Long-read Sequencing and de novo Genome Assembly of Three Aspergillus fumigatus Genomes.
Aspergillus fumigatus
Azole resistance
Fungal genome
Oxford nanopore sequencing
de novo genome assembly
Journal
Mycopathologia
ISSN: 1573-0832
Titre abrégé: Mycopathologia
Pays: Netherlands
ID NLM: 7505689
Informations de publication
Date de publication:
Aug 2023
Aug 2023
Historique:
received:
24
03
2023
accepted:
21
04
2023
medline:
31
7
2023
pubmed:
25
5
2023
entrez:
25
5
2023
Statut:
ppublish
Résumé
Aspergillus fumigatus is a genetically diverse fungal species, which is near ubiquitous in its global distribution and is the major cause of the life-threatening disease invasive aspergillosis. We present 3 de novo genome assemblies that were selected to be representative of the genetic diversity of clinical and environmental A. fumigatus. Sequencing using long-read Oxford Nanopore and subsequent assembly of the genomes yielded 10-23 contigs with an N50 of 4.05 Mbp to 4.93 Mbp.
Identifiants
pubmed: 37227556
doi: 10.1007/s11046-023-00740-2
pii: 10.1007/s11046-023-00740-2
pmc: PMC10386934
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
409-412Subventions
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : Wellcome Trust
ID : WPIA_P82512
Pays : United Kingdom
Informations de copyright
© 2023. The Author(s).
Références
WHO fungal priority pathogens list to guide research, Development and Public Health Action (2022) World Health Organization. World Health Organization. 2022. https://www.who.int/publications/i/item/9789240060241 Accessed 17 Jan 2023.
Bongomin F, Gago S, Oladele RO, Denning DW. Global and multi-national prevalence of fungal diseases—estimate precision. J Fungi. 2017;3(4):57.
doi: 10.3390/jof3040057
Fisher MC, Hawkins NJ, Sanglard D, Gurr SJ. Worldwide emergence of resistance to antifungal drugs challenges human health and food security. Science. 2018;360(6390):739–42.
doi: 10.1126/science.aap7999
pubmed: 29773744
Rhodes J, Abdolrasouli A, Dunne K, Sewell TR, Zhang Y, Ballard E, Brackin AP, van Rhijn N, Chown H, Tsitsopoulou A, Posso RB. Population genomics confirms acquisition of drug-resistant Aspergillus fumigatus infection by humans from the environment. Nat Microbiol. 2022;7(5):663–74.
doi: 10.1038/s41564-022-01091-2
pubmed: 35469019
pmcid: 9064804
Sewell TR, Zhu J, Rhodes J, Hagen F, Meis JF, Fisher MC, Jombart T. Nonrandom distribution of azole resistance across the global population of Aspergillus fumigatus. MBio. 2019;10(3):e00392-e419.
doi: 10.1128/mBio.00392-19
pubmed: 31113894
pmcid: 6529631
Nierman WC, Pain A, Anderson MJ, Wortman JR, Kim HS, Arroyo J, Berriman M, Abe K, Archer DB, Bermejo C, Bennett J. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature. 2005;438(7071):1151–6.
doi: 10.1038/nature04332
pubmed: 16372009
Fedorova ND, Khaldi N, Joardar VS, Maiti R, Amedeo P, Anderson MJ, Crabtree J, Silva JC, Badger JH, Albarraq A, Angiuoli S. Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genet. 2008;4(4):e1000046.
doi: 10.1371/journal.pgen.1000046
pubmed: 18404212
pmcid: 2289846
Aspergillus fumigatus genome list - genome - NCBI. National Center for Biotechnology Information https://www.ncbi.nlm.nih.gov/genome/browse/#!/eukaryotes/18/ . Acessed 2 Feb 2023.
Wick RR, Judd LM, Gorrie CL, Holt KE. Completing bacterial genome assemblies with multiplex MinION sequencing. Microb Genomics. 2017;3(10):e000132.
doi: 10.1099/mgen.0.000132
De Coster W, D’hert S, Schultz DT, Cruts M, Van Broeckhoven C. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics. 2018;34(15):2666–9.
doi: 10.1093/bioinformatics/bty149
pubmed: 29547981
pmcid: 6061794
Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 2017;27(5):722–36.
doi: 10.1101/gr.215087.116
pubmed: 28298431
pmcid: 5411767
Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE. 2014;9(11):e112963.
doi: 10.1371/journal.pone.0112963
pubmed: 25409509
pmcid: 4237348
Chan PP, Lin BY, Mak AJ, Lowe TM. tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic Acids Res. 2021;49(16):9077–96.
doi: 10.1093/nar/gkab688
pubmed: 34417604
pmcid: 8450103
Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008;24(5):637–44.
doi: 10.1093/bioinformatics/btn013
pubmed: 18218656
Seppey M, Manni M, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness. Methods Mol Biol. 2019;1962:227–45. https://doi.org/10.1007/978-1-4939-9173-0_14 .
doi: 10.1007/978-1-4939-9173-0_14
pubmed: 31020564
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinform. 2009;10:1–9.
doi: 10.1186/1471-2105-10-421