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Eukaryotes

Genome Sequence of Ustilaginoidea virens IPU010, a Rice Pathogenic Fungus Causing False Smut

Toshitaka Kumagai, Tomoko Ishii, Goro Terai, Myco Umemura, Masayuki Machida, Kiyoshi Asai
Toshitaka Kumagai
aFermlab Inc., Koto-ku, Tokyo, Japan
bTechnology Research Association of Highly Efficient Gene Design, Sapporo, Hokkaido, Japan
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Tomoko Ishii
bTechnology Research Association of Highly Efficient Gene Design, Sapporo, Hokkaido, Japan
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Goro Terai
bTechnology Research Association of Highly Efficient Gene Design, Sapporo, Hokkaido, Japan
cINTEC Inc., Koto-ku, Tokyo, Japan
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Myco Umemura
bTechnology Research Association of Highly Efficient Gene Design, Sapporo, Hokkaido, Japan
dBioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
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Masayuki Machida
bTechnology Research Association of Highly Efficient Gene Design, Sapporo, Hokkaido, Japan
dBioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
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Kiyoshi Asai
bTechnology Research Association of Highly Efficient Gene Design, Sapporo, Hokkaido, Japan
eDepartment of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
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DOI: 10.1128/genomeA.00306-16
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ABSTRACT

Ustilaginoidea virens is a rice pathogenic fungus that causes false smut disease, a disease that seriously damages the yield and quality of the grain. Analysis of the U. virens IPU010 33.6-Mb genome sequence will aid in the understanding of the pathogenicity of the strain, particularly in regard to effector proteins and secondary metabolic genes.

GENOME ANNOUNCEMENT

Ustilaginoidea virens is a plant pathogenic fungus that causes false smut disease in rice. The disease is widespread in the major rice-growing areas of Asia, including Japan, and seriously damages both the yield and quality of the grain (1, 2). The fungus is considered as a biotrophic pathogen (3) that obtains nutrition from living host cells and secretes effector proteins to suppress or regulate the immune response of plants to invasion (4). In this report, the genome sequence of the U. virens strain IPU010 was determined. It was isolated from a rice field in Shiga Prefecture, Japan (MAFF 236576, transferred from the National Institute of Agrobiological Science [NIAS], Japan).

DNA of the strain was extracted using NucleoBond AGX100 (TaKaRa Bio, Inc., Kusatsu, Shiga, Japan) after 9 days of cultivation at 25°C in 100 mL of potato dextrose broth (Difco). Extracted DNA was sheared to a size of ~20 kb using the g-TUBE (Covaris, Wobum, MA, USA). The DNA libraries were prepared from 10 µg of the sheared DNA with the SMRTBell template prep kit 1.0 reagents (Pacific Biosciences, Menlo Park, CA, USA) and size-selected according to the manufacturer's protocol. The libraries were sequenced on a PacBio RS II instrument with the DNA sequencing reagent 4.0 and single-molecule real-time (SMRT) cells 8 Pac V3 (Pacific Biosciences). A total of 1.7 Gbp sequence data in 160,206 PacBio subreads were obtained from 2 cells of the SMRT cell. The prepared DNA was also sequenced using the Illumina MiSeq platform with the TruSeq DNA LT sample prep kit (Illumina, San Diego, CA, USA) to obtain 13.4-M paired-end (insertion length 557 bp, total 7.9 Gbp) short-read data, according to the manufacturers' instructions.

The de novo genome assembly proceeded using the hybrid approach (5). First, Platanus (6) was used to perform De Bruijn graph assembly on the Illumina MiSeq reads and a total of 42.5Mbp highly accurate 34,389 fragments were retrieved. Next, DBG2OLC (7) was used to align these fragments onto the PacBio reads for consensus calling, resulting in a genome of 33.6 Mb in 139 contigs with an N50 value of 529,978 bp and an average G+C content of 51.3%. A total of 6,451 protein-coding genes were predicted using a combination of the gene prediction programs ALN (8) and GlimmerHMM (9).

The annotated genome sequence of U. virens IPU010 will contribute to the understanding of the pathogenicity of U. virens, which is important to the effort of securing reliable supplies of rice. Examining the genes responsible for biosynthesis of ustiloxins, which are the major mycotoxins produced by U. virens (10), is particularly important in terms of food safety. The ustiloxin biosynthetic gene cluster has recently been identified in the U. virens UV-8b genome (11, 12), and a homologous region to it is also found in the current genome sequence of IPU010. Analyses of genes co-expressed with the ustiloxin gene cluster will contribute greatly to controlling the toxicity of the fungus.

Nucleotide sequence accession numbers.This whole-genome shotgun project has been deposited in DDBJ/EMBL/GenBank under the accession no. BBTG00000000. The version described in this paper is the second version, BBTG02000000.

ACKNOWLEDGMENT

This work was supported by the Commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI), Japan.

FOOTNOTES

    • Received 9 March 2016.
    • Accepted 11 March 2016.
    • Published 5 May 2016.
  • Copyright © 2016 Kumagai et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

REFERENCES

  1. 1.↵
    1. Ashizawa T,
    2. Takahashi M,
    3. Moriwaki J,
    4. Hirayae K
    . 2010. Quantification of the rice false smut pathogen Ustilaginoidea virens from soil in Japan using real-time PCR. Eur J Plant Pathol 128:221–232. doi:10.1007/s10658-010-9647-4.
    OpenUrlCrossRef
  2. 2.↵
    1. Sun X,
    2. Kang S,
    3. Zhang Y,
    4. Tan X,
    5. Yu Y,
    6. He H,
    7. Zhang X,
    8. Liu Y,
    9. Wang S,
    10. Sun W,
    11. Cai L,
    12. Li S
    . 2013. Genetic diversity and population structure of rice pathogen Ustilaginoidea virens in China. PLoS One 8:e76879. doi:10.1371/journal.pone.0076879.
    OpenUrlCrossRefPubMed
  3. 3.↵
    1. Chao J,
    2. Jin J,
    3. Wang D,
    4. Han R,
    5. Zhu R,
    6. Zhu Y,
    7. Li S
    . 2014. Cytological and transcriptional dynamics analysis of host plant revealed stage-specific biological processes related to compatible rice-Ustilaginoidea virens interaction. PLoS One 9:e91391. doi:10.1371/journal.pone.0091391.
    OpenUrlCrossRefPubMed
  4. 4.↵
    1. Koeck M,
    2. Hardham AR,
    3. Dodds PN
    . 2011. The role of effectors of biotrophic and hemibiotrophic fungi in infection. Cell Microbiol 13:1849–1857. doi:10.1111/j.1462-5822.2011.01665.x.
    OpenUrlCrossRefPubMed
  5. 5.↵
    1. Chakraborty M,
    2. Baldwin-Brown JG,
    3. Long AD,
    4. Emerson JJ
    . 16 October 2015. A practical guide to de novo genome assembly using long reads. bioRxiv. doi:10.1101/029306.
    OpenUrlAbstract/FREE Full Text
  6. 6.↵
    1. Kajitani R,
    2. Toshimoto K,
    3. Noguchi H,
    4. Toyoda A,
    5. Ogura Y,
    6. Okuno M,
    7. Yabana M,
    8. Harada M,
    9. Nagayasu E,
    10. Maruyama H,
    11. Kohara Y,
    12. Fujiyama A,
    13. Hayashi T,
    14. Itoh T
    . 2014. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res 24:1384–1395. doi:10.1101/gr.170720.113.
    OpenUrlAbstract/FREE Full Text
  7. 7.↵
    1. Ye C,
    2. Hill CM,
    3. Ruan J,
    4. Ma ZS
    . 2014. DBG2OLC: efficient assembly of large genomes using the compressed overlap graph. arXiv:1410.2801. http://arxiv.org/abs/1410.2801.
  8. 8.↵
    1. Gotoh O
    . 2000. Homology-based gene structure prediction: simplified matching algorithm using a translated codon (tron) and improved accuracy by allowing for long gaps. Bioinformatics 16:190–202. doi:10.1093/bioinformatics/16.3.190.
    OpenUrlCrossRefPubMedWeb of Science
  9. 9.↵
    1. Majoros WH,
    2. Pertea M,
    3. Salzberg SL
    . 2004. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 20:2878–2879. doi:10.1093/bioinformatics/bth315.
    OpenUrlCrossRefPubMedWeb of Science
  10. 10.↵
    1. Nakamura K,
    2. Izumiyama N,
    3. Ohtsubo K,
    4. Koiso Y,
    5. Iwasaki S,
    6. Sonoda R,
    7. Fujita Y,
    8. Yaegashi H,
    9. Sato Z
    . 1994. “Lupinosis”-like lesions in mice caused by ustiloxin, produced by Ustilaginoieda virens: a morphological study. Nat Toxins 2:22–28. doi:10.1002/nt.2620020106.
    OpenUrlCrossRefPubMed
  11. 11.↵
    1. Zhang Y,
    2. Zhang K,
    3. Fang A,
    4. Han Y,
    5. Yang J,
    6. Xue M,
    7. Bao J,
    8. Hu D,
    9. Zhou B,
    10. Sun X,
    11. Li S,
    12. Wen M,
    13. Yao N,
    14. Ma LJ,
    15. Liu Y,
    16. Zhang M,
    17. Huang F,
    18. Luo C,
    19. Zhou L,
    20. Li J,
    21. Chen Z,
    22. Miao J,
    23. Wang S,
    24. Lai J,
    25. Xu JR,
    26. Hsiang T,
    27. Peng YL,
    28. Sun W
    . 2014. Specific adaptation of Ustilaginoidea virens in occupying host florets revealed by comparative and functional genomics. Nat Commun 5:3849. doi:10.1038/ncomms4849.
    OpenUrlCrossRefPubMed
  12. 12.↵
    1. Tsukui T,
    2. Nagano N,
    3. Umemura M,
    4. Kumagai T,
    5. Terai G,
    6. Machida M,
    7. Asai K
    . 2015. Ustiloxins, fungal cyclic peptides, are ribosomally synthesized in Ustilaginoidea virens. Bioinformatics 31:981–985. doi:10.1093/bioinformatics/btu753.
    OpenUrlCrossRefPubMed
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Genome Sequence of Ustilaginoidea virens IPU010, a Rice Pathogenic Fungus Causing False Smut
Toshitaka Kumagai, Tomoko Ishii, Goro Terai, Myco Umemura, Masayuki Machida, Kiyoshi Asai
Genome Announcements May 2016, 4 (3) e00306-16; DOI: 10.1128/genomeA.00306-16

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Genome Sequence of Ustilaginoidea virens IPU010, a Rice Pathogenic Fungus Causing False Smut
Toshitaka Kumagai, Tomoko Ishii, Goro Terai, Myco Umemura, Masayuki Machida, Kiyoshi Asai
Genome Announcements May 2016, 4 (3) e00306-16; DOI: 10.1128/genomeA.00306-16
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