Page 83 - Read Online

Page 14 of 16 Renzi et al. Microbiome Res Rep 2024;3:2 https://dx.doi.org/10.20517/mrr.2023.27

Environ Microbiol 2017;83:e00905-17. DOI PubMed PMC
75. Kiss L. Limits of nuclear ribosomal DNA internal transcribed spacer (ITS) sequences as species barcodes for Fungi. Proc Natl Acad
Sci U S A 2012;109:E1811; author reply E1812. DOI PubMed PMC
76. Stielow JB, Lévesque CA, Seifert KA, et al. One fungus, which genes? Development and assessment of universal primers for
potential secondary fungal DNA barcodes. Persoonia 2015;35:242-63. DOI
77. James TY, Kauff F, Schoch CL, et al. Reconstructing the early evolution of fungi using a six-gene phylogeny. Nature 2006;443:818-
22. DOI PubMed
78. Matheny PB, Liu YJ, Ammirati JF, Hall BD. Using RPB1 sequences to improve phylogenetic inference among mushrooms (Inocybe,
Agaricales). Am J Bot 2002;89:688-98. DOI PubMed
79. Meyer W, Irinyi L, Hoang MTV, et al. Database establishment for the secondary fungal DNA barcode translational elongation factor
1
1α (TEF1α) . Genome 2019;62:160-9. DOI
80. Větrovský T, Kolařík M, Žifčáková L, Zelenka T, Baldrian P. The rpb2 gene represents a viable alternative molecular marker for the
analysis of environmental fungal communities. Mol Ecol Resour 2016;16:388-401. DOI PubMed
81. Morrison GA, Fu J, Lee GC, et al. Nanopore sequencing of the fungal intergenic spacer sequence as a potential rapid diagnostic
assay. J Clin Microbiol 2020;58:e01972-20. DOI PubMed PMC
82. Geiser DM, Frisvad JC, Taylor JW. Evolutionary relationships in Aspergillus section Fumigati inferred from partial β-tubulin and
hydrophobin DNA sequences. Mycologia 1998;90:831-45. DOI
83. Hu T, Chitnis N, Monos D, Dinh A. Next-generation sequencing technologies: an overview. Hum Immunol 2021;82:801-11. DOI
PubMed
84. Quince C, Walker AW, Simpson JT, Loman NJ, Segata N. Shotgun metagenomics, from sampling to analysis. Nat Biotechnol
2017;35:833-44. DOI PubMed
85. Morgan XC, Huttenhower C. Meta’omic analytic techniques for studying the intestinal microbiome. Gastroenterology
2014;146:1437-48.e1. DOI PubMed
86. Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 2012;486:207-14. DOI
PubMed PMC
87. Nash AK, Auchtung TA, Wong MC, et al. The gut mycobiome of the Human Microbiome Project healthy cohort. Microbiome
2017;5:153. DOI PubMed PMC
88. Hoang MTV, Irinyi L, Hu Y, Schwessinger B, Meyer W. Long-reads-based metagenomics in clinical diagnosis with a special focus
on fungal infections. Front Microbiol 2021;12:708550. DOI PubMed PMC
89. Pollard MO, Gurdasani D, Mentzer AJ, Porter T, Sandhu MS. Long reads: their purpose and place. Hum Mol Genet 2018;27:R234-
41. DOI PubMed PMC
90. Mantere T, Kersten S, Hoischen A. Long-read sequencing emerging in medical genetics. Front Genet 2019;10:426. DOI PubMed
PMC
91. Sui Y, Wisniewski M, Droby S, Piombo E, Wu X, Yue J. Genome sequence, assembly, and characterization of the antagonistic yeast
candida oleophila used as a biocontrol agent against post-harvest diseases. Front Microbiol 2020;11:295. DOI PubMed PMC
92. Cuomo CA, Shea T, Yang B, Rao R, Forche A. Whole genome sequence of the heterozygous clinical isolate candida krusei 81-B-5.
G3 2017;7:2883-9. DOI PubMed PMC
93. Luo R, Zimin A, Workman R, et al. First draft genome sequence of the pathogenic fungus Lomentospora prolificans (Formerly
Scedosporium prolificans). G3 2017;7:3831-6. DOI PubMed PMC
94. Vale-Silva L, Beaudoing E, Tran VDT, Sanglard D. Comparative genomics of two sequential candida glabrata clinical isolates. G3
2017;7:2413-26. DOI PubMed PMC
95. Panthee S, Hamamoto H, Ishijima SA, Paudel A, Sekimizu K. Utilization of hybrid assembly approach to determine the genome of an
opportunistic pathogenic fungus, candida albicans TIMM 1768. Genome Biol Evol 2018;10:2017-22. DOI PubMed PMC
96. Rhodes J, Abdolrasouli A, Farrer RA, et al. Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen
Candida auris. Emerg Microbes Infect 2018;7:43. DOI PubMed PMC
97. Morand SC, Bertignac M, Iltis A, et al. Complete genome sequence of Malassezia restricta CBS 7877, an opportunist pathogen
involved in dandruff and seborrheic dermatitis. Microbiol Resour Announc 2019;8:e01543-18. DOI PubMed PMC
98. Schultzhaus Z, Cuomo CA, Wang Z. Genome sequence of the black yeast exophiala lecanii-corni. Microbiol Resour Announc
2019;8:e01709-18. DOI PubMed PMC
99. Pchelin IM, Azarov DV, Churina MA, et al. Whole genome sequence of first Candida auris strain, isolated in Russia. Med Mycol
2020;58:414-6. DOI
100. Arnaud MB, Chibucos MC, Costanzo MC, et al. The aspergillus genome database, a curated comparative genomics resource for gene,
protein and sequence information for the Aspergillus research community. Nucleic Acids Res 2010;38:D420-7. DOI PubMed PMC
101. Ratnasingham S, Hebert PD. bold: The barcode of life data system (http://www.barcodinglife.org). Mol Ecol Notes 2007;7:355-64.
DOI PubMed PMC
102. Inglis DO, Arnaud MB, Binkley J, et al. The Candida genome database incorporates multiple Candida species: multispecies search
and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata. Nucleic Acids Res
2012;40:D667-74. DOI PubMed PMC
103. Güldener U, Münsterkötter M, Kastenmüller G, et al. CYGD: the comprehensive yeast genome database. Nucleic Acids Res