov AV. 2011. Alternatives to Trichoderma reesei in biofuel production. Trends Biotechnol 29:419–425.
3.
Fujii T, Fang X, Inoue H, Murakami K, Sawayama S. 2009. Enzymatic hydrolyzing performance of Acremonium cellulolyticus and Trichoderma reesei against three lignocellulosic materials. Biotechnol Biofuels 2:24.
4.
Fang X, Yano S, Inoue H, Sawayama S. 2009. Strain improvement of Acremonium cellulolyticus for cellulase production by mutation. J Biosci Bioeng 107:256–261.
5.
Inoue H, Decker SR, Taylor LE, Yano S, Sawayama S. 2014. Identification and characterization of core cellulolytic enzymes from Talaromyces cellulolyticus (formerly Acremonium cellulolyticus) critical for hydrolysis of lignocellulosic biomass. Biotechnol Biofuels 7:151.
6.
Fujii T, Hoshino T, Inoue H, Yano S. 2014. Taxonomic revision of the cellulose-degrading fungus Acremonium cellulolyticus nomen nudum to Talaromyces based on phylogenetic analysis. FEMS Microbiol Lett 351:32–41.
7.
Fujii T, Iwata K, Murakami K, Yano S, Sawayama S. 2012. Isolation of uracil auxotrophs of the fungus Acremonium cellulolyticus and the development of a transformation system with the pyrF gene. Biosci Biotechnol Biochem 76:245–249.
8.
Fujii T, Inoue H, Ishikawa K. 2014. Characterization of the xylanase regulator protein gene, xlnR, in Talaromyces cellulolyticus (formerly known as Acremonium cellulolyticus). Biosci Biotechnol Biochem 78:1564–1567.
9.
Fujii T, Inoue H, Ishikawa K. 2013. Enhancing cellulase and hemicellulase production by genetic modification of the carbon catabolite repressor gene, creA, in Acremonium cellulolyticus. AMB Express 3:73.
10.
Inoue H, Fujii T, Yoshimi M, Taylor LE II, Decker SR, Kishishita S, Nakabayashi M, Ishikawa K. 2013. Construction of a starch-inducible homologous expression system to produce cellulolytic enzymes from Acremonium cellulolyticus. J Ind Microbiol Biotechnol 40:823–830.
11.
Watanabe M, Inoue H, Inoue B, Yoshimi M, Fujii T, Ishikawa K. 2014. Xylanase (GH11) from Acremonium cellulolyticus: homologous expression and characterization. AMB Express 4:27.
12.
Stanke M, Morgenstern B. 2005. AUGUSTUS: a Web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Res 33:W465–W467.
13.
Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM, Cullen D, Danchin EG, Grigoriev IV, Harris P, Jackson M, Kubicek CP, Han CS, Ho I, Larrondo LF, de Leon AL, Magnuson JK, Merino S, Misra M, Nelson B, Putnam N, Robbertse B, Salamov AA, Schmoll M, Terry A, Thayer N, Westerholm-Parvinen A, Schoch CL, Yao J, Barabote R, Nelson MA, Detter C, Bruce D, Kuske CR, Xie G, Richardson P, Rokhsar DS, Lucas SM, Rubin EM, Dunn-Coleman N, Ward M, Brettin TS. 2008. Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol 26:553–560.
14.
Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B. 2009. The carbohydrate-active enzymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res 37:D233–D238.
15.
Gao MT, Yano S, Inoue H, Sakanishi K. 2012. Production of ethanol from potato pulp: investigation of the role of the enzyme from Acremonium cellulolyticus in conversion of potato pulp into ethanol. Proc Biochem 47:2110–2115.

Information & Contributors

Information

Published In

cover image Genome Announcements
Genome Announcements
Volume 3Number 126 February 2015
eLocator: e00014-15
PubMed: 25720677

History

Received: 7 January 2015
Accepted: 13 January 2015
Published online: 26 February 2015

Contributors

Authors

Tatsuya Fujii
Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Higashi-Hiroshima, Hiroshima, Japan
Hideaki Koike
Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
Shigeki Sawayama
Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
Shinichi Yano
Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Higashi-Hiroshima, Hiroshima, Japan
Hiroyuki Inoue
Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Higashi-Hiroshima, Hiroshima, Japan

Notes

Address correspondence to Hiroyuki Inoue, [email protected].

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