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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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Proteins with Orthologs in the Three Most Closely Related Aspergilli (A. fumigatus, N. fischeri and A. clavatus).These proteins constitute the Affc-core group, and proteins with no orthologs in N. fischeri and A. clavatus constitute the A. fumigatus-specific group (Afum). The proteins in the Affc-core can be further divided into two groups, Aspergillus-core (Asp-core), which has orthologs in all of the other aspergilli, and the Affc-specific group, which is comprised of the rest of the Affc-core.
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pgen-1000046-g005: Proteins with Orthologs in the Three Most Closely Related Aspergilli (A. fumigatus, N. fischeri and A. clavatus).These proteins constitute the Affc-core group, and proteins with no orthologs in N. fischeri and A. clavatus constitute the A. fumigatus-specific group (Afum). The proteins in the Affc-core can be further divided into two groups, Aspergillus-core (Asp-core), which has orthologs in all of the other aspergilli, and the Affc-specific group, which is comprised of the rest of the Affc-core.

Mentions: Comparative genomic analysis has showed that the three Aspergillus genomes contain a large number of species-specific genes, which is consistent with previous comparative studies [7]. We have identified 7514 orthologous core and 818, 1402 and 1151 species-specific genes in the Af293, N. fischeri and A. clavatus genomes, respectively (Figure 5). Numbers of core- and species-specific genes, however, depend on selection of genomes from which they were derived. Thus, adding new genomes to this comparison resulted in fewer core and specific genes as shown for Af293 in Table S6. The availability of additional sequenced Aspergillus genomes allowed us to explore these patterns in a more systematic manner by comparing A. fumigatus Af293 genes with different lineage specificity (i.e. number of orthologs in other species).


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)

Proteins with Orthologs in the Three Most Closely Related Aspergilli (A. fumigatus, N. fischeri and A. clavatus).These proteins constitute the Affc-core group, and proteins with no orthologs in N. fischeri and A. clavatus constitute the A. fumigatus-specific group (Afum). The proteins in the Affc-core can be further divided into two groups, Aspergillus-core (Asp-core), which has orthologs in all of the other aspergilli, and the Affc-specific group, which is comprised of the rest of the Affc-core.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1000046-g005: Proteins with Orthologs in the Three Most Closely Related Aspergilli (A. fumigatus, N. fischeri and A. clavatus).These proteins constitute the Affc-core group, and proteins with no orthologs in N. fischeri and A. clavatus constitute the A. fumigatus-specific group (Afum). The proteins in the Affc-core can be further divided into two groups, Aspergillus-core (Asp-core), which has orthologs in all of the other aspergilli, and the Affc-specific group, which is comprised of the rest of the Affc-core.
Mentions: Comparative genomic analysis has showed that the three Aspergillus genomes contain a large number of species-specific genes, which is consistent with previous comparative studies [7]. We have identified 7514 orthologous core and 818, 1402 and 1151 species-specific genes in the Af293, N. fischeri and A. clavatus genomes, respectively (Figure 5). Numbers of core- and species-specific genes, however, depend on selection of genomes from which they were derived. Thus, adding new genomes to this comparison resulted in fewer core and specific genes as shown for Af293 in Table S6. The availability of additional sequenced Aspergillus genomes allowed us to explore these patterns in a more systematic manner by comparing A. fumigatus Af293 genes with different lineage specificity (i.e. number of orthologs in other species).

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