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Title: What Can Comparative Genomics Tell Us About Species Concepts in the Genus Aspergillus?

Author
item ROKAS, A - VANDERBILT UNIV NASHVILLE
item PAYNE, G - NCSU RALEIGH
item FEDOROVA, N - JCVI ROCKVILLE MD
item BAKER, S - PAC NW NATL LAB
item MACHIDA, M - NIAIST JAPAN
item Yu, Jiujiang
item GEORGIANNA, D - NCSU RALEIGH
item DEAN, RALPH - NCSU RALEIGH
item Bhatnagar, Deepak
item Cleveland, Thomas
item WORTMAN, J - JCVI ROCKVILLE MD
item MAITI, R - JCVI ROCKVILLE MD
item JOARDAR, V - JCVI ROCKVILLE MD
item AMEDEO, P - JCVI ROCKVILLE MD
item DENNING, D - UNIV OF MANCHESTER UK
item NIERMAN, W - JCVI ROCKVILLE MD

Submitted to: Studies in Mycology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/15/2007
Publication Date: 6/1/2007
Citation: Rokas, A., Payne, G., Fedorova, N.D., Baker, S.E., Machida, M., Yu, J., Georgianna, D.R., Dean, R.A., Bhatnagar, D., Cleveland, T.E., Wortman, J.R., Maiti, R., Joardar, V., Amedeo, P., Denning, D.W., Nierman, W.C. 2007. What Can Comparative Genomics Tell Us About Species Concepts in the Genus Aspergillus?. Studies in Mycology. 59:11-17.

Interpretive Summary: Recent research efforts in several labs across the globe have resulted in deciphering the complete genetic make-up of several fungal species in the Aspergillus family. Among these are some that are significant in agriculture producing toxins in crops (Aspergillus flavus), in human health (Aspergillus fumigatus), or in the fermentation industry (Aspergillus oryzae). Comparisons of these sequences of all the DNA in these individual fungi highlight the potential usefulness of genomics for the accurate identification of species boundaries in the genus Aspergillus. Genomics can aid Aspergillus taxonomy (i.e. classification of this group of fungi) by serving as a source of novel and unprecedented amounts of comparative data, as a resource for the development of additional diagnostic tools, and finally as a knowledge database about the biological differences between strains and species. In other words, genomics, as presented in this study, can provide an arsenal of data and molecular tools to aid scientists to define more accurately lines of separation between species in the genus Aspergillus, and to also understand (from gene function studies) why each of the related fungi belonging to the family Aspergillus have different functionalities.

Technical Abstract: Understanding the nature of species’ boundaries is a fundamental question in evolutionary biology. The availability of genomes from several species of the genus Aspergillus allows us for the first time to examine the demarcation of fungal species at the whole-genome level. Here, we examine four case studies, two of which involve intra-specific comparisons, whereas the other two deal with inter-specific genomic comparisons between closely related species. These four comparisons reveal significant variation in the nature of species boundaries across Aspergillus. For example, comparisons between A. fumigatus and Neosartorya fischeri (the teleomorph of A. fischerianus) and between A. oryzae and A. flavus suggest that measures of sequence similarity and species-specific genes are significantly higher for the A. fumigatus– N. fischeri pair. Importantly, the values obtained from the comparison between A. oryzae and A. flavus are remarkably similar to those obtained from an intra-specific comparison of A. fumigatus strains, giving support to the proposal that A. oryzae represents a distinct ecotype of A. flavus and not a distinct species. We argue that genomic data can aid Aspergillus taxonomy by serving as a source of novel and unprecedented amounts of comparative data, as a resource for the development of additional diagnostic tools, and finally, as a knowledge database about the biological differences between strains and species.