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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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Examples for the variable C-terminal domain structures found in the [SG]-P-C-[KR]-P proteins. The [SG]-P-C-[KR]-P proteins feature a predicted signal peptide followed by the [SG]-P-C-[KR]-P motif, a serine/threonine rich stretch of variable length and a C-terminal domain. A representative member of the predicted tribes is shown on the right. The number of tribe members is given in the far right column followed by the mean  ratio and the percentage of tribe members that are under site-specific diversifying selection predicted by CODEML. Meme motifs are given with their respective number (see supplementary material, Supplementary Material online, for motifs) and Pfam domain hits are given with their identifier. PA14_2 (Pfam PF10528) is a GLEYA domain found in fungal adhesins and CBM_4_9 (Pfam PF02018) is found in carbohydrate-active enzymes.
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evv092-F5: Examples for the variable C-terminal domain structures found in the [SG]-P-C-[KR]-P proteins. The [SG]-P-C-[KR]-P proteins feature a predicted signal peptide followed by the [SG]-P-C-[KR]-P motif, a serine/threonine rich stretch of variable length and a C-terminal domain. A representative member of the predicted tribes is shown on the right. The number of tribe members is given in the far right column followed by the mean ratio and the percentage of tribe members that are under site-specific diversifying selection predicted by CODEML. Meme motifs are given with their respective number (see supplementary material, Supplementary Material online, for motifs) and Pfam domain hits are given with their identifier. PA14_2 (Pfam PF10528) is a GLEYA domain found in fungal adhesins and CBM_4_9 (Pfam PF02018) is found in carbohydrate-active enzymes.

Mentions: The C-terminal region for the [SG]-P-C-[KR]-P proteins is composed of a variety of different domain structures, which indicates the functional diversity and potential specialization of members in this group. We collected the C-terminal protein sequences and clustered them into families using TRIBE-MCL. This resulted in 25 predicted tribes covering 113 of the 118 genes. We were able to obtain ratios for 116 genes and to calculate the likelihood of site-specific diversifying selection for 108 genes. The percentage of genes that are under site-specific diversifying selection (20.2%) is substantially higher than genome-wide means (table 1). We ran MEME and Pfam searches to inspect the variable C-terminal domain structures. Figure 5 shows examples of the diverse domain structures for the [SG]-P-C-[KR]-P proteins with a representative member (see supplementary material, Supplementary Material online, for full results). One tribe (FGSG_04739, FGSG_04858, FVEG_05717, FVEG_07656, FVEG_11011, and FOXG_13582, FOXG_02535) shares sequence similarity in the C-terminal region with the GLEYA domain (PA14_2, Pfam PF10528) found in fungal adhesins. The mean ratio for this tribe is 0.15, which is not elevated compared with the genome-wide means and therefore suggests a conserved function. In contrast, another tribe (FGSG_07629, FVEG_03625, FOXG_01333, and FOXG_05752) contains a carbohydrate binding domain (CBM_4_9, Pfam PF02018) found in carbohydrate-active enzymes. This tribe has an elevated ratio of 0.62 and FGSG_07629, FVEG_03625, and FOXG_05752 show site-specific diversifying selection on amino acids in the C-terminal region. Taken together, this exemplifies the diversification of the [SG]-P-C-[KR]-P proteins through their C-terminals or a potential acquisition of the N-terminal SG]-P-C-[KR]-P motif through convergent evolution.Fig. 5.—


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)

Examples for the variable C-terminal domain structures found in the [SG]-P-C-[KR]-P proteins. The [SG]-P-C-[KR]-P proteins feature a predicted signal peptide followed by the [SG]-P-C-[KR]-P motif, a serine/threonine rich stretch of variable length and a C-terminal domain. A representative member of the predicted tribes is shown on the right. The number of tribe members is given in the far right column followed by the mean  ratio and the percentage of tribe members that are under site-specific diversifying selection predicted by CODEML. Meme motifs are given with their respective number (see supplementary material, Supplementary Material online, for motifs) and Pfam domain hits are given with their identifier. PA14_2 (Pfam PF10528) is a GLEYA domain found in fungal adhesins and CBM_4_9 (Pfam PF02018) is found in carbohydrate-active enzymes.
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evv092-F5: Examples for the variable C-terminal domain structures found in the [SG]-P-C-[KR]-P proteins. The [SG]-P-C-[KR]-P proteins feature a predicted signal peptide followed by the [SG]-P-C-[KR]-P motif, a serine/threonine rich stretch of variable length and a C-terminal domain. A representative member of the predicted tribes is shown on the right. The number of tribe members is given in the far right column followed by the mean ratio and the percentage of tribe members that are under site-specific diversifying selection predicted by CODEML. Meme motifs are given with their respective number (see supplementary material, Supplementary Material online, for motifs) and Pfam domain hits are given with their identifier. PA14_2 (Pfam PF10528) is a GLEYA domain found in fungal adhesins and CBM_4_9 (Pfam PF02018) is found in carbohydrate-active enzymes.
Mentions: The C-terminal region for the [SG]-P-C-[KR]-P proteins is composed of a variety of different domain structures, which indicates the functional diversity and potential specialization of members in this group. We collected the C-terminal protein sequences and clustered them into families using TRIBE-MCL. This resulted in 25 predicted tribes covering 113 of the 118 genes. We were able to obtain ratios for 116 genes and to calculate the likelihood of site-specific diversifying selection for 108 genes. The percentage of genes that are under site-specific diversifying selection (20.2%) is substantially higher than genome-wide means (table 1). We ran MEME and Pfam searches to inspect the variable C-terminal domain structures. Figure 5 shows examples of the diverse domain structures for the [SG]-P-C-[KR]-P proteins with a representative member (see supplementary material, Supplementary Material online, for full results). One tribe (FGSG_04739, FGSG_04858, FVEG_05717, FVEG_07656, FVEG_11011, and FOXG_13582, FOXG_02535) shares sequence similarity in the C-terminal region with the GLEYA domain (PA14_2, Pfam PF10528) found in fungal adhesins. The mean ratio for this tribe is 0.15, which is not elevated compared with the genome-wide means and therefore suggests a conserved function. In contrast, another tribe (FGSG_07629, FVEG_03625, FOXG_01333, and FOXG_05752) contains a carbohydrate binding domain (CBM_4_9, Pfam PF02018) found in carbohydrate-active enzymes. This tribe has an elevated ratio of 0.62 and FGSG_07629, FVEG_03625, and FOXG_05752 show site-specific diversifying selection on amino acids in the C-terminal region. Taken together, this exemplifies the diversification of the [SG]-P-C-[KR]-P proteins through their C-terminals or a potential acquisition of the N-terminal SG]-P-C-[KR]-P motif through convergent evolution.Fig. 5.—

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