Genome-Wide Analysis in Three Fusarium Pathogens Identifies Rapidly Evolving Chromosomes and Genes Associated with Pathogenicity.
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.
Affiliation: CSIRO Agriculture Flagship, Centre for Environment and Life Sciences, Perth, Western Australia, Australia firstname.lastname@example.org.Show MeSH
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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.—
Affiliation: CSIRO Agriculture Flagship, Centre for Environment and Life Sciences, Perth, Western Australia, Australia email@example.com.