Genomic characteristics and genetic manipulation of the marine yeast Scheffersomyces spartinae

Abdel-Mawgoud A, Stephanopoulos G (2020) Improving CRISPR/Cas9-mediated genome editing efficiency in Yarrowia lipolytica using direct tRNA-sgRNA fusions. Metab Eng 62:106–115

Article  CAS  PubMed  Google Scholar 

Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. Babraham Bioinformatics, Babraham Institute, Cambridge

Google Scholar 

Atzmüller D, Ullmann N, Zwirzitz A (2020) Identification of genes involved in xylose metabolism of Meyerozyma guilliermondii and their genetic engineering for increased xylitol production. AMB Exp 10:78

Article  Google Scholar 

Bang S, Pazirandeh M (1999) Physical properties and heavy metal uptake of encapsulated Escherichia coli expressing a metal binding gene (NCP). J Microencapsul 16:489–499

Article  CAS  PubMed  Google Scholar 

Barros KO, Mader M, Krause DJ, Pangilinan J, Andreopoulos B, Lipzen A, Mondo SJ, Grigoriev IV, Rosa CA, Sato TK (2024) Oxygenation influences xylose fermentation and gene expression in the yeast genera Spathaspora and Scheffersomyces. Biotechnol Biof Biop 17:20

CAS  Google Scholar 

Breyer E, Espada-Hinojosa S, Reitbauer M, Karunarathna SC, Baltar F (2023) Physiological properties of three pelagic fungi isolated from the Atlantic Ocean. J Fungi 9:439

Article  CAS  Google Scholar 

Chatterjee N, Walker GC (2017) Mechanisms of DNA damage, repair, and mutagenesis. Environ Mol Mutagen 58:235–263

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen Y, Nie F, Xie S-Q, Zheng Y-F, Bray T, Dai Q, Wang Y-X, Xing J-f, Huang Z-J, Wang D-P (2020) Fast and accurate assembly of Nanopore reads via progressive error correction and adaptive read selection. BioRxiv: 2020.2002. 2001.930107

Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 6:80–92

Article  CAS  PubMed  PubMed Central  Google Scholar 

Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676

Article  CAS  PubMed  Google Scholar 

Cui Z, Zheng H, Zhang J, Jiang Z, Zhu Z, Liu X, Qi Q, Hou J (2021) A CRISPR/Cas9-mediated, homology-independent tool developed for targeted genome integration in Yarrowia lipolytica. Appl Environ Microbiol 87:e02666-e2620

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, de Montigny J, Marck C, Neuvéglise C, Talla E, Goffard N, Frangeul L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich J-M, Beyne E, Bleykasten C, Boisramé A, Boyer J, Cattolico L, Confanioleri F, de Daruvar A, Despons L, Fabre E, Fairhead C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequin C, Jauniaux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur I, Ma L, Muller H, Nicaud J-M, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard G-F, Straub M-L, Suleau A, Swennen D, Tekaia F, Wésolowski-Louvel M, Westhof E, Wirth B, Zeniou-Meyer M, Zivanovic I, Bolotin-Fukuhara M, Thierry A, Bouchier C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P, Souciet J-L (2004) Genome evolution in yeasts. Nature 430:35–44

Article  PubMed  Google Scholar 

Förstemann K, Lingner J (2001) Molecular basis for telomere repeat divergence in budding yeast. Mol Cell Biol 21:7277–7286

Article  PubMed  PubMed Central  Google Scholar 

Fujimura H (1998) Growth inhibition of Saccharomyces cerevisiae by the immunosuppressant leflunomide is due to the inhibition of uracil uptake via Fur4p. Mol Gen Genet 260:102–107

Article  CAS  PubMed  Google Scholar 

Gedvilaite A, Sasnauskas K (1994) Control of the expression of the ADE2 gene of the yeast Saccharomyces cerevisiae. Curr Genet 25:475–479

Article  CAS  PubMed  Google Scholar 

Gietz RD, Schiestl RH (2007) High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method. Nat Protoc 2:31–34

Article  CAS  PubMed  Google Scholar 

Gillings M, Holley M, Selleck M (2006) Molecular identification of species comprising an unusual biofilm from a groundwater treatment plant. Biofilms 3:19–24

Article  Google Scholar 

Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M (1996) Life with 6000 genes. Science 274:546–567

Article  CAS  PubMed  Google Scholar 

Goldstein AL, McCusker JH (1999) Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae. Yeast 15:1541–1553

Article  CAS  PubMed  Google Scholar 

Gueldener U, Heinisch J, Koehler G, Voss D, Hegemann J (2002) A second set of loxP marker cassettes for Cre-mediated multiple gene knockouts in budding yeast. Nucleic Acids Res 30:e23

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hu J, Fan J, Sun Z, Liu S (2020) NextPolish: a fast and efficient genome polishing tool for long-read assembly. Bioinformatics 36:2253–2255

Article  CAS  PubMed  Google Scholar 

Ji Q, Mai J, Ding Y, Wei Y, Ledesma-Amaro R, Ji X-J (2020) Improving the homologous recombination efficiency of Yarrowia lipolytica by grafting heterologous component from Saccharomyces cerevisiae. Meta Eng Commun 11:e00152

Article  Google Scholar 

Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK (2012) VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 22:568–576

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kurtzman CP, Suzuki M (2010) Phylogenetic analysis of ascomycete yeasts that form coenzyme Q-9 and the proposal of the new genera Babjeviella, Meyerozyma, Millerozyma, Priceomyces, and Scheffersomyces. Mycoscience 51:2–14

Article  CAS  Google Scholar 

Kwak S, Jin Y-S (2017) Production of fuels and chemicals from xylose by engineered Saccharomyces cerevisiae: a review and perspective. Microb Cell Fact 16:82

Article  PubMed  PubMed Central  Google Scholar 

Lee TJ, Liu Y-C, Liu W-A, Lin Y-F, Lee H-H, Ke H-M, Huang J-P, Lu M-YJ, Hsieh C-L, Chung K-F (2022) Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages. Genome Res 32:864–877

CAS  PubMed  PubMed Central  Google Scholar 

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Subgroup GPDP (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079

Article  PubMed  PubMed Central  Google Scholar 

Li C, Shi K, Zhang Y, Wang G (2019) Nocardioides silvaticus sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 69:68–73

Article  CAS  PubMed  Google Scholar 

Li K-J, Qi L, Zhu Y-X, He M, Xiang Q, Zheng D-Q (2024) Spontaneous and environment induced genomic alterations in yeast model. Cell Insight 4:100209

Article  PubMed  PubMed Central  Google Scholar 

Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:1303.3997

Lowe TM, Chan PP (2016) tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 44:W54–W57

Article  CAS  PubMed  PubMed Central  Google Scholar 

Madden K, Snyder M (1998) Cell polarity and morphogenesis in budding yeast. Annu Rev Microbiol 52:687–744

Article  CAS  PubMed  Google Scholar 

Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A (2018) MUMmer4: a fast and versatile genome alignment system. PLoS Comp Biol 14:e1005944

Article  Google Scholar 

Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17:10–12

Comments (0)

No login
gif