Abstract
Cryptococcus curvatus ATCC 20509 is a commonly used nonmodel oleaginous yeast capable of converting a variety of carbon sources into fatty acids. Here, we present the draft genome sequence of this popular organism to provide a means for more in-depth studies of its fatty acid production potential.
GENOME ANNOUNCEMENT
Cryptococcus curvatus ATCC 20509 is an oleaginous yeast strain capable of assimilating xylose, lactose, glucose, and sucrose, as well as a variety of agricultural and food-processing wastes, as carbon sources (1–3). Lipid production in C. curvatus ATCC 20509 can be induced under nitrogen-limiting conditions (4) and favors the synthesis of 18-carbon-chain-length fatty acids (5). The utility of these fatty acids for the production of biofuels and other high-value products, in tandem with its ability to grow using low- or negative-cost feedstocks, makes it a potential candidate for use in industrial fermentation processes. In this context, the C. curvatus ATCC 20509 draft genome sequence provides a supplemental point of comparison in relation to other oleaginous yeasts for elucidating the genetic mechanisms underlying fatty acid synthesis potentials and the metabolic controls governing the enactment of oleaginous metabolism.
To prepare for sequencing, C. curvatus ATCC 20509 was grown under standard laboratory conditions in YPD broth (10 g/liter yeast extract, 20 g/liter peptone, 20 g/liter glucose) at 25°C and 150 rpm. Cells were lysed during mid-log-phase growth by treatment with a buffer containing 8 M urea, 0.5 M NaCl, 20 mM Tris, 20 mM EDTA, and 2% SDS, and the DNA was isolated by phenol-chloroform–isoamyl alcohol extraction as previously described (6). Following isolation, RNA was removed via RNase treatment, and the DNA was ethanol precipitated. The purified DNA was used to generate shotgun and mate-pair libraries with insert sizes of approximately 323 bp and 6 kb, respectively. Genome sequencing was performed using an Illumina HiSeq 2500 platform. The shotgun library produced 6,150,342 reads. The mate-pair library produced 10,284,626 reads. The AllPaths LG whole-genome shotgun assembler (release version R49403) (7) was used for creation of a de novo genome assembly. This assembly represents an 87.8× coverage level from a total of 16 scaffolds (145 contigs). The average scaffold read length was 1.24 Mbp. The scaffold N50 was 3 Mbp, and the maximum scaffold length was 5.25 Mb. The total sequence length of the resulting draft genome was 19.9 Mbp, and the overall G+C content was determined to be 60.7%.
Accession number(s).
This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under accession no. MATS00000000. The version described in this paper is the first version, MATS01000000.
ACKNOWLEDGMENTS
We thank the Department of Energy’s Joint Genome Institute for genome sequencing and assembly.
This work was supported by Laboratory Directed Research and Development funding from Oak Ridge National Laboratory. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the U.S. Department of Energy under contract DE-AC05-00OR22725.
Footnotes
Citation Close D, Ojumu J. 2016. Draft genome sequence of the oleaginous yeast Cryptococcus curvatus ATCC 20509. Genome Announc 4(6):e01235-16. doi:10.1128/genomeA.01235-16.
REFERENCES
- 1.Bednarski W, Leman J, Tomasik J. 1986. Utilization of beet molasses and whey for fat biosynthesis by a yeast. Agric Wastes 18:19–26. doi: 10.1016/0141-4607(86)90104-6. [DOI] [Google Scholar]
- 2.Gong Z, Shen H, Yang X, Wang Q, Xie H, Zhao ZK. 2014. Lipid production from corn stover by the oleaginous yeast Cryptococcus curvatus. Biotechnol Biofuels 7:158. doi: 10.1186/s13068-13014-10158-y. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Gonzalez-Garcia Y, Hernandez R, Zhang G, Escalante FM, Holmes W, French WT. 2013. Lipids accumulation in Rhodotorula glutinis and Cryptococcus curvatus growing on distillery wastewater as culture medium. Environ Prog Sustain J Energ 32:69–74. [Google Scholar]
- 4.Hassan M, Blanc PJ, Granger L, Pareilleux A, Goma G. 1996. Influence of nitrogen and iron limitations on lipid production by Cryptococcus curvatus grown in batch and fed-batch culture. Proc Biochem 31:355–361. doi: 10.1016/0032-9592(95)00077-1. [DOI] [Google Scholar]
- 5.Gong Z, Shen H, Wang Q, Yang X, Xie H, Zhao ZK. 2013. Efficient conversion of biomass into lipids by using the simultaneous saccharification and enhanced lipid production process. Biotechnol Biofuels 6:36. doi: 10.1186/1754-6834-1186-1136. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Sansinforiano ME, Padilla JA, Hermoso de Mendoza J, Hermoso de Mendoza M, Fernandez-Garcia JL, Martínez-Tranćon M, Rabasco A, Parejo JC. 1998. Rapid and easy method to extract and preserve DNA from Cryptococcus neoformans and other pathogenic yeasts. Mycoses 41:195–198. doi: 10.1111/j.1439-0507.1998.tb00323.x. [DOI] [PubMed] [Google Scholar]
- 7.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]