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Genome-Wide Analysis in Three Fusarium Pathogens Identifies Rapidly Evolving Chromosomes and Genes Associated with Pathogenicity.

Sperschneider J, Gardiner DM, Thatcher LF, Lyons R, Singh KB, Manners JM, Taylor JM - Genome Biol Evol (2015)

Bottom Line: We found a two-speed genome structure both on the chromosome and gene group level.Members of two gene groups evolve rapidly, namely those that encode proteins with an N-terminal [SG]-P-C-[KR]-P sequence motif and proteins that are conserved predominantly in pathogens.Specifically, 29 F. graminearum genes are rapidly evolving, in planta induced and encode secreted proteins, strongly pointing toward effector function.

View Article: PubMed Central - PubMed

Affiliation: CSIRO Agriculture Flagship, Centre for Environment and Life Sciences, Perth, Western Australia, Australia jana.sperschneider@csiro.au.

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Distribution of genes under diversifying selection across the F. graminearum and F. oxysporum f. sp. lycopersici genomes and regions of macrosynteny based on predicted orthologies. A Circos plot is shown which visualizes the four F. graminearum chromosomes followed by the 15 chromosomes of F. oxysporum f. sp. lycopersici displayed as merged supercontigs with ticks in kilobase (kb) units. The following bands are visualized: (I) Recombination frequency (blue bars) and SNP density (line) for F. graminearum (Cuomo et al. 2007), (II) line plot of  ratios in 50 kb bins, (III) scatter plot and heat map of genes with more than two orthologs that are predicted to undergo site specific diversifying selection using CODEML, and (IV) heat map that visualizes regions for which no ortholog information is available in dark blue. Bundled links for all orthologs between F. graminearum and F. oxysporum f. sp. lycopersici are shown as ribbons, colored according to their chromosomal origin in F. graminearum. Note that  ratios for F. graminearum and F. oxysporum f. sp. lycopersici are not shown on the same scale for clarity.
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evv092-F2: Distribution of genes under diversifying selection across the F. graminearum and F. oxysporum f. sp. lycopersici genomes and regions of macrosynteny based on predicted orthologies. A Circos plot is shown which visualizes the four F. graminearum chromosomes followed by the 15 chromosomes of F. oxysporum f. sp. lycopersici displayed as merged supercontigs with ticks in kilobase (kb) units. The following bands are visualized: (I) Recombination frequency (blue bars) and SNP density (line) for F. graminearum (Cuomo et al. 2007), (II) line plot of ratios in 50 kb bins, (III) scatter plot and heat map of genes with more than two orthologs that are predicted to undergo site specific diversifying selection using CODEML, and (IV) heat map that visualizes regions for which no ortholog information is available in dark blue. Bundled links for all orthologs between F. graminearum and F. oxysporum f. sp. lycopersici are shown as ribbons, colored according to their chromosomal origin in F. graminearum. Note that ratios for F. graminearum and F. oxysporum f. sp. lycopersici are not shown on the same scale for clarity.

Mentions: One of our aims was to identify chromosomal regions in F. graminearum, F. oxysporum f. sp. lycopersici, and F. verticillioides that are under diversifying selection in the genus and might point to regions involved in host–pathogen coevolution. We first plotted ratios as well as links between orthologs for F. graminearum and F. oxysporum f. sp. lycopersici (fig. 2, track II). This revealed known regions of macrosynteny, which have been attributed to ancient chromosome fusion events (Cuomo et al. 2007; Ma et al. 2010). As expected, regions without predicted orthologies in F. oxysporum f. sp. lycopersici are found most strikingly on the dispensable chromosomes 3, 6, 14, and 15 as well as at the lineage-specific ends of chromosomes 1 and 2 (fig. 2, track IV). In F. graminearum, regions without predicted orthologies occur predominantly in the subtelomeric regions of the chromosomes as well as in the center of chromosome 4. In F. verticillioides, regions without predicted orthologies are found in the subtelomeric regions particularly of chromosome 1, 4, 6, and 10 as well as in a small region of around 100 kb in the center of chromosome 7 (supplementary fig. S1, Supplementary Material online, track III).Fig. 2.—


Genome-Wide Analysis in Three Fusarium Pathogens Identifies Rapidly Evolving Chromosomes and Genes Associated with Pathogenicity.

Sperschneider J, Gardiner DM, Thatcher LF, Lyons R, Singh KB, Manners JM, Taylor JM - Genome Biol Evol (2015)

Distribution of genes under diversifying selection across the F. graminearum and F. oxysporum f. sp. lycopersici genomes and regions of macrosynteny based on predicted orthologies. A Circos plot is shown which visualizes the four F. graminearum chromosomes followed by the 15 chromosomes of F. oxysporum f. sp. lycopersici displayed as merged supercontigs with ticks in kilobase (kb) units. The following bands are visualized: (I) Recombination frequency (blue bars) and SNP density (line) for F. graminearum (Cuomo et al. 2007), (II) line plot of  ratios in 50 kb bins, (III) scatter plot and heat map of genes with more than two orthologs that are predicted to undergo site specific diversifying selection using CODEML, and (IV) heat map that visualizes regions for which no ortholog information is available in dark blue. Bundled links for all orthologs between F. graminearum and F. oxysporum f. sp. lycopersici are shown as ribbons, colored according to their chromosomal origin in F. graminearum. Note that  ratios for F. graminearum and F. oxysporum f. sp. lycopersici are not shown on the same scale for clarity.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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evv092-F2: Distribution of genes under diversifying selection across the F. graminearum and F. oxysporum f. sp. lycopersici genomes and regions of macrosynteny based on predicted orthologies. A Circos plot is shown which visualizes the four F. graminearum chromosomes followed by the 15 chromosomes of F. oxysporum f. sp. lycopersici displayed as merged supercontigs with ticks in kilobase (kb) units. The following bands are visualized: (I) Recombination frequency (blue bars) and SNP density (line) for F. graminearum (Cuomo et al. 2007), (II) line plot of ratios in 50 kb bins, (III) scatter plot and heat map of genes with more than two orthologs that are predicted to undergo site specific diversifying selection using CODEML, and (IV) heat map that visualizes regions for which no ortholog information is available in dark blue. Bundled links for all orthologs between F. graminearum and F. oxysporum f. sp. lycopersici are shown as ribbons, colored according to their chromosomal origin in F. graminearum. Note that ratios for F. graminearum and F. oxysporum f. sp. lycopersici are not shown on the same scale for clarity.
Mentions: One of our aims was to identify chromosomal regions in F. graminearum, F. oxysporum f. sp. lycopersici, and F. verticillioides that are under diversifying selection in the genus and might point to regions involved in host–pathogen coevolution. We first plotted ratios as well as links between orthologs for F. graminearum and F. oxysporum f. sp. lycopersici (fig. 2, track II). This revealed known regions of macrosynteny, which have been attributed to ancient chromosome fusion events (Cuomo et al. 2007; Ma et al. 2010). As expected, regions without predicted orthologies in F. oxysporum f. sp. lycopersici are found most strikingly on the dispensable chromosomes 3, 6, 14, and 15 as well as at the lineage-specific ends of chromosomes 1 and 2 (fig. 2, track IV). In F. graminearum, regions without predicted orthologies occur predominantly in the subtelomeric regions of the chromosomes as well as in the center of chromosome 4. In F. verticillioides, regions without predicted orthologies are found in the subtelomeric regions particularly of chromosome 1, 4, 6, and 10 as well as in a small region of around 100 kb in the center of chromosome 7 (supplementary fig. S1, Supplementary Material online, track III).Fig. 2.—

Bottom Line: We found a two-speed genome structure both on the chromosome and gene group level.Members of two gene groups evolve rapidly, namely those that encode proteins with an N-terminal [SG]-P-C-[KR]-P sequence motif and proteins that are conserved predominantly in pathogens.Specifically, 29 F. graminearum genes are rapidly evolving, in planta induced and encode secreted proteins, strongly pointing toward effector function.

View Article: PubMed Central - PubMed

Affiliation: CSIRO Agriculture Flagship, Centre for Environment and Life Sciences, Perth, Western Australia, Australia jana.sperschneider@csiro.au.

Show MeSH
Related in: MedlinePlus