|Venter, J. Craig|
Submitted to: PLoS Genetics
Publication Type: Review Article
Publication Acceptance Date: 3/4/2008
Publication Date: 4/11/2008
Citation: Fedorova, N.D., Khaldi, N., Joardar, V., Maiti, R., Amedeo, P., Anderson, M.J., Crabtree, J., Silva, J.C., Badger, J., Albarraq, A., Angiuoli, S., Bussey, H., Bowyer, P., Cotty, P.J., Dyer, P.S., Egan, A., Galens, K., Fraser-Liggett, C.M., Haas, B.J., Inman, J.M., Kent, R., Lemieux, S., Malavazi, I., Orvis, J., Roemer, T., Ronning, C.M., Sundaram, J.P., Sutton, G., Turner, G., Venter, J.C., White, O.R., Whitty, B.R., Youngman, P., Wolfe, K.H., Goldman, G.H., Wortman, J.R., Jiang, B., Denning, D.W., Nierman, W.C. 2008. Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus. PLoS Genetics. 4(4):e1000046:1-13 Interpretive Summary:
Technical Abstract: We present the genome sequences of a new clinical isolate, CEA10, of an important human pathogen, Aspergillus fumigatus, and two closely related, but rarely pathogenic species, Neosartorya fischeri NRRL181 and Aspergillus clavatus NRRL1. Comparative genomic analysis of CEA10 with the recently sequenced A. fumigatus isolate Af293 has identified core, variable and unique regions in each genome. While the core regions are 99.8% identical at the nucleotide level, identity over some variable regions can be as low 40%. Further comparison has revealed that A. fumigatus contains isolate- and species-specific genes, which comprise ~2% and 9% of the genome, respectively. These lineage-specific genes differ in variability, dispensability and size from the core genes and encode accessory functions. Subsequent phylogenetic analysis demonstrated that these genes emergence though duplication, accelerated diversification and/or gene loss (DDL). Most lineage-specific genes cluster in large chromosomal islands, which display a strong subtelomeric bias, have low gene density, and harbour a disproportionate number of pseudogenes, transposons and other repetitive elements. These regions may function as designated “gene dumps” and, simultaneously, as “gene factories”. Although A. fumigatus was chosen as the primary focus of this study, similar chromosomal structures were observed in the genomes of N. fischeri and A. clavatus, suggesting that all three species are poised for the rapid adaptation to heterogeneous environments such as soil, compost piles or a mammalian host.