Abstract
Umbelopsis isabellina is a fungus in the subdivision Mucoromycotina, many members of which have been shown to be oleaginous and have become important organisms for producing oil because of their high level of intracellular lipid accumulation from various feedstocks. The genome sequence of U. isabellina NBRC 7884 was determined and annotated, and this information might provide insights into the oleaginous properties of this fungus.
GENOME ANNOUNCEMENT
Umbelopsis isabellina is a Mucoromycotina fungus belonging to the order Mucorales, which includes the genera Rhizopus, Mucor, Cunninghamella, etc. Interestingly, U. isabellina was formerly classified in the order Mortierellales, but a molecular phylogenetic analysis has shown that Umbelopsis species belong in the Mucorales order (1).
Many fungi in the subdivision Mucoromycotina, including the well-known pathogen Rhizopus oryzae, have been shown to be oleaginous (2, 3). Both U. isabellina and Cunninghamella echinulata accumulate lipids to more than 40% of their biomass (4). Because of their high levels of intracellular triacylglyceride accumulation, versatility in nutrient utilization, and high growth rate, Mucoromycotina fungi are becoming increasingly important as potential producers of biofuels and high-value chemicals (5, 6). The genome sequences of at least two Murocomycotina fungi have been published—R. oryzae (7) and the Mortierellales fungus Mortierella alpina (3). Moreover, other genome sequences are currently accessible through the Joint Genome Institute (JGI) Mycocosm Genome Portal (8), including Mucor circinelloides, Umbelopsis rammanianna, and Phycomyces blakesleeanum. However, the numbers of Mucormycotina genome sequences are still much lower than those of other lineages of Dikarya fungi. The comparative study of the Mucoromycotina fungi could be useful for determining the genetic factors related to oleaginous characteristics because they share oleaginous characteristics. However, only small regions of microsynteny have been observed among the genome sequences currently available (our unpublished data).
The fungal strain used in this study, U. isabellina NBRC 7884, was obtained from the Japanese Biological Resource Center, NITE (http://www.nbrc.nite.go.jp/). Whole-genome sequencing was performed using a mate-paired library with an insert size of approximately 3 kb and a read length of 55 bases with the SOLiD 5500xl system (Life Technologies). The total short reads were filtered according to quality (9), resulting in approximately 200-fold coverage (85,662,706 reads), and assembled by SOLiD De Novo Accessory Tools 2.0 (Life Technologies), which contains the Velvet assembler (10), with a k-mer size of 37. The assembly generated 84 scaffolds (≥1 kb) with an N50 value of 554,975 bp and a maximum length of 1,873,367 bp. The assembled genome of 22,588,838 bp was covered by 84 scaffolds, including 53 scaffolds of >100 kb and 4 scaffolds of >1 Mb, with a G+C content of 41.79%.
A total of 9,081 protein-coding genes were predicted, based on the homologies to known genes and the statistical features of the genes, by applying a combination of gene-finding software tools (11). Functional annotation of the genes was predicted by a homology search (BLASTp) against an NCBI-nr protein database. A total of 6,911 of 9,081 protein-coding genes (76.1%) were homologous to sequences in the annotated genes of U. ramanniana sequenced by the Department of Energy (DOE) Joint Genome Institute (8) (BLASTp E value, 1e−5; sequence length, ≤20% difference; and sequence identity, ≥25%).
Nucleotide sequence accession numbers.
This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession numbers BAVE01000001 through BAVE01000084. The version described in this paper is the first version.
ACKNOWLEDGMENTS
This work was performed through a grant-in-aid of the Ministry of Economy, Trade and Industry (METI), Japan. This work was also supported by a grant-in-aid of the U.S. Department of Energy (DOE). A portion of this research was performed at EMSL, a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research and located at the Pacific Northwest National Laboratory. H.K. is an EMSL Wiley Visiting Scientist.
Footnotes
Citation Takeda I, Tamano K, Yamane N, Ishii T, Miura A, Umemura M, Terai G, Baker SE, Koike H, Machida M. 2014. Genome sequence of the Mucoromycotina fungus Umbelopsis isabellina, an effective producer of lipids. Genome Announc. 2(1):e00071-14. doi:10.1128/genomeA.00071-14.
REFERENCES
- 1. Voigt K, Wöstemeyer J. 2001. Phylogeny and origin of 82 zygomycetes from all 54 genera of the Mucorales and Mortierellales based on combined analysis of actin and translation elongation factor EF-1alpha genes. Gene 270:113–120. 10.1016/S0378-1119(01)00464-4 [DOI] [PubMed] [Google Scholar]
- 2. Vorapreeda T, Thammarongtham C, Cheevadhanarak S, Laoteng K. 2012. Alternative routes of acetyl-CoA synthesis identified by comparative genomic analysis: involvement in the lipid production of oleaginous yeast and fungi. Microbiology 158:217–228. 10.1099/mic.0.051946-0 [DOI] [PubMed] [Google Scholar]
- 3. Wang L, Chen W, Feng Y, Ren Y, Gu Z, Chen H, Wang H, Thomas MJ, Zhang B, Berquin IM, Li Y, Wu J, Zhang H, Song Y, Liu X, Norris JS, Wang S, Du P, Shen J, Wang N, Yang Y, Wang W, Feng L, Ratledge C, Zhang H, Chen YQ. 2011. Genome characterization of the oleaginous fungus mortierella alpina. PLoS One 6:e28319. 10.1371/journal.pone.0028319 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4. Fakas S, Papanikolaou S, Batsos A, Galiotou-Panayotou M, Mallouchos A, Aggelis G. 2009. Evaluating renewable carbon sources as substrates for single cell oil production by Cunninghamella echinulata and Mortierella isabellina. Biomass Bioenerg. 33:573–580. 10.1016/j.biombioe.2008.09.006 [DOI] [Google Scholar]
- 5. Rossi M, Amaretti A, Raimondi S, Leonardi A. 2011. Getting lipids biodiesel from oleaginous fungi, p 71–92 In Stoytcheva M. (ed), Biodiesel—feedstocks and processing technologies. InTech, Rijeka, Croatia [Google Scholar]
- 6. Ratledge C. 2004. Fatty acid biosynthesis in microorganisms being used for single cell oil production. Biochimie 86:807–815. 10.1016/j.biochi.2004.09.017 [DOI] [PubMed] [Google Scholar]
- 7. Ma LJ, Ibrahim AS, Skory C, Grabherr MG, Burger G, Butler M, Elias M, Idnurm A, Lang BF, Sone T, Abe A, Calvo SE, Corrochano LM, Engels R, Fu J, Hansberg W, Kim JM, Kodira CD, Koehrsen MJ, Liu B, Miranda-Saavedra D, O’Leary S, Ortiz-Castellanos L, Poulter R, Rodriguez-Romero J, Ruiz-Herrera J, Shen YQ, Zeng Q, Galagan J, Birren BW, Cuomo CA, Wickes BL. 2009. Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication. PLoS Genet. 5:e1000549. 10.1371/journal.pgen.1000549 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Grigoriev IV, Nordberg H, Shabalov I, Aerts A, Cantor M, Goodstein D, Kuo A, Minovitsky S, Nikitin R, Ohm RA, Otillar R, Poliakov A, Ratnere I, Riley R, Smirnova T, Rokhsar D, Dubchak I. 2012. The genome portal of the Department of Energy Joint Genome Institute. Nucleic Acids Res. 40:D26–D32. 10.1093/nar/gkr947 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. Umemura M, Koyama Y, Takeda I, Hagiwara H, Ikegami T, Koike H, Machida M. 2013. Fine de novo sequencing of a fungal genome using only SOLiD short read data: verification on Aspergillus oryzae RIB40. PLoS One 8:e63673. 10.1371/journal.pone.0063673 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821–829. 10.1101/gr.074492.107 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11. Machida M, Asai K, Sano M, Tanaka T, Kumagai T, Terai G, Kusumoto K, Arima T, Akita O, Kashiwagi Y, Abe K, Gomi K, Horiuchi H, Kitamoto K, Kobayashi T, Takeuchi M, Denning DW, Galagan JE, Nierman WC, Yu J, Archer DB, Bennett JW, Bhatnagar D, Cleveland TE, Fedorova ND, Gotoh O, Horikawa H, Hosoyama A, Ichinomiya M, Igarashi R, Iwashita K, Juvvadi PR, Kato M, Kato Y, Kin T, Kokubun A, Maeda H, Maeyama N, Maruyama J, Nagasaki H, Nakajima T, Oda K, Okada K, Paulsen I, Sakamoto K, Sawano T, Takahashi M, Takase K, Terabayashi Y, Wortman JR, Yamada O, Yamagata Y, Anazawa H, Hata Y, Koide Y, Komori T, Koyama Y, Minetoki T, Suharnan S, Tanaka A, Isono K, Kuhara S, Ogasawara N, Kikuchi H. 2005. Genome sequencing and analysis of Aspergillus oryzae. Nature 438:1157–1161. 10.1038/nature04300 [DOI] [PubMed] [Google Scholar]