Duplications and losses in gene families of rust pathogens highlight putative effectors
Amanda L. Pendleton, Katherine E. Smith, Nicolas Feau, Francis M. Martin, Igor V. Grigoriev, Richard Hamelin, C. Dana Nelson, J. Gordon Burleigh, and John M. Davis
2014 June 26, Front Plant Sci. 26;5:299. doi: 10.3389/fpls.2014.00299. eCollection 2014.
Rust fungi are a group of fungal pathogens that cause some of the world’s most destructive diseases of trees and crops. A shared characteristic among rust fungi is obligate biotrophy, the inability to complete a lifecycle without a host. This dependence on a host species likely affects patterns of gene expansion, contraction, and innovation within rust pathogen genomes. The establishment of disease by biotrophic pathogens is reliant upon effector proteins that are encoded in the fungal genome and secreted from the pathogen into the host’s cell apoplast or within the cells. This study uses a comparative genomic approach to elucidate putative effectors and determine their evolutionary histories. We used OrthoMCL to identify nearly 20,000 gene families in proteomes of 16 diverse fungal species, which include 15 basidiomycetes and one ascomycete. We inferred patterns of duplication and loss for each gene family and identified families with distinctive patterns of expansion/contraction associated with the evolution of rust fungal genomes. To recognize potential contributors for the unique features of rust pathogens, we identified families harboring secreted proteins that: (i) arose or expanded in rust pathogens relative to other fungi, or (ii) contracted or were lost in rust fungal genomes. While the origin of rust fungi appears to be associated with considerable gene loss, there are many gene duplications associated with each sampled rust fungal genome. We also highlight two putative effector gene families that have expanded in Cqf that we hypothesize have roles in pathogenicity.
Conserved proteins and families within only four Pucciniomycete pathogen genomes are mostly species-specific. Gene family (OrthoMCL) conservation within Pucciniomycete pathogens; Mixia osmundae (Mos), Cronartium quercuum f.sp. fusiforme (Cqf), Melampsora larici-populina (Mlp), and Puccinia graminis f.sp. tritici (Pgt). The values indicate the total number of (A) gene models or (B) gene families conserved in only these four species and absent in the remaining 12 fungal taxa included in the OrthoMCL analysis.
Gene loss and gain in the Basidiomycota fungal lineage highlights shared loss in the rust pathogen lineage and high levels of species-specific gain. Mapping putative gene duplications and losses across 16 fungal taxa. Values in blue are associated with gains/duplications, whereas orange indicates loss. Outside of parentheses are the number of gain or loss events that have occurred on the branch preceding a node, and within parentheses are the number of gene families associated with duplications or losses. The node denoted with R indicates the last common ancestor of the rust pathogens.
Pendleton Amanda L., Smith Katherine E., Feau Nicolas, Martin Francis Michel, Grigoriev Igor V., Hamelin Richard, Nelson C. Dana, Burleigh J. Gordon, Davis John M. 2014. Duplications and losses in gene families of rust pathogens highlight putative effectors. Frontiers in Plant Science 5(299): 1-13. DOI=10.3389/fpls.2014.00299