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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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Phylogenetic relationships of the Fusarium genomes used for the prediction of diversifying selection with species complex information and host ranges. Nine Fusarium genomes were used for the prediction of diversifying selection in the genus. One hundred genes were randomly chosen that have predicted one-to-one orthologies amongst all Fusarium genomes and a phmmer hit with E-value of zero in Trichoderma reesei (Martinez et al. 2008). Protein sequences were concatenated and a multiple sequence alignment was calculated using PRANK with the +F option (Loytynoja and Goldman 2005). The tree was constructed using Phyml with branch support values shown (Guindon et al. 2010). Trichoderma reesei was used as an outgroup to root the phylogenetic tree.
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evv092-F1: Phylogenetic relationships of the Fusarium genomes used for the prediction of diversifying selection with species complex information and host ranges. Nine Fusarium genomes were used for the prediction of diversifying selection in the genus. One hundred genes were randomly chosen that have predicted one-to-one orthologies amongst all Fusarium genomes and a phmmer hit with E-value of zero in Trichoderma reesei (Martinez et al. 2008). Protein sequences were concatenated and a multiple sequence alignment was calculated using PRANK with the +F option (Loytynoja and Goldman 2005). The tree was constructed using Phyml with branch support values shown (Guindon et al. 2010). Trichoderma reesei was used as an outgroup to root the phylogenetic tree.

Mentions: To identify processes under strong evolutionary pressure in the Fusarium genus, we performed a genome-wide analysis of diversifying selection for three reference Fusarium genomes: F. graminearum, F. oxysporum f. sp. lycopersici, and Fusarium verticillioides, using orthologs from a set of nine Fusarium genomes (table 1). F. graminearum, F. oxysporum f. sp. lycopersici, and F. verticillioides were chosen because of their distribution across different species complexes, the availability of chromosomal data and the maturity of their gene models and annotations. The phylogenetic relationships and variation in host specificity are shown in figure 1.Fig. 1.—


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)

Phylogenetic relationships of the Fusarium genomes used for the prediction of diversifying selection with species complex information and host ranges. Nine Fusarium genomes were used for the prediction of diversifying selection in the genus. One hundred genes were randomly chosen that have predicted one-to-one orthologies amongst all Fusarium genomes and a phmmer hit with E-value of zero in Trichoderma reesei (Martinez et al. 2008). Protein sequences were concatenated and a multiple sequence alignment was calculated using PRANK with the +F option (Loytynoja and Goldman 2005). The tree was constructed using Phyml with branch support values shown (Guindon et al. 2010). Trichoderma reesei was used as an outgroup to root the phylogenetic tree.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evv092-F1: Phylogenetic relationships of the Fusarium genomes used for the prediction of diversifying selection with species complex information and host ranges. Nine Fusarium genomes were used for the prediction of diversifying selection in the genus. One hundred genes were randomly chosen that have predicted one-to-one orthologies amongst all Fusarium genomes and a phmmer hit with E-value of zero in Trichoderma reesei (Martinez et al. 2008). Protein sequences were concatenated and a multiple sequence alignment was calculated using PRANK with the +F option (Loytynoja and Goldman 2005). The tree was constructed using Phyml with branch support values shown (Guindon et al. 2010). Trichoderma reesei was used as an outgroup to root the phylogenetic tree.
Mentions: To identify processes under strong evolutionary pressure in the Fusarium genus, we performed a genome-wide analysis of diversifying selection for three reference Fusarium genomes: F. graminearum, F. oxysporum f. sp. lycopersici, and Fusarium verticillioides, using orthologs from a set of nine Fusarium genomes (table 1). F. graminearum, F. oxysporum f. sp. lycopersici, and F. verticillioides were chosen because of their distribution across different species complexes, the availability of chromosomal data and the maturity of their gene models and annotations. The phylogenetic relationships and variation in host specificity are shown in figure 1.Fig. 1.—

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