ABSTRACT
Talaromyces atroroseus is a known producer of Monascus colorants suitable for the food industry. Furthermore, genetic tools have been established that facilitate elucidation and engineering of its biosynthetic pathways. Here, we report the draft genome of a potential fungal cell factory, T. atroroseus IBT 11181 (CBS 123796).
GENOME ANNOUNCEMENT
The genus Talaromyces primarily contains saprophytic fungi and encompasses medically and industrially relevant species such as the opportunistic human pathogen T. marneffei (formerly Penicillium marneffei), species with high production of cellulolytic enzymes, i.e., T. cellulolyticus (1), as well as the interesting pigment-producing species T. atroroseus (2). Several strains of T. atroroseus and closely related species are recognized as potential cell factories for Monascus pigment production, as they may serve as mycotoxin-free alternatives to Monascus spp. (2–4).
T. atroroseus IBT 11181 was originally isolated from red sweet bell pepper bought in a Danish supermarket and is deposited in the CBS collection at CBS-KNAW, Utrecht, the Netherlands, as CBS 123796 and CBS 238.95. We intend to implement this isolate as a model for T. atroroseus by investigating its growth physiology (5), by establishing genetic tools (6), and by reporting here the full-genome sequence of T. atroroseus IBT 11181.
Genomic DNA was extracted from the mycelium with a slightly modified protocol of the cetyltrimethylammonium bromide method used by Fulton et al. (7). The T. atroroseus IBT 11181 genome was sequenced using an Illumina HiSeq 2000 platform on a 180-bp paired-end library and a 6-kb mate-paired library both with reads of 2 × 100 bp by Beijing Genome Institute (BGI), Hong Kong. Sequencing depth was 193×, and assembly of the genome was performed with the ALLPATHS-LG algorithm (8). The final assembly resulted in 48 scaffolds with a G+C content of 44.35% and a total assembly size of 30.85 Mb corresponding to 93% of the estimated genome size from k-mer spectral analysis. The minimum number of sequences making up 50% of the genome assembly was seven, and the N50 length was 1,577,401 bp. The CEGMA pipeline (9) identified 242 of the 248 core eukaryotic genes, assessing the genome assembly completeness to be 97.58%. This indicated that the draft genome assembly was good with a high completeness and was valid to use for whole-genome analysis.
Gene-calling of the genome was performed using a pipeline of first masking the genome with RepeatMasker version 4.0.5 (Institute for Systems Biology, Seattle, WA, USA; http://www.repeatmasker.org), and then gene-calling with AUGUSTUS version 3.0.3 (10, 11), FGENESH version 3.1.2 (SoftBerry) (12), and GeneMark-ES (13). The individual ab initio gene predictions were merged into a consensus gene prediction using EVidenceModeler (14), resulting in a total of 9,519 protein-encoding genes serving as the final gene prediction. The genome sequence reported here represents a useful resource for further research into the metabolism of T. atroroseus and its potential as a cell factory for colorant production.
Accession number(s).
This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number LFMY00000000. The version described in this paper is the first version, LFMY01000000.
ACKNOWLEDGMENT
This work was supported by grant 09-064967 from the Danish Council for Independent Research, Technology, and Production Sciences.
Footnotes
Citation Thrane U, Rasmussen KB, Petersen B, Rasmussen S, Sicheritz-Pontén T, Mortensen UH. 2017. Genome sequence of Talaromyces atroroseus, which produces red colorants for the food industry. Genome Announc 5:e01736-16. https://doi.org/10.1128/genomeA.01736-16.
REFERENCES
- 1.Inoue H, Decker SR, Taylor LE 2nd, 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. doi: 10.1186/s13068-014-0151-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Frisvad JC, Yilmaz N, Thrane U, Rasmussen KB, Houbraken J, Samson RA. 2013. Talaromyces atroroseus, a new species efficiently producing industrially relevant red pigments. PLoS One 8:e84102. doi: 10.1371/journal.pone.0084102. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Mapari SAS, Nielsen KF, Larsen TO, Frisvad JC, Meyer AS, Thrane U. 2005. Exploring fungal biodiversity for the production of water-soluble pigments as potential natural food colorants. Curr Opin Biotechnol 16:231–238. doi: 10.1016/j.copbio.2005.03.004. [DOI] [PubMed] [Google Scholar]
- 4.Mapari SAS, Meyer AS, Thrane U, Frisvad JC. 2009. Identification of potentially safe promising fungal cell factories for the production of polyketide natural food colorants using chemotaxonomic rationale. Microb Cell Fact 8:24. doi: 10.1186/1475-2859-8-24. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Mapari SAS, Thrane U, Meyer AS. 2010. Fungal polyketide azaphilone pigments as future natural food colorants? Trends Biotechnol 28:300–307. doi: 10.1016/j.tibtech.2010.03.004. [DOI] [PubMed] [Google Scholar]
- 6.Nielsen ML, Isbrandt T, Rasmussen KB, Thrane U, Hoof JB, Larsen TO, Mortensen UH. 2017. Genes linked to production of secondary metabolites in Talaromyces atroroseus revealed using CRISPR-Cas9. PLoS One 12:e0169712. doi: 10.1371/journal.pone.0169712. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Fulton TM, Chunwongse J, Tanksley SD. 1995. Microprep protocol for extraction of DNA from tomato and other herbaceous plants. Plant Mol Biol Rep 13:207–209. doi: 10.1007/BF02670897. [DOI] [Google Scholar]
- 8.Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, Berlin AM, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, Jaffe DB. 2011. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A 108:1513–1518. doi: 10.1073/pnas.1017351108. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Parra G, Bradnam K, Korf I. 2007. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23:1061–1067. doi: 10.1093/bioinformatics/btm071. [DOI] [PubMed] [Google Scholar]
- 10.Stanke M, Schöffmann O, Morgenstern B, Waack S. 2006. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics 7:62. doi: 10.1186/1471-2105-7-62. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Stanke M, Diekhans M, Baertsch R, Haussler D. 2008. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24:637–644. doi: 10.1093/bioinformatics/btn013. [DOI] [PubMed] [Google Scholar]
- 12.Salamov AA, Solovyev VV. 2000. Ab initio gene finding in drosophila genomic DNA. Genome Res 10:516–522. doi: 10.1101/gr.10.4.516. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Ter-Hovhannisyan V, Lomsadze A, Chernoff YO, Borodovsky M. 2008. Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Res 18:1979–1990. doi: 10.1101/gr.081612.108. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Buell CR, Wortman JR. 2008. Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol 9:R7. doi: 10.1186/gb-2008-9-1-r7. [DOI] [PMC free article] [PubMed] [Google Scholar]