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A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi

James K Hane12, Thierry Rouxel3, Barbara J Howlett4, Gert HJ Kema5, Stephen B Goodwin6 and Richard P Oliver7*

Author Affiliations

1 CSIRO Plant Industry, Centre for Environment and Life Sciences, Private Bag 5, Perth, 6193, Australia

2 Faculty of Health Sciences, Murdoch University, Perth, 6150, Australia

3 INRA-Bioger, Avenue Lucien Brétignières, BP 01, Thiverval-Grignon, 78850, France

4 School of Botany, The University of Melbourne, Melbourne, 3010, Australia

5 Wageningen UR, Plant Research International, Department of Biointeractions and Plant Health, PO Box 69, Wageningen, 6700 AB, The Netherlands

6 USDA-ARS, Crop Production and Pest Control Research Unit, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054, USA

7 Australian Centre for Necrotrophic Fungal Pathogens, Curtin University, Perth, 6845, Australia

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Genome Biology 2011, 12:R45  doi:10.1186/gb-2011-12-5-r45

Published: 24 May 2011

Additional files

Additional file 1:

Supplementary Figure S1. The origins of the different types of syntenic relationships. Immediately after a speciation event, equivalent chromosomes in two daughter species retain the gene content, order and orientation of the parent species. (a) Diagrammatic representation of a chromosome with sequential elements A to Z. (b) A dot plot comparing the chromosomes in (a), with letters substituted for dots. The unbroken series of letters on the diagonal indicates macrosynteny. (c, d) Loss of sequences from each chromosome (c) will degrade the diagonal co-linearity when visualized as a dot plot (d).

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Additional file 2:

Supplementary Figure S2. (a, b) Correspondence between promer-derived dot plots (a) and blastp-derived protein comparisons of annotated genes (b) between Phaeosphaeria nodorum and Leptosphaeria maculans. Sequence pairs ('boxes') in (a) containing non-random distributions of 'dots' correspond to those in (b), indicating that the back-translated genome matches in (a) correspond to regions of conserved gene content.

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Additional file 3:

Supplementary File 1. Predictions of synteny between all species involved in this study in an Excel file.

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This file can be viewed with: Microsoft Excel Viewer

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Additional file 4:

Supplementary Figure S3. Presence of both macrosyntenic and mesosyntenic conservation patterns between the genomes of Fusarium oxysporum and Nectria haematococca. Core chromosomes (indicated by black bars along the axes) are macrosyntenic between the two species. Dispensable chromosomes (red bars along the axes) are either non-syntenic (N. haematococca chromosomes 15 to 17) or mesosyntenic (N. haematococca chromosomes 7 and 11 to 14, F. oxysporum chromosome 14). The majority of chromosomes 3 and 6 of F. oxysporum had no similarity to the chromosomes of N. haematococca except for regions near their telomeres.

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Open Data

Additional file 5:

Supplementary Figure S4. Degradation of whole-genome synteny in the classes Saccharomycetes and Schizosaccharomyces. Whole-genome dot plots have been limited to scaffolds or chromosomes greater than 500 kb. Species of the Saccharomyces and Schizosaccharomyces do not exhibit whole-genome conservation with each other. Certain species within each class exhibit macrosynteny whereas others exhibit no synteny.

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Additional file 6:

Supplementary Figure S5. Degradation of whole-genome synteny between a member of the class Agaricales and related orders. Whole-genome dot plots have been limited to scaffolds or chromosomes greater than 500 kb. Species in the Agaricales exhibited macrosynteny with each other. However, the Agaricales exhibited no synteny with the closest related classes represented in this study, the Exobasidiomycetes and Pucciniomycetes.

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Additional file 7:

Supplementary Figure S6. Evidence of degraded mesosynteny between the genomes of two homothallic Sordariomycete species, Fusarium graminearum (order Hypocreales) and Chaetomium globosum (order Sordariales). These two species are estimated to have diverged approximately 225 Mya. Sequence matches (dots) are arranged in blocked clusters typical of mesosynteny. Chromosomes and scaffolds do not share a one-to-one relationship, with multiple mesosyntenic clusters appearing in the same row or column.

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Open Data