title: Complete genome sequence and transcriptome regulation of the pentose utilizing yeast Sugiyamaella lignohabitans.
abstract: Efficient conversion of hexoses and pentoses into value-added chemicals represents one core step for establishing economically feasible biorefineries from lignocellulosic material. While extensive research efforts have recently provided advances in the overall process performance, the quest for new microbial cell factories and novel enzymes sources is still open. As demonstrated recently the yeast Sugiyamaella lignohabitans (formerly Candida lignohabitans) represents a promising microbial cell factory for the production of organic acids from lignocellulosic hydrolysates. We report here the de novo genome assembly of S. lignohabitans using the Single Molecule Real-Time platform, with gene prediction refined by using RNA-seq. The sequencing revealed a 15.98 Mb genome, subdivided into four chromosomes. By phylogenetic analysis, Blastobotrys (Arxula) adeninivorans and Yarrowia lipolytica were found to be close relatives of S. lignohabitans Differential gene expression was evaluated in typical growth conditions on glucose and xylose and allowed a first insight into the transcriptional response of S. lignohabitans to different carbon sources and different oxygenation conditions. Novel sequences for enzymes and transporters involved in the central carbon metabolism, and therefore of potential biotechnological interest, were identified. These data open the way for a better understanding of the metabolism of S. lignohabitans and provide resources for further metabolic engineering.
authors.affiliation: Department of Biotechnology, BOKU-VIBT University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
authors.forename: Martina
authors.initials: M
authors.lastname: Bellasio
authors.affiliation: Austrian Centre of Industrial Biotechnology (ACIB), University of Applied Sciences FH Campus Wien, 1190 Vienna, Austria School of Bioengineering, University of Applied Sciences FH Campus Wien, 1190 Vienna, Austria.
authors.forename: Armin
authors.initials: A
authors.lastname: Peymann
authors.affiliation: Department of Biotechnology, BOKU-VIBT University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria Austrian Centre of Industrial Biotechnology (ACIB), University of Applied Sciences FH Campus Wien, 1190 Vienna, Austria.
authors.forename: Matthias G
authors.initials: MG
authors.lastname: Steiger
authors.affiliation: Department of Biotechnology, BOKU-VIBT University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria Austrian Centre of Industrial Biotechnology (ACIB), University of Applied Sciences FH Campus Wien, 1190 Vienna, Austria.
authors.forename: Minoska
authors.initials: M
authors.lastname: Valli
authors.affiliation: Department of Genetics and Applied Microbiology, University of Debrecen, 4032 Debrecen, Egyetem tér1, Hungary.
authors.forename: Matthias
authors.initials: M
authors.lastname: Sipiczki
authors.affiliation: Department of Biotechnology, BOKU-VIBT University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria Austrian Centre of Industrial Biotechnology (ACIB), University of Applied Sciences FH Campus Wien, 1190 Vienna, Austria.
authors.forename: Michael
authors.initials: M
authors.lastname: Sauer
authors.affiliation: Austrian Centre of Industrial Biotechnology (ACIB), University of Applied Sciences FH Campus Wien, 1190 Vienna, Austria School of Bioengineering, University of Applied Sciences FH Campus Wien, 1190 Vienna, Austria.
authors.forename: Alexandra B
authors.initials: AB
authors.lastname: Graf
authors.affiliation: Department of Biotechnology, BOKU-VIBT University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria hans.marx@boku.ac.at.
authors.forename: Hans
authors.initials: H
authors.lastname: Marx
authors.affiliation: Department of Biotechnology, BOKU-VIBT University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria Austrian Centre of Industrial Biotechnology (ACIB), University of Applied Sciences FH Campus Wien, 1190 Vienna, Austria.
authors.forename: Diethard
authors.initials: D
authors.lastname: Mattanovich
mesh_terms: D015825:Chromosomes, Fungal; D020869:Gene Expression Profiling; D016681:Genome, Fungal; D005947:Glucose / Q000378:metabolism; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D010429:Pentoses / Q000378:metabolism*; D010802:Phylogeny; D004718:Saccharomycetales / Q000145:classification / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D017385:Sequence Homology; D014994:Xylose / Q000378:metabolism
chemical_list: D010429:Pentoses; D014994:Xylose; D005947:Glucose
keywords: RNA-Seq; SMRT sequencing; Sugiyamaella lignohabitans; complete genome sequence; microbial cell factory; xylose utilization