Abstract
This is the first report of the genome sequence of Trichosporon asahii environmental strain CBS 8904, which was isolated from maize cobs. Comparison of the genome sequence with that of clinical strain CBS 2479 revealed that they have >99% chromosomal and mitochondrial sequence identity, yet CBS 8904 has 368 specific genes. Analysis of clusters of orthologous groups predicted that 3,307 genes belong to 23 functional categories and 703 genes were predicted to have a general function.
GENOME ANNOUNCEMENT
Trichosporon asahii is an important yeast fungus that exists widely under natural conditions (2) and forms colonies in some human tissues and organs (3, 11). T. asahii can invade the human body and cause disease (7, 12, 15). It is widely used in food fermentation (4, 6, 8, 10, 13) and other industrial production (9, 14, 16) processes. CBS 8904 is an environmental strain of T. asahii that was isolated in 1998 from maize cobs (http://www.cbs.knaw.nl/collections/BioloMICS.aspx?Table=CBS%20strain%20database&Name=CBS%208904&Fields=All&ExactMatch=T). To date, the genome sequence of this T. asahii environmental strain has not been published.
Whole-genome sequencing of T. asahii CBS 8904 was performed with a combined strategy of 454 sequencing (5) and Solexa sequencing technology (1). A genomic library containing 8-kb inserts was constructed, and 935,617 paired-end reads were generated by using the GS FLX system, giving 21.1-fold coverage of the genome. Overall, 83.26% of the reads were assembled into 194 scaffolds totaling 1.9 Mbp by using Newbler version 2.3 (454 Life Sciences, Branford, CT). A total of 51,221,338 reads were generated to reach a depth of 204-fold coverage with an Illumina Solexa Genome Analyzer IIx and mapped to the scaffolds by using the Burrows-Wheeler alignment tool.
The genome of T. asahii strain CBS 8904 contains 25,015,122 bp of nuclear chromosomal DNA and 32,568 bp of mitochondrial DNA. The average GC content is 59% in the chromosomal DNA and 29% in the mitochondrial DNA. Overall, the chromosomal DNA contains 8,507 protein-encoding genes and 530 tRNA-encoding genes. The mitochondrial DNA has 22 protein-encoding genes and 25 tRNA-encoding genes.
Comparison with the previously published genome of T. asahii CBS 2479 (NCBI GenBank accession number ALBS00000000) revealed that the chromosomes of CBS 8904 and CBS 2479 have 99.59% identity and the mitochondria of these two strains have 99.99% identity. CBS 8904 has 8,161 orthologous coding sequences in common with CBS 2479, and CBS 8904 has 368 specific genes compared with CBS 2479, most of which are of unknown function. Analysis of clusters of orthologous groups of T. asahii CBS 8904 predicted that 3,307 of the protein-encoding genes belong to 23 functional categories, i.e., cell motility (n = 4); extracellular structures (n = 5); nuclear structure (n = 26); defense mechanisms (n = 29); cell wall/membrane/envelope biogenesis (n = 38); nucleotide transport and metabolism (n = 58); coenzyme transport and metabolism (n = 68); chromatin structure and dynamics (n = 76); cytoskeleton (n = 84); inorganic ion transport and metabolism (n = 103); secondary metabolite biosynthesis, transport, and catabolism (n = 112); cell cycle control, cell division, and chromosome partitioning (n = 139); replication, recombination, and repair (n = 153); RNA processing and modification (n = 178); amino acid transport and metabolism (n = 202); energy production and conversion (n = 230); carbohydrate transport and metabolism (n = 230); lipid transport and metabolism (n = 214); intracellular trafficking, secretion, and vesicular transport (n = 238); transcription (n = 248); translation, ribosomal structure, and biogenesis (n = 263); signal transduction mechanisms (n = 249); and posttranslational modification, protein turnover, and chaperones (n = 360). A total of 703 genes were predicted to have only a general function, and the functions of 709 genes were unknown.
Nucleotide sequence accession numbers.
This whole-genome shotgun sequencing project has been deposited in DDBJ/EMBL/GenBank under accession no. AMBO00000000. The version described in this paper is the first one (AMBO01000000).
ACKNOWLEDGMENT
This work was supported by a grant from the key projects of the Twelfth Five-Year Plan of the Chinese People's Liberation Army (BWS11J059).
Footnotes
R.Y.Y., H.T.L., and H.Z. contributed equally to this work.
REFERENCES
- 1. Bentley DR, et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2. Chagas-Neto TC, Chaves GM, Colombo AL. 2008. Update on the genus Trichosporon. Mycopathologia 166:121–132 [DOI] [PubMed] [Google Scholar]
- 3. Itoh T, Hosokawa H, Kohdera U, Toyazaki N, Asada Y. 1996. Disseminated infection with Trichosporon asahii. Mycoses 39:195–199 [DOI] [PubMed] [Google Scholar]
- 4. Jespersen L, Nielsen DS, Hønholt S, Jakobsen M. 2005. Occurrence and diversity of yeasts involved in fermentation of West African cocoa beans. FEMS Yeast Res. 5:441–453 [DOI] [PubMed] [Google Scholar]
- 5. Margulies M, et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Nielsen DS, Hønholt S, Tano-Debrah K, Jespersen L. 2005. Yeast populations associated with Ghanaian cocoa fermentations analysed using denaturing gradient gel electrophoresis (DGGE). Yeast 22:271–284 [DOI] [PubMed] [Google Scholar]
- 7. Nishiura Y, et al. 1997. Assignment and serotyping of Trichosporon species: the causative agents of summer-type hypersensitivity pneumonitis. J. Med. Vet. Mycol. 35:45–52 [DOI] [PubMed] [Google Scholar]
- 8. Ongol MP, Asano K. 2009. Main microorganisms involved in the fermentation of Ugandan ghee. Int. J. Food Microbiol. 133:286–291 [DOI] [PubMed] [Google Scholar]
- 9. Rodríguez-Bustamante E, Maldonado-Robledo G, Ortiz MA, Díaz-Avalos C, Sanchez S. 2005. Bioconversion of lutein using a microbial mixture—maximizing the production of tobacco aroma compounds by manipulation of culture medium. Appl. Microbiol. Biotechnol. 68:174–182 [DOI] [PubMed] [Google Scholar]
- 10. Suzzi G, et al. 2003. Yeasts associated with manteca. FEMS Yeast Res. 3:159–166 [DOI] [PubMed] [Google Scholar]
- 11. Takamura S, Oono T, Kanzaki H, Arata J. 1999. Disseminated trichosporonosis with Trichosporon asahii. Eur. J. Dermatol. 9:577–579 [PubMed] [Google Scholar]
- 12. Tashiro T, et al. 1995. Trichosporon beigelii pneumonia in patients with hematologic malignancies. Chest 108:190–195 [DOI] [PubMed] [Google Scholar]
- 13. Wang HY, Gao YB, Fan QW, Xu Y. 2011. Characterization and comparison of microbial community of different typical Chinese liquor Daqus by PCR-DGGE. Lett. Appl. Microbiol. 53:134–140 [DOI] [PubMed] [Google Scholar]
- 14. Wang Y, Li J, Xu Y. 2011. Characterization of novel β-glucosidases with transglycosylation properties from Trichosporon asahii. J. Agric. Food Chem. 59:11219–11227 [DOI] [PubMed] [Google Scholar]
- 15. Yang R, et al. 2003. Disseminated trichosporonosis in China. Mycoses 46:519–523 [DOI] [PubMed] [Google Scholar]
- 16. Zheng S, Sun J, Han H. 2011. Effect of dissolved oxygen changes on activated sludge fungal bulking during lab-scale treatment of acidic industrial wastewater. Environ. Sci. Technol. 45:8928–8934 [DOI] [PubMed] [Google Scholar]