Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1

Ravin NV, Eldarov MA, Kadnikov VV, Beletsky AV, Schneider J, Mardanova ES, Smekalova EM, Zvereva MI, Dontsova OA, Mardanov AV, Skryabin KG (2013)
BMC Genomics 14(1): 837.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
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Ravin, Nikolai V.; Eldarov, Michael A.; Kadnikov, Vitaly V.; Beletsky, Alexey V.; Schneider, JessicaUniBi; Mardanova, Eugenia S.; Smekalova, Elena M.; Zvereva, Maria I.; Dontsova, Olga A.; Mardanov, Andrey V.; Skryabin, Konstantin G.
Abstract / Bemerkung
Background: Hansenula polymorpha DL1 is a methylotrophic yeast, widely used in fundamental studies of methanol metabolism, peroxisome biogenesis and function, and also as a microbial cell factory for production of recombinant proteins and metabolic engineering towards the goal of high temperature ethanol production. Results: We have sequenced the 9 Mbp H. polymorpha DL1 genome and performed whole genome analysis for the H. polymorpha transcriptome obtained from both methanol- and glucose-grown cells. RNA-seq analysis revealed the complex and dynamic character of the H. polymorpha transcriptome under the two studied conditions, identified abundant and highly unregulated expression of 40% of the genome in methanol grown cells, and revealed alternative splicing events. We have identified subtelomerically biased protein families in H. polymorpha, clusters of LTR elements at G + C-poor chromosomal loci in the middle of each of the seven H. polymorpha chromosomes, and established the evolutionary position of H. polymorpha DL1 within a separate yeast clade together with the methylotrophic yeast Pichia pastoris and the non-methylotrophic yeast Dekkera bruxellensis. Intergenome comparisons uncovered extensive gene order reshuffling between the three yeast genomes. Phylogenetic analyses enabled us to reveal patterns of evolution of methylotrophy in yeasts and filamentous fungi. Conclusions: Our results open new opportunities for in-depth understanding of many aspects of H. polymorpha life cycle, physiology and metabolism as well as genome evolution in methylotrophic yeasts and may lead to novel improvements toward the application of H. polymorpha DL-1 as a microbial cell factory.
Yeast; RNA-seq; Methylotrophic yeasts; Hansenula polymorpha; Genome; evolution
BMC Genomics
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Ravin NV, Eldarov MA, Kadnikov VV, et al. Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1. BMC Genomics. 2013;14(1): 837.
Ravin, N. V., Eldarov, M. A., Kadnikov, V. V., Beletsky, A. V., Schneider, J., Mardanova, E. S., Smekalova, E. M., et al. (2013). Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1. BMC Genomics, 14(1), 837. doi:10.1186/1471-2164-14-837
Ravin, Nikolai V., Eldarov, Michael A., Kadnikov, Vitaly V., Beletsky, Alexey V., Schneider, Jessica, Mardanova, Eugenia S., Smekalova, Elena M., et al. 2013. “Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1”. BMC Genomics 14 (1): 837.
Ravin, N. V., Eldarov, M. A., Kadnikov, V. V., Beletsky, A. V., Schneider, J., Mardanova, E. S., Smekalova, E. M., Zvereva, M. I., Dontsova, O. A., Mardanov, A. V., et al. (2013). Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1. BMC Genomics 14:837.
Ravin, N.V., et al., 2013. Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1. BMC Genomics, 14(1): 837.
N.V. Ravin, et al., “Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1”, BMC Genomics, vol. 14, 2013, : 837.
Ravin, N.V., Eldarov, M.A., Kadnikov, V.V., Beletsky, A.V., Schneider, J., Mardanova, E.S., Smekalova, E.M., Zvereva, M.I., Dontsova, O.A., Mardanov, A.V., Skryabin, K.G.: Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1. BMC Genomics. 14, : 837 (2013).
Ravin, Nikolai V., Eldarov, Michael A., Kadnikov, Vitaly V., Beletsky, Alexey V., Schneider, Jessica, Mardanova, Eugenia S., Smekalova, Elena M., Zvereva, Maria I., Dontsova, Olga A., Mardanov, Andrey V., and Skryabin, Konstantin G. “Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1”. BMC Genomics 14.1 (2013): 837.

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Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL., Genome Biol. 14(4), 2013
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Roberts A, Pimentel H, Trapnell C, Pachter L., Bioinformatics 27(17), 2011
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Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.
Thorvaldsdottir H, Robinson JT, Mesirov JP., Brief. Bioinformatics 14(2), 2012
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RAPYD--rapid annotation platform for yeast data.
Schneider J, Blom J, Jaenicke S, Linke B, Brinkrolf K, Neuweger H, Tauch A, Goesmann A., J. Biotechnol. 155(1), 2010
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Assessing the gene space in draft genomes.
Parra G, Bradnam K, Ning Z, Keane T, Korf I., Nucleic Acids Res. 37(1), 2008
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Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.
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MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
Unipro UGENE: a unified bioinformatics toolkit.
Okonechnikov K, Golosova O, Fursov M; UGENE team, Varlamov A, Vaskin Y, Efremov I, Grehov G, Kandrov D, Rasputin K, Syabro M, Tleukenov T., Bioinformatics 28(8), 2012
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Versatile and open software for comparing large genomes.
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