Draft genome sequence of Ustilago trichophora RK089, a promising malic acid producer

Genome Announcements

Volumn 4, Issue 4, 2016, Pages

  Zambanini, Thiemo ^a   Buescher, Joerg M ^b   Meurer, Guido ^b   Wierckx, Nick ^a   Blank, Lars M ^a  

^a RWTH AACHEN UNIVERSITY   (Germany)

^b BRAIN AG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85010223240     PISSN: None     EISSN: 21698287     Source Type: Journal    
DOI: 10.1128/genomeA.00749-16     Document Type: Article

References (20)

1. Geiser E, Wiebach V, Wierckx N, Blank LM. 2014. Prospecting the biodiversity of the fungal family Ustilaginaceae for the production of value-added chemicals. BMC fungal biol. Biotechnol 1:2.
2. Maassen N, Panakova M, Wierckx N, Geiser E, Zimmermann M, Bölker M, Klinner U, Blank LM. 2013. Influence of carbon and nitrogen concentration on itaconic acid production by the smut fungus Ustilago maydis. Eng Life Sci 14:129-134.
3. Klement T, Milker S, Jäger G, Grande PM, Domínguez de Maria P, Büchs J. 2012. Biomass pretreatment affects Ustilago maydis in producing itaconic acid. Microb Cell Fact 11:43. http://dx.doi.org/10.1186/1475-2859-11-43.
4. Klement T, Büchs J. 2013. Itaconic acid-a biotechnological process in change. Bioresour Technol 135:422-431. http://dx.doi.org/10.1016/j.biortech.2012.11.141.
5. Feldbrügge M, Kellner R, Schipper K. 2013. The biotechnological use and potential of plant pathogenic smut fungi. Appl Microbiol Biotechnol 97:3253-3265. http://dx.doi.org/10.1007/s00253-013-4777-1.
6. Bölker M, Basse CW, Schirawski J. 2008. Ustilago maydis secondary metabolism-from genomics to biochemistry. Fungal Genet Biol 45(Suppl 1):S88-S93. http://dx.doi.org/10.1016/j.fgb.2008.05.007.
7. Zambanini T, Sarikaya E, Kleineberg W, Buescher JM, Meurer G, Wierckx N, Blank LM. 2016. Efficient malic acid production from glycerol with Ustilago trichophora TZ1. Biotechnol Biofuels 9:67. http://dx.doi.org/10.1186/s13068-016-0483-4.
8. Zambanini T, Kleineberg W, Sarikaya E, Buescher JM, Meurer G, Wierckx N, Blank LM. 2016. Enhanced malic acid production from glycerol with high-cell-density Ustilago trichophora TZ1 cultivations. Biotechnol Biofuels. 2016. http://dx.doi.org/10.1186/s13068-016-0483-4.
9. Kunze. 1830. Ustilago trichophora. Flora 1:369.
10. Fullerton RA, Langdon RFN. 1969. A study of some smuts of Echinochloa spp. Proc Linn Soc NSW 93:281-293.
11. Stoll M, Piepenbring M, Begerow D, Oberwinkler F. 2003. Molecular phylogeny of Ustilago and Sporisorium species (Basidiomycota, Ustilaginales) based on internal transcribed spacer (ITS) sequences. Can J Bot 81:976-984. http://dx.doi.org/10.1139/b03-094.
12. Stoll M, Begerow D, Oberwinkler F. 2005. Molecular phylogeny of Ustilago, Sporisorium, and related taxa based on combined analyses of rDNA sequences. Mycol Res 109:342-356. http://dx.doi.org/10.1017/S0953756204002229.
13. Zhang JZ, Guan PG, Tao G, Ojaghian MR, Hyde KD. 2013. Ultrastructure and phylogeny of Ustilago coicis. J Zhejiang Univ Sci 14:336-345. http://dx.doi.org/10.1631/jzus.B1200239.
14. Chikhi R, Medvedev P. 2014. Informed and automated k-mer size selection for genome assembly. Bioinformatics 30:31-37. http://dx.doi.org/10.1093/bioinformatics/btt310.
15. Chaisson MJ, Tesler G. 2012. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics 13:238. http://dx.doi.org/10.1186/1471-2105-13-238.
16. Boetzer M, Pirovano W. 2014. SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information. BMC Bioinformatics 15:211. http://dx.doi.org/10.1186/1471-2105-15-211.
17. Boetzer M, PirovanoW. 2012. Toward almost closed genomes with Gap-Filler. Genome Biol 13:R56. http://dx.doi.org/10.1186/gb-2012-13-6-r56.
18. Geiser E, Przybilla SK, Friedrich A, Buckel W, Wierckx N, Blank LM, Bölker M. 2016. Ustilago maydis produces itaconic acid via the unusual intermediate trans-aconitate. Microb Biotechnol 9:116-126. http://dx.doi.org/10.1111/1751-7915.12329.
19. Teichmann B, Linne U, Hewald S, Marahiel MA, Bölker M. 2007. A biosynthetic gene cluster for a secreted cellobiose lipid with antifungal activity from Ustilago maydis. Mol Microbiol 66:525-533. http://dx.doi.org/10.1111/j.1365-2958.2007.05941.x.
20. Hewald S, Linne U, Scherer M, Marahiel MA, Kämper J, Bölker M. 2006. Identification of a gene cluster for biosynthesis of mannosylerythritol lipids in the basidiomycetous fungus Ustilago maydis. Appl Environ Microbiol 72:5469-5477. http://dx.doi.org/10.1128/AEM.00506-06.