title: Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1.
abstract: 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.
authors.forename: Nikolai V
authors.initials: NV
authors.lastname: Ravin
authors.forename: Michael A
authors.initials: MA
authors.lastname: Eldarov
authors.forename: Vitaly V
authors.initials: VV
authors.lastname: Kadnikov
authors.forename: Alexey V
authors.initials: AV
authors.lastname: Beletsky
authors.forename: Jessica
authors.initials: J
authors.lastname: Schneider
authors.forename: Eugenia S
authors.initials: ES
authors.lastname: Mardanova
authors.forename: Elena M
authors.initials: EM
authors.lastname: Smekalova
authors.forename: Maria I
authors.initials: MI
authors.lastname: Zvereva
authors.forename: Olga A
authors.initials: OA
authors.lastname: Dontsova
authors.forename: Andrey V
authors.initials: AV
authors.lastname: Mardanov
authors.affiliation: Centre "Bioengineering" of RAS, Prosp, 60-let Oktyabrya, bld, 7-1, Moscow 117312, Russia. biengi@biengi.ac.ru.
authors.forename: Konstantin G
authors.initials: KG
authors.lastname: Skryabin
mesh_terms: D017398:Alternative Splicing; D000975:Antioxidants / Q000378:metabolism; D015825:Chromosomes, Fungal; D016000:Cluster Analysis; D003062:Codon; D004251:DNA Transposable Elements; D019143:Evolution, Molecular; D005227:Fatty Acids / Q000378:metabolism; D020440:Gene Duplication; D020869:Gene Expression Profiling; D005800:Genes, Fungal; D016681:Genome, Fungal; D005947:Glucose / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D000432:Methanol / Q000378:metabolism; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D010084:Oxidation-Reduction; D010427:Pentose Phosphate Pathway; D020675:Peroxisomes / Q000378:metabolism; D010802:Phylogeny; D022821:RNA Splice Sites; D004718:Saccharomycetales / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA; D016615:Telomere / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: D000975:Antioxidants; D003062:Codon; D004251:DNA Transposable Elements; D005227:Fatty Acids; D022821:RNA Splice Sites; D014157:Transcription Factors; D005947:Glucose; D000432:Methanol