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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.

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

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XylA shows signatures of site-specific diversifying selection. An alignment of XylA (FGSG_10999) protein sequences in the Fusarium genus reveals a high conservation on the amino acid level, visualized by Jalview (Waterhouse et al. 2009). However, two sites (shown as red columns) are predicted to undergo diversifying selection by CODEML (model M7/M8). Additionally, four sites (shown as blue columns) have a posterior probability larger than 0.5 as estimated using the CODEML model M7/M8 empirical Bayes method, including Val151 (shown at position 162 in this alignment). F. graminearum: FGSG, F. pseudograminearum: FPSE, F. culmorum: FCUL, F. incarnatum–F. equiseti: FIFE, F. fujikuroi: FFUJ, F. oxysporum Fo5176: FOXB, F. oxysporum f. sp. lycopersici: FOXG, F. verticillioides: FVEG, F. acuminatum: FACU.
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evv092-F4: XylA shows signatures of site-specific diversifying selection. An alignment of XylA (FGSG_10999) protein sequences in the Fusarium genus reveals a high conservation on the amino acid level, visualized by Jalview (Waterhouse et al. 2009). However, two sites (shown as red columns) are predicted to undergo diversifying selection by CODEML (model M7/M8). Additionally, four sites (shown as blue columns) have a posterior probability larger than 0.5 as estimated using the CODEML model M7/M8 empirical Bayes method, including Val151 (shown at position 162 in this alignment). F. graminearum: FGSG, F. pseudograminearum: FPSE, F. culmorum: FCUL, F. incarnatum–F. equiseti: FIFE, F. fujikuroi: FFUJ, F. oxysporum Fo5176: FOXB, F. oxysporum f. sp. lycopersici: FOXG, F. verticillioides: FVEG, F. acuminatum: FACU.

Mentions: FGSG_10999 is a family 11 endo-beta-1,4-xylanase, also referred to as XylA. Xylan is a significant component especially in the cell wall of cereal plants and xylan-degrading enzymes are thought to play a role in pathogen attack, particularly of monocots (Belien et al. 2006). Functional studies of microbial endoxylanases and their plant inhibitors suggest a coevolutionary process in which plants evolve proteinaceous inhibitors of endoxylanases to combat microbial attack while microbial pathogens evolve endoxylanases with distinct sensitivities toward the respective plant inhibitors (Belien et al. 2005). XylA in particular has been shown to be inhibited by the Triticum aestivum xylanase inhibitor TAXI-I, but unexpectedly not by the xylanase inhibitor protein XIP-I (Belien et al. 2005). Insensitivity of XylA to XIP-1 has been attributed a handful of amino acid changes in XylA, in particular Val151 (Belien et al. 2007). CODEML returns two sites under diversifying selection (fig. 4). Furthermore, we do not detect significant site-specific diversifying selection for XylB (FGSG_03624), which is a necrotizing factor but is not essential for virulence (Sella et al. 2013). This emphasizes the diversification of endoxylanases and that subtle amino acid changes can be a driving force in the coevolutionary arms race between plant and pathogen.Fig. 4.—


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)

XylA shows signatures of site-specific diversifying selection. An alignment of XylA (FGSG_10999) protein sequences in the Fusarium genus reveals a high conservation on the amino acid level, visualized by Jalview (Waterhouse et al. 2009). However, two sites (shown as red columns) are predicted to undergo diversifying selection by CODEML (model M7/M8). Additionally, four sites (shown as blue columns) have a posterior probability larger than 0.5 as estimated using the CODEML model M7/M8 empirical Bayes method, including Val151 (shown at position 162 in this alignment). F. graminearum: FGSG, F. pseudograminearum: FPSE, F. culmorum: FCUL, F. incarnatum–F. equiseti: FIFE, F. fujikuroi: FFUJ, F. oxysporum Fo5176: FOXB, F. oxysporum f. sp. lycopersici: FOXG, F. verticillioides: FVEG, F. acuminatum: FACU.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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evv092-F4: XylA shows signatures of site-specific diversifying selection. An alignment of XylA (FGSG_10999) protein sequences in the Fusarium genus reveals a high conservation on the amino acid level, visualized by Jalview (Waterhouse et al. 2009). However, two sites (shown as red columns) are predicted to undergo diversifying selection by CODEML (model M7/M8). Additionally, four sites (shown as blue columns) have a posterior probability larger than 0.5 as estimated using the CODEML model M7/M8 empirical Bayes method, including Val151 (shown at position 162 in this alignment). F. graminearum: FGSG, F. pseudograminearum: FPSE, F. culmorum: FCUL, F. incarnatum–F. equiseti: FIFE, F. fujikuroi: FFUJ, F. oxysporum Fo5176: FOXB, F. oxysporum f. sp. lycopersici: FOXG, F. verticillioides: FVEG, F. acuminatum: FACU.
Mentions: FGSG_10999 is a family 11 endo-beta-1,4-xylanase, also referred to as XylA. Xylan is a significant component especially in the cell wall of cereal plants and xylan-degrading enzymes are thought to play a role in pathogen attack, particularly of monocots (Belien et al. 2006). Functional studies of microbial endoxylanases and their plant inhibitors suggest a coevolutionary process in which plants evolve proteinaceous inhibitors of endoxylanases to combat microbial attack while microbial pathogens evolve endoxylanases with distinct sensitivities toward the respective plant inhibitors (Belien et al. 2005). XylA in particular has been shown to be inhibited by the Triticum aestivum xylanase inhibitor TAXI-I, but unexpectedly not by the xylanase inhibitor protein XIP-I (Belien et al. 2005). Insensitivity of XylA to XIP-1 has been attributed a handful of amino acid changes in XylA, in particular Val151 (Belien et al. 2007). CODEML returns two sites under diversifying selection (fig. 4). Furthermore, we do not detect significant site-specific diversifying selection for XylB (FGSG_03624), which is a necrotizing factor but is not essential for virulence (Sella et al. 2013). This emphasizes the diversification of endoxylanases and that subtle amino acid changes can be a driving force in the coevolutionary arms race between plant and pathogen.Fig. 4.—

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