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Stud Mycol 59(1): 11-17 2007
DOI: 10.3114/sim.2007.59.02
Copyright © 2007 CBS Fungal Biodiversity Centre
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What can comparative genomics tell us about species concepts in the genus Aspergillus?

A. Rokas1,*, G. Payne2, N.D. Fedorova3, S.E. Baker4, M. Machida5, J. Yu6, D. Ryan Georgianna2, Ralph A. Dean2, Deepak Bhatnagar6, T.E. Cleveland6, J.R. Wortman3, R. Maiti3, V. Joardar3, P. Amedeo3, D.W. Denning7 and W.C. Nierman3

1 Vanderbilt University, Department of Biological Sciences, Nashville, TN 37235, U.S.A.
2 North Carolina State University, Department of Plant Pathology, Raleigh, NC 27695, U.S.A.
3 The J. Craig Venter Institute, Rockville, MD 20850, U.S.A.
4 Pacific Northwest National Laboratory, Fungal Biotechnology Team, Richland, WA 99352, U.S.A.
5 National Institute of Advanced Industrial Science and Technologies, Research Institute of Cell Engineering, Tsukuba, Ibaraki 305-8566, Japan
6 USDA/ARS/SRRC, New Orleans, LA 70124, U.S.A.
7 University of Manchester, School of Medicine, Manchester, M13 9PL, U.K.

* Correspondence: Antonis Rokas, antonis.rokas{at}vanderbilt.edu

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 intraspecific comparisons, whereas the other two deal with interspecific 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.

Keywords comparative genomics / genetic diversity / genome sequences / identifcation of species boundaries




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 Mol Biol EvolHome page
J. G. Gibbons and A. Rokas
Comparative and Functional Characterization of Intragenic Tandem Repeats in 10 Aspergillus Genomes
Mol. Biol. Evol., March 1, 2009; 26(3): 591 - 602.
[Abstract] [Full Text] [PDF]


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