A telomere-to-telomere genome assembly for Meyerozyma guilliermondii ATCC 6260: closing gaps and resolving a translocation in the reference sequence

References

1. Papon N, Savini V, Lanoue A, Simkin AJ, Crèche J et al. Candida guilliermondii: biotechnological applications, perspectives for biological control, emerging clinical importance and recent advances in genetics. Curr Genet 2013; 59:73–90 [View Article] [PubMed]
   [Google Scholar]
2. Butler G, Rasmussen MD, Lin MF, Santos MAS, Sakthikumar S et al. Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature 2009; 459:657–662 [View Article] [PubMed]
   [Google Scholar]
3. Santos MAS, Gomes AC, Santos MC, Carreto LC, Moura GR. The genetic code of the fungal CTG clade. C R Biol 2011; 334:607–611 [View Article] [PubMed]
   [Google Scholar]
4. Oh S-H, Schliep K, Isenhower A, Rodriguez-Bobadilla R, Vuong VM et al. Using genomics to shape the definition of the agglutinin-like sequence (ALS) family in the Saccharomycetales. Front Cell Infect Microbiol 2021; 11:794529 [View Article] [PubMed]
   [Google Scholar]
5. Eid J, Fehr A, Gray J, Luong K, Lyle J et al. Real-time DNA sequencing from single polymerase molecules. Science 2009; 323:133–138 [View Article] [PubMed]
   [Google Scholar]
6. Hoyer LL, Freeman BA, Hogan EK, Hernandez AG. Use of a Candida albicans SC5314 PacBio HiFi reads dataset to close gaps in the reference genome assembly, reveal a subtelomeric gene family, and produce accurate phased allelic sequences. Front Cell Infect Microbiol 2024; 14:1329438 [View Article] [PubMed]
   [Google Scholar]
7. Hoyer LL. Visualization of yeast chromosomes using clamped homogeneous electric field (CHEF) electrophoresis. Protocols.io; 2023 https://dx.doi.org/10.17504/protocols.io.8epv5jdpdl1b/v1
8. Hoyer LL. Extraction of yeast high-molecular-weight genomic DNA v1. Protocols.io; 2023 https://doi.org/10.17504/protocols.io.rm7vzb1b4vx1/v1
9. Wick RR, Menzel P. Filtlong 2019 https://github.com/rrwick/Filtlong
10. Cheng H, Concepcion GT, Feng X, Zhang H, Li H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods 2021; 18:170–175 [View Article] [PubMed]
    [Google Scholar]
11. Palmer JM, Stajich J. Funannotate v1.8.13 2025 https://github.com/nextgenusfs/funannotate
12. EMBOSS Transeq EMBOSS TRANSEQ Sequence Translation (ST); 2025 https://www.ebi.ac.uk/jdispatcher/st/emboss_transeq
13. Madeira F, Pearce M, Tivey ARN, Basutkar P, Lee J et al. Search and sequence analysis tools services from EMBL-EBI in 2022. Nucleic Acids Res 2022; 50:W276–W279 [View Article] [PubMed]
    [Google Scholar]
14. Jones P, Binns D, Chang H-Y, Fraser M, Li W et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 2014; 30:1236–1240 [View Article] [PubMed]
    [Google Scholar]
15. Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol 2021; 38:5825–5829 [View Article] [PubMed]
    [Google Scholar]
16. Cantalapiedra CP, Hernandez-Plaza A, Coelho LP, Szklarczyk D, Forslund SK et al. eggNOG-mapper web. n.d http://eggnog-mapper.embl.de
17. Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol Biol Evol 2021; 38:4647–4654 [View Article] [PubMed]
    [Google Scholar]
18. Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL et al. MUMmer4: a fast and versatile genome alignment system. PLoS Comput Biol 2018; 14:e1005944 [View Article] [PubMed]
    [Google Scholar]
19. Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 2018; 34:3094–3100 [View Article]
    [Google Scholar]
20. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J et al. The sequence alignment/map (SAM) format and SAMtools. Bioinformatics 2009; 25:2078–2079 [View Article] [PubMed]
    [Google Scholar]
21. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES et al. Integrative genomics viewer. Nat Biotechnol 2011; 29:24–26 [View Article] [PubMed]
    [Google Scholar]
22. McEachern MJ, Blackburn EH. A conserved sequence motif within the exceptionally diverse telomeric sequences of budding yeasts. Proc Natl Acad Sci USA 1994; 91:3453–3457 [View Article] [PubMed]
    [Google Scholar]