The structure of the Cyberlindnera jadinii genome and its relation to Candida utilis analyzed by the occurrence of single nucleotide polymorphisms

Journal of Biotechnology

Volumn 211, Issue , 2015, Pages 20-30

  Rupp, Oliver ^a,b   Brinkrolf, Karina ^b   Buerth, Christoph ^c   Kunigo, Maya ^c   Schneider, Jessica ^b   Jaenicke, Sebastian ^b   Goesmann, Alexander ^a,b   Pühler, Alfred ^b   Jaeger, Karl Erich ^c,d   Ernst, Joachim F ^c  

^a JUSTUS LIEBIG UNIVERSITY   (Germany)

^b BIELEFELD UNIVERSITY   (Germany)

^c HEINRICH HEINE UNIVERSITY   (Germany)

^d FORSCHUNGSZENTRUM JÜLICH   (Germany)

Author keywords

Candida utilis; Cyberlindnera jadinii; Genome sequence; Level of ploidy; SNP (single nucleotide polymorphism) calling

Indexed keywords

CANDIDA; COMPUTER KEYBOARDS; GENETIC ENGINEERING; NUCLEOTIDES; YEAST;

CANDIDA UTILIS; CYBERLINDNERA JADINII; GENOME SEQUENCES; LEVEL OF PLOIDY; SINGLE NUCLEOTIDE POLYMORPHISMS;

GENES;

CELL NUCLEUS DNA; FUNGAL DNA;

ARTICLE; CHROMOSOME; CONTROLLED STUDY; CYBERLINDNERA JADINII; DIPLOIDY; DNA CONTENT; FLUORESCENCE ACTIVATED CELL SORTING; FUNGAL GENOME; FUNGAL STRAIN; HAPLOIDY; MOLECULAR PHYLOGENY; NEXT GENERATION SEQUENCING; NONHUMAN; PLOIDY; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; TETRAPLOIDY; TRIPLOIDY; ASCOMYCETES; CANDIDA; DNA BASE COMPOSITION; DNA SEQUENCE; FLOW CYTOMETRY; FUNGAL GENE; GENE ONTOLOGY; GENETICS; REPRODUCIBILITY; SEQUENCE HOMOLOGY;

PICHIA JADINII;

ASCOMYCOTA; BASE COMPOSITION; CANDIDA; DIPLOIDY; DNA, FUNGAL; FLOW CYTOMETRY; GENE ONTOLOGY; GENES, FUNGAL; GENOME, FUNGAL; PLOIDIES; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 84937110261     PISSN: 01681656     EISSN: 18734863     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2015.06.423     Document Type: Article

References (37)

1. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
2. Amberg D., Burke D., Strathem J. Methods in Yeast Genetics 2005, Cold Spring Habor Laboratory Press. 1st ed.
3. Bansal V., Bafna V. HapCUT: an efficient and accurate algorithm for the haplotype assembly problem. Bioinformatics 2008, 24:i153-159.
4. Bekatorou A., Psarianos C., Koutinas A.A. Production of food grade yeasts. Food Technol. Biotechnol. 2006, 44:407-415.
5. Blom J., Albaum S.P., Doppmeier D., Pühler A., Vorhölter F.J., Zakrzewski M., Goesmann A. EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinform. 2009, 10:154.
6. Borodovsky, M., Lomsadze, A., 2011. Eukaryotic gene prediction using GeneMark.hmm-E and GeneMark-ES. Curr. Protoc. Bioinform. Chapter 4, Unit 4, 6, 1-10.
7. Buerth C., Heilmann C.J., Klis F.M., de Koster C.G., Ernst J.F., Tielker D. Growth-dependent secretome of Candida utilis. Microbiology 2011, 157:2493-2503.
8. Donmez N., Brudno M. SCARPA: scaffolding reads with practical algorithms. Bioinformatics 2013, 29:428-434.
9. Falcon S., Gentleman R. Using GOstats to test gene lists for GO term association. Bioinformatics 2007, 23:257-258.
10. Gerstein A.C., Otto S.P. Ploidy and the causes of genomic evolution. J. Hered. 2009, 100:571-581.
11. Haas B.J., Salzberg S.L., Zhu W., Pertea M., Allen J.E., Orvis J., White O., Buell C.R., Wortman J.R. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 2008, 9:R7.
12. Hilker R., Stadermann K.B., Doppmeier D., Kalinowski J., Stoye J., Straube J., Winnebald J., Goesmann A. ReadXplorer-visualization and analysis of mapped sequences. Bioinformatics 2014, 30:2247-2254.
13. Hong Y.R., Chen Y.L., Farh L., Yang W.J., Liao C.H., Shiuan D. Recombinant Candida utilis for the production of biotin. Appl. Microbiol. Biotechnol. 2006, 71:211-221.
14. Ikushima S., Fujii T., Kobayashi O. Efficient gene disruption in the high-ploidy yeast Candida utilis using the Cre-loxP system. Biosci. Biotechnol. Biochem. 2009, 73:879-884.
15. Kondo K., Saito T., Kajiwara S., Takagi M., Misawa N. A transformation system for the yeast Candida utilis: use of a modified endogenous ribosomal protein gene as a drug-resistant marker and ribosomal DNA as an integration target for vector DNA. J. Bacteriol. 1995, 177:7171-7177.
16. Korf I. Gene finding in novel genomes. BMC Bioinform. 2004, 5:59.
17. Küberl A., Schneider J., Thallinger G.G., Anderl I., Wibberg D., Hajek T., Jaenicke S., Brinkrolf K., Goesmann A., Szczepanowski R., Pühler A., Schwab H., Glieder A., Pichler H. High-quality genome sequence of Pichia pastoris CBS7435. J. Biotechnol. 2011, 154:312-320.
18. Kunigo M., Buerth C., Tielker D., Ernst J.F. Heterologous protein secretion by Candida utilis. Appl. Microbiol. Biotechnol. 2013, 97:7357-7368.
19. Kurtz S., Phillippy A., Delcher A.L., Smoot M., Shumway M., Antonescu C., Salzberg S.L. Versatile and open software for comparing large genomes. Genome Biol. 2004, 5:R12.
20. Kurtzman, Robnett, Basehoar-Powers The Yeasts - A Taxonomic Study 2011, Elsevier, London, Burlington, San Diego. 5 ed.
21. Kurtzman C.P., Johnson C.J., Smiley M.J. Determination of conspecificity of Candida utilis and Hansenula jadinii through DNA reassociation. Mycologia 1979, 11:844-847.
22. Langmead B., Salzberg S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 2013, 9:357-359.
23. McKenna A., Hanna M., Banks E., Sivachenko A., Cibulskis K., Kernytsky A., Garimella K., Altshuler D., Gabriel S., Daly M., DePristo M.A. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010, 20:1297-1303.
24. Minter D.W. Cyberlindnera, a replacement name for Lindnera Kurtzman et al. nom. illegit. Mycotaxon 2009, 110:473-476.
25. Mukherjee P.K., Chandra J., Retuerto M., Sikaroodi M., Brown R.E., Jurevic R., Salata R.A., Lederman M.M., Gillevet P.M., Ghannoum M.A. Oral mycobiome analysis of HIV-infected patients: identification of Pichia as an antagonist of opportunistic fungi. PLoS Pathog. 2014, 10:e1003996.
26. Perez P., Rincón S.A. Rho GTPases: regulation of cell polarity and growth in yeasts. Biochem. J. 2010, 426:243-253.
27. Rupp O., Becker J., Brinkrolf K., Timmermann C., Borth N., Pühler A., Noll T., Goesmann A. Construction of a public CHO cell line transcript database using versatile bioinformatics analysis pipelines. PLoS One 2014, 9:e85568.
28. Sherman F., Fink G.R., Hicks J.B. Methods in Yeast Genetics 1986, Cold Spring Habor Laboratory Press, New York.
29. Slater G.S., Birney E. Automated generation of heuristics for biological sequence comparison. BMC Bioinform. 2005, 6:31.
30. Stanke M., Waack, S Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 2003, 19(Suppl. 2):ii215-ii225.
31. Stoltenburg R., Klinner U., Ritzerfeld P., Zimmermann M., Emeis C.C. Genetic diversity of the yeast Candida utilis. Curr. Genet. 1992, 22:441-446.
32. Tamakawa H., Ikushima S., Yoshida S. Efficient production of L-lactic acid from xylose by a recombinant Candida utilis strain. J. Biosci. Bioeng. 2012, 113:73-75.
33. Tomita Y., Ikeo K., Tamakawa H., Gojobori T., Ikushima S. Genome and transcriptome analysis of the food-yeast Candida utilis. PLoS One 2012, 7:e37226.
34. Trapnell C., Pachter L., Salzberg S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25:1105-1111.
35. Trapnell C., Roberts A., Goff L., Pertea G., Kim D., Kelley D.R., Pimentel H., Salzberg S.L., Rinn J.L., Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 2012, 7:562-578.
36. Tsai I.J., Otto T.D., Berriman M. Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biol. 2013, 11:R41.
37. Yamada Y., Matsuda M., Mikata K. The phylogenetic relationships of Pichia jadinii, formerly classified in the genus Hansenula, and related species based on the partial sequences of 18S and 26S ribosomal RNAs (Saccharomycetaceae). Biosci. Biotechnol. Biochem. 1995, 59:518-520.