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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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Related in: MedlinePlus

A comparison of diversifying selection acting on the F. graminearum, F. oxysporum f. sp. lycopersici, and F. verticillioides chromosomes. Percentages of genes under site-specific diversifying selection for specific chromosomes are shown in red. These were compared with the percentages of genes under site-specific diversifying selection for the remaining chromosomes, shown in blue. Statistical significance for each group compared with the remainder of the genome was assessed with a Fisher’s exact test at a significance threshold of P < 0.05. (A) Fusarium graminearum chromosome 2 has the highest percentage of rapidly evolving genes. (B) For F. oxysporum f. sp. lycopersici, significantly higher numbers of rapidly evolving genes are found on the dispensable chromosomes 3, 6, 14, and 15 as well as chromosomes 2b. (C) F. verticillioides chromosome 2 has the highest percentage of rapidly evolving genes.
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evv092-F3: A comparison of diversifying selection acting on the F. graminearum, F. oxysporum f. sp. lycopersici, and F. verticillioides chromosomes. Percentages of genes under site-specific diversifying selection for specific chromosomes are shown in red. These were compared with the percentages of genes under site-specific diversifying selection for the remaining chromosomes, shown in blue. Statistical significance for each group compared with the remainder of the genome was assessed with a Fisher’s exact test at a significance threshold of P < 0.05. (A) Fusarium graminearum chromosome 2 has the highest percentage of rapidly evolving genes. (B) For F. oxysporum f. sp. lycopersici, significantly higher numbers of rapidly evolving genes are found on the dispensable chromosomes 3, 6, 14, and 15 as well as chromosomes 2b. (C) F. verticillioides chromosome 2 has the highest percentage of rapidly evolving genes.

Mentions: We used statistical testing to determine the significance of differences in the number of genes under site-specific diversifying selection for the individual chromosomes in comparison to the remainder of the genome. On the dispensable F. oxysporum f. sp. lycopersici chromosomes, the percentage of genes that could be analyzed for site-specific diversifying selection is lower than for the core chromosomes (∼30–40% on dispensable chromosomes have a CODEML result compared with 69.7% genome-wide). Nevertheless, F. oxysporum f. sp. lycopersici has a significantly higher percentage of rapidly evolving genes on the dispensable chromosomes 3, 6, 14, and 15 as well as on chromosomes 2b (fig. 3B). Interestingly, the highest percentage of rapidly evolving genes for F. graminearum is found on chromosome 2 (fig. 3A). For F. verticillioides high percentages of rapidly evolving genes are located on chromosome 2, 7, 8, 6, 10, and 4 (fig. 3C).Fig. 3.—


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)

A comparison of diversifying selection acting on the F. graminearum, F. oxysporum f. sp. lycopersici, and F. verticillioides chromosomes. Percentages of genes under site-specific diversifying selection for specific chromosomes are shown in red. These were compared with the percentages of genes under site-specific diversifying selection for the remaining chromosomes, shown in blue. Statistical significance for each group compared with the remainder of the genome was assessed with a Fisher’s exact test at a significance threshold of P < 0.05. (A) Fusarium graminearum chromosome 2 has the highest percentage of rapidly evolving genes. (B) For F. oxysporum f. sp. lycopersici, significantly higher numbers of rapidly evolving genes are found on the dispensable chromosomes 3, 6, 14, and 15 as well as chromosomes 2b. (C) F. verticillioides chromosome 2 has the highest percentage of rapidly evolving genes.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4494044&req=5

evv092-F3: A comparison of diversifying selection acting on the F. graminearum, F. oxysporum f. sp. lycopersici, and F. verticillioides chromosomes. Percentages of genes under site-specific diversifying selection for specific chromosomes are shown in red. These were compared with the percentages of genes under site-specific diversifying selection for the remaining chromosomes, shown in blue. Statistical significance for each group compared with the remainder of the genome was assessed with a Fisher’s exact test at a significance threshold of P < 0.05. (A) Fusarium graminearum chromosome 2 has the highest percentage of rapidly evolving genes. (B) For F. oxysporum f. sp. lycopersici, significantly higher numbers of rapidly evolving genes are found on the dispensable chromosomes 3, 6, 14, and 15 as well as chromosomes 2b. (C) F. verticillioides chromosome 2 has the highest percentage of rapidly evolving genes.
Mentions: We used statistical testing to determine the significance of differences in the number of genes under site-specific diversifying selection for the individual chromosomes in comparison to the remainder of the genome. On the dispensable F. oxysporum f. sp. lycopersici chromosomes, the percentage of genes that could be analyzed for site-specific diversifying selection is lower than for the core chromosomes (∼30–40% on dispensable chromosomes have a CODEML result compared with 69.7% genome-wide). Nevertheless, F. oxysporum f. sp. lycopersici has a significantly higher percentage of rapidly evolving genes on the dispensable chromosomes 3, 6, 14, and 15 as well as on chromosomes 2b (fig. 3B). Interestingly, the highest percentage of rapidly evolving genes for F. graminearum is found on chromosome 2 (fig. 3A). For F. verticillioides high percentages of rapidly evolving genes are located on chromosome 2, 7, 8, 6, 10, and 4 (fig. 3C).Fig. 3.—

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