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Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus.

Fedorova ND, Khaldi N, Joardar VS, Maiti R, Amedeo P, Anderson MJ, Crabtree J, Silva JC, Badger JH, Albarraq A, Angiuoli S, Bussey H, Bowyer P, Cotty PJ, Dyer PS, Egan A, Galens K, Fraser-Liggett CM, Haas BJ, Inman JM, Kent R, Lemieux S, Malavazi I, Orvis J, Roemer T, Ronning CM, Sundaram JP, Sutton G, Turner G, Venter JC, White OR, Whitty BR, Youngman P, Wolfe KH, Goldman GH, Wortman JR, Jiang B, Denning DW, Nierman WC - PLoS Genet. (2008)

Bottom Line: The most divergent loci appear to contain heterokaryon incompatibility (het) genes associated with fungal programmed cell death such as developmental regulator rosA.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".

View Article: PubMed Central - PubMed

Affiliation: The J. Craig Venter Institute, Rockville, Maryland, United States of America.

ABSTRACT
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".

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Alignment of the A1163, N. fischeri, and A. clavatus Assemblies against the Eight Af293 Chromosomes.The first three tracks from the top for each reference chromosome show syntenic blocks (horizontal bars) identified in the target genomes, A. fumigatus A1163, N. fischeri, and A. clavatus. Each assembly from the target genomes is represented by a single color. Syntenic blocks are numbered based on the target genome assembly ID and the position of the block in the target genome assembly. Tracks 4 and 5 show Asp-core gene density and blocks (horizontal bars), respectively, in the Af293 genome. Tracks 6 and 7 show Afum-specific gene density and blocks (horizontal bars), respectively. Tracks 8 and 9 show the density of clustered secondary metabolite biosynthesis genes and transposable elements, respectively, found in Af293. Pink vertical bars represent putative centromeres, the purple vertical bar in chromosome 4 represents a region of ribosomal DNA, and horizontal black bars beneath each chromosome designate sequencing gaps.
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pgen-1000046-g003: Alignment of the A1163, N. fischeri, and A. clavatus Assemblies against the Eight Af293 Chromosomes.The first three tracks from the top for each reference chromosome show syntenic blocks (horizontal bars) identified in the target genomes, A. fumigatus A1163, N. fischeri, and A. clavatus. Each assembly from the target genomes is represented by a single color. Syntenic blocks are numbered based on the target genome assembly ID and the position of the block in the target genome assembly. Tracks 4 and 5 show Asp-core gene density and blocks (horizontal bars), respectively, in the Af293 genome. Tracks 6 and 7 show Afum-specific gene density and blocks (horizontal bars), respectively. Tracks 8 and 9 show the density of clustered secondary metabolite biosynthesis genes and transposable elements, respectively, found in Af293. Pink vertical bars represent putative centromeres, the purple vertical bar in chromosome 4 represents a region of ribosomal DNA, and horizontal black bars beneath each chromosome designate sequencing gaps.

Mentions: The genome of A. fumigatus strain A1163 was sequenced by the whole genome random sequencing method [22]. Its genome (29.2 Mb) is 1.4% larger than the genome of the first sequenced strain Af293 (28.8 Mb) (Table 1). About 98% of each genome can be aligned with high confidence. Alignment of the A1163 genome against the eight Af293 chromosomes has revealed 17 large syntenic blocks, which correspond roughly to the 16 Af293 chromosomal arms (Figure 3). The syntenic blocks were defined as regions containing at least five syntenic orthologs separated by no more than 20 genes without orthologs.


Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus.

Fedorova ND, Khaldi N, Joardar VS, Maiti R, Amedeo P, Anderson MJ, Crabtree J, Silva JC, Badger JH, Albarraq A, Angiuoli S, Bussey H, Bowyer P, Cotty PJ, Dyer PS, Egan A, Galens K, Fraser-Liggett CM, Haas BJ, Inman JM, Kent R, Lemieux S, Malavazi I, Orvis J, Roemer T, Ronning CM, Sundaram JP, Sutton G, Turner G, Venter JC, White OR, Whitty BR, Youngman P, Wolfe KH, Goldman GH, Wortman JR, Jiang B, Denning DW, Nierman WC - PLoS Genet. (2008)

Alignment of the A1163, N. fischeri, and A. clavatus Assemblies against the Eight Af293 Chromosomes.The first three tracks from the top for each reference chromosome show syntenic blocks (horizontal bars) identified in the target genomes, A. fumigatus A1163, N. fischeri, and A. clavatus. Each assembly from the target genomes is represented by a single color. Syntenic blocks are numbered based on the target genome assembly ID and the position of the block in the target genome assembly. Tracks 4 and 5 show Asp-core gene density and blocks (horizontal bars), respectively, in the Af293 genome. Tracks 6 and 7 show Afum-specific gene density and blocks (horizontal bars), respectively. Tracks 8 and 9 show the density of clustered secondary metabolite biosynthesis genes and transposable elements, respectively, found in Af293. Pink vertical bars represent putative centromeres, the purple vertical bar in chromosome 4 represents a region of ribosomal DNA, and horizontal black bars beneath each chromosome designate sequencing gaps.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2289846&req=5

pgen-1000046-g003: Alignment of the A1163, N. fischeri, and A. clavatus Assemblies against the Eight Af293 Chromosomes.The first three tracks from the top for each reference chromosome show syntenic blocks (horizontal bars) identified in the target genomes, A. fumigatus A1163, N. fischeri, and A. clavatus. Each assembly from the target genomes is represented by a single color. Syntenic blocks are numbered based on the target genome assembly ID and the position of the block in the target genome assembly. Tracks 4 and 5 show Asp-core gene density and blocks (horizontal bars), respectively, in the Af293 genome. Tracks 6 and 7 show Afum-specific gene density and blocks (horizontal bars), respectively. Tracks 8 and 9 show the density of clustered secondary metabolite biosynthesis genes and transposable elements, respectively, found in Af293. Pink vertical bars represent putative centromeres, the purple vertical bar in chromosome 4 represents a region of ribosomal DNA, and horizontal black bars beneath each chromosome designate sequencing gaps.
Mentions: The genome of A. fumigatus strain A1163 was sequenced by the whole genome random sequencing method [22]. Its genome (29.2 Mb) is 1.4% larger than the genome of the first sequenced strain Af293 (28.8 Mb) (Table 1). About 98% of each genome can be aligned with high confidence. Alignment of the A1163 genome against the eight Af293 chromosomes has revealed 17 large syntenic blocks, which correspond roughly to the 16 Af293 chromosomal arms (Figure 3). The syntenic blocks were defined as regions containing at least five syntenic orthologs separated by no more than 20 genes without orthologs.

Bottom Line: The most divergent loci appear to contain heterokaryon incompatibility (het) genes associated with fungal programmed cell death such as developmental regulator rosA.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".

View Article: PubMed Central - PubMed

Affiliation: The J. Craig Venter Institute, Rockville, Maryland, United States of America.

ABSTRACT
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".

Show MeSH