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Title: What can comparative genomics tell us about species concepts in the genus Aspergillus?

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 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,more » and finally as a knowledge database about the biological differences between strains and species.« less

Authors:
; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
985066
Report Number(s):
PNNL-SA-58814
Journal ID: ISSN 0166-0616; ISSN 1872-9797; BM0102070; TRN: US201016%%1752
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Studies in Mycology, 59:11-17; Journal Volume: 59; Journal Issue: 1
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; ASPERGILLUS; AVAILABILITY; BIOLOGY; GENES; STRAINS; TAXONOMY; fungi; genomics; Aspergillus

Citation Formats

Rokas, Antonis, payne, gary, Federova, Natalie D., Baker, Scott E., Machida, Masa, yu, Jiujiang, georgianna, D. R., Dean, Ralph A., Bhatnagar, Deepak, Cleveland, T. E., Wortman, Jennifer R., Maiti, R., Joardar, V., Amedeo, Paolo, Denning, David W., and Nierman, William C. What can comparative genomics tell us about species concepts in the genus Aspergillus?. United States: N. p., 2007. Web. doi:10.3114/sim.2007.59.02.
Rokas, Antonis, payne, gary, Federova, Natalie D., Baker, Scott E., Machida, Masa, yu, Jiujiang, georgianna, D. R., Dean, Ralph A., Bhatnagar, Deepak, Cleveland, T. E., Wortman, Jennifer R., Maiti, R., Joardar, V., Amedeo, Paolo, Denning, David W., & Nierman, William C. What can comparative genomics tell us about species concepts in the genus Aspergillus?. United States. doi:10.3114/sim.2007.59.02.
Rokas, Antonis, payne, gary, Federova, Natalie D., Baker, Scott E., Machida, Masa, yu, Jiujiang, georgianna, D. R., Dean, Ralph A., Bhatnagar, Deepak, Cleveland, T. E., Wortman, Jennifer R., Maiti, R., Joardar, V., Amedeo, Paolo, Denning, David W., and Nierman, William C. Sat . "What can comparative genomics tell us about species concepts in the genus Aspergillus?". United States. doi:10.3114/sim.2007.59.02.
@article{osti_985066,
title = {What can comparative genomics tell us about species concepts in the genus Aspergillus?},
author = {Rokas, Antonis and payne, gary and Federova, Natalie D. and Baker, Scott E. and Machida, Masa and yu, Jiujiang and georgianna, D. R. and Dean, Ralph A. and Bhatnagar, Deepak and Cleveland, T. E. and Wortman, Jennifer R. and Maiti, R. and Joardar, V. and Amedeo, Paolo and Denning, David W. and Nierman, William C.},
abstractNote = {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.},
doi = {10.3114/sim.2007.59.02},
journal = {Studies in Mycology, 59:11-17},
number = 1,
volume = 59,
place = {United States},
year = {Sat Dec 15 00:00:00 EST 2007},
month = {Sat Dec 15 00:00:00 EST 2007}
}