Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus.
We present the genome sequences of a new clinical isolate of the important human pathogen, Aspergillus fumigatus, A1163, and two closely related but rarely pathogenic species, Neosartorya fischeri NRRL181 and Aspergillus clavatus NRRL1. Comparative genomic analysis of A1163 with the recently sequenc...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2008-04-01
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| Series: | PLoS Genetics |
| Online Access: | http://europepmc.org/articles/PMC2289846?pdf=render |
| _version_ | 1819055563187683328 |
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| author | Natalie D Fedorova Nora Khaldi Vinita S Joardar Rama Maiti Paolo Amedeo Michael J Anderson Jonathan Crabtree Joana C Silva Jonathan H Badger Ahmed Albarraq Sam Angiuoli Howard Bussey Paul Bowyer Peter J Cotty Paul S Dyer Amy Egan Kevin Galens Claire M Fraser-Liggett Brian J Haas Jason M Inman Richard Kent Sebastien Lemieux Iran Malavazi Joshua Orvis Terry Roemer Catherine M Ronning Jaideep P Sundaram Granger Sutton Geoff Turner J Craig Venter Owen R White Brett R Whitty Phil Youngman Kenneth H Wolfe Gustavo H Goldman Jennifer R Wortman Bo Jiang David W Denning William C Nierman |
| author_facet | Natalie D Fedorova Nora Khaldi Vinita S Joardar Rama Maiti Paolo Amedeo Michael J Anderson Jonathan Crabtree Joana C Silva Jonathan H Badger Ahmed Albarraq Sam Angiuoli Howard Bussey Paul Bowyer Peter J Cotty Paul S Dyer Amy Egan Kevin Galens Claire M Fraser-Liggett Brian J Haas Jason M Inman Richard Kent Sebastien Lemieux Iran Malavazi Joshua Orvis Terry Roemer Catherine M Ronning Jaideep P Sundaram Granger Sutton Geoff Turner J Craig Venter Owen R White Brett R Whitty Phil Youngman Kenneth H Wolfe Gustavo H Goldman Jennifer R Wortman Bo Jiang David W Denning William C Nierman |
| author_sort | Natalie D Fedorova |
| collection | DOAJ |
| description | We present the genome sequences of a new clinical isolate of the important human pathogen, Aspergillus fumigatus, A1163, and two closely related but rarely pathogenic species, Neosartorya fischeri NRRL181 and Aspergillus clavatus NRRL1. Comparative genomic analysis of A1163 with the recently sequenced A. fumigatus isolate Af293 has identified core, variable and up to 2% unique genes in each genome. While the core genes are 99.8% identical at the nucleotide level, identity for variable genes can be as low 40%. The most divergent loci appear to contain heterokaryon incompatibility (het) genes associated with fungal programmed cell death such as developmental regulator rosA. Cross-species comparison has revealed that 8.5%, 13.5% and 12.6%, respectively, of A. fumigatus, N. fischeri and A. clavatus genes are species-specific. These genes are significantly smaller in size than core genes, contain fewer exons and exhibit a subtelomeric bias. Most of them cluster together in 13 chromosomal islands, which are enriched for pseudogenes, transposons and other repetitive elements. At least 20% of A. fumigatus-specific genes appear to be functional and involved in carbohydrate and chitin catabolism, transport, detoxification, secondary metabolism and other functions that may facilitate the adaptation to heterogeneous environments such as soil or a mammalian host. Contrary to what was suggested previously, their origin cannot be attributed to horizontal gene transfer (HGT), but instead is likely to involve duplication, diversification and differential gene loss (DDL). The role of duplication in the origin of lineage-specific genes is further underlined by the discovery of genomic islands that seem to function as designated "gene dumps" and, perhaps, simultaneously, as "gene factories". |
| first_indexed | 2024-12-21T13:09:30Z |
| format | Article |
| id | doaj.art-faa9cdea440a44ac8cfb2dcbcab87503 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-12-21T13:09:30Z |
| publishDate | 2008-04-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-faa9cdea440a44ac8cfb2dcbcab875032022-12-21T19:02:56ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042008-04-0144e100004610.1371/journal.pgen.1000046Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus.Natalie D FedorovaNora KhaldiVinita S JoardarRama MaitiPaolo AmedeoMichael J AndersonJonathan CrabtreeJoana C SilvaJonathan H BadgerAhmed AlbarraqSam AngiuoliHoward BusseyPaul BowyerPeter J CottyPaul S DyerAmy EganKevin GalensClaire M Fraser-LiggettBrian J HaasJason M InmanRichard KentSebastien LemieuxIran MalavaziJoshua OrvisTerry RoemerCatherine M RonningJaideep P SundaramGranger SuttonGeoff TurnerJ Craig VenterOwen R WhiteBrett R WhittyPhil YoungmanKenneth H WolfeGustavo H GoldmanJennifer R WortmanBo JiangDavid W DenningWilliam C NiermanWe present the genome sequences of a new clinical isolate of the important human pathogen, Aspergillus fumigatus, A1163, and two closely related but rarely pathogenic species, Neosartorya fischeri NRRL181 and Aspergillus clavatus NRRL1. Comparative genomic analysis of A1163 with the recently sequenced A. fumigatus isolate Af293 has identified core, variable and up to 2% unique genes in each genome. While the core genes are 99.8% identical at the nucleotide level, identity for variable genes can be as low 40%. The most divergent loci appear to contain heterokaryon incompatibility (het) genes associated with fungal programmed cell death such as developmental regulator rosA. Cross-species comparison has revealed that 8.5%, 13.5% and 12.6%, respectively, of A. fumigatus, N. fischeri and A. clavatus genes are species-specific. These genes are significantly smaller in size than core genes, contain fewer exons and exhibit a subtelomeric bias. Most of them cluster together in 13 chromosomal islands, which are enriched for pseudogenes, transposons and other repetitive elements. At least 20% of A. fumigatus-specific genes appear to be functional and involved in carbohydrate and chitin catabolism, transport, detoxification, secondary metabolism and other functions that may facilitate the adaptation to heterogeneous environments such as soil or a mammalian host. Contrary to what was suggested previously, their origin cannot be attributed to horizontal gene transfer (HGT), but instead is likely to involve duplication, diversification and differential gene loss (DDL). The role of duplication in the origin of lineage-specific genes is further underlined by the discovery of genomic islands that seem to function as designated "gene dumps" and, perhaps, simultaneously, as "gene factories".http://europepmc.org/articles/PMC2289846?pdf=render |
| spellingShingle | Natalie D Fedorova Nora Khaldi Vinita S Joardar Rama Maiti Paolo Amedeo Michael J Anderson Jonathan Crabtree Joana C Silva Jonathan H Badger Ahmed Albarraq Sam Angiuoli Howard Bussey Paul Bowyer Peter J Cotty Paul S Dyer Amy Egan Kevin Galens Claire M Fraser-Liggett Brian J Haas Jason M Inman Richard Kent Sebastien Lemieux Iran Malavazi Joshua Orvis Terry Roemer Catherine M Ronning Jaideep P Sundaram Granger Sutton Geoff Turner J Craig Venter Owen R White Brett R Whitty Phil Youngman Kenneth H Wolfe Gustavo H Goldman Jennifer R Wortman Bo Jiang David W Denning William C Nierman Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. PLoS Genetics |
| title | Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. |
| title_full | Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. |
| title_fullStr | Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. |
| title_full_unstemmed | Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. |
| title_short | Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. |
| title_sort | genomic islands in the pathogenic filamentous fungus aspergillus fumigatus |
| url | http://europepmc.org/articles/PMC2289846?pdf=render |
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