Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis

Department of Biological Sciences, Bowling Green State University, Боулинг-Грин, Ohio, United States
Science (Impact Factor: 33.61). 10/2006; 313(5791):1261-6. DOI: 10.1126/science.1128796
Source: PubMed


Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oömycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oömycete avirulence genes.

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Available from: Sucheta Tripathy, Oct 13, 2015
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    • "The half-size ABCG proteins, sometimes called WBC transporters as the prototypical members of the group white brown complex transporter in D. melanogaster, are needed for eye pigment formation (Kovalchuk and Driessen, 2010). However, animal genome does not show any full-length ABCG protein while the genomes of plants, fungi, oomycetes, brown algae and slime molds have been reported to contain a large group of full-length subfamily G transporters (Tyler et al., 2006; Cock et al., 2010). The maximum number of members exists under rice subfamily G among all the plant lineages taken under study, of which only eleven members are FT and rest are HT. "
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    ABSTRACT: ATP-binding cassette (ABC) transporter is a large gene superfamily that utilizes the energy released from ATP hydrolysis for transporting myriad of substrates across the biological membranes. Although many investigations have been done on the structural and functional analysis of the ABC transporters in Oryza sativa, much less is known about molecular phylogenetic and global expression pattern of the complete ABC family in rice. In this study, we have carried out a comprehensive phylogenetic analysis constructing neighbor-joining and maximum-likelihood trees based on various statistical methods of different ABC protein subfamily of five plant lineages including Chlamydomonas reinhardtii (green algae), Physcomitrella patens (moss), Selaginella moellendorffii (lycophyte), Arabidopsis thaliana (dicot) and Oryza sativa (monocot) to explore the origin and evolutionary patterns of these ABC genes. We have identified several conserved motifs in Nucleotide binding domain (NBD) of ABC proteins among all plant lineages during evolution. Amongst the different ABC protein subfamilies, ‘ABCE’ has not yet been identified in lower plant genomes (algae, moss and lycophytes). The result indicated that gene duplication and diversification process acted upon these genes as a major operative force creating new groups and subgroups and functional divergence during evolution. We have demonstrated that rice ABCI subfamily consists of only half size transporters that represented highly dynamic members showing maximum sequence variations among the other rice ABC subfamilies. The evolutionary and the expression analysis contribute to a deep insight into the evolution and diversity of rice ABC proteins and their roles in response to salt stress that facilitate our further understanding on rice ABC transporters.
    Computational Biology and Chemistry 11/2014; 54. DOI:10.1016/j.compbiolchem.2014.11.005 · 1.12 Impact Factor
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    • "Cacao black pod disease, caused by several species of the Straminipile genus Phytophthora (Kroon et al., 2004; Tyler et al., 2006) is the most common disease of cacao causing global yield losses estimated at 30% (Guest, 2007). In Cameroon, the most widespread species is Phytophthora megakarya Brassier & Griffin (Mfegue, 2012), which is endemic to West Africa and present in all four of the largest cocoa producing countries in this region, Ivory Coast, Ghana, Nigeria and Cameroon (Guest, 2007). "
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    ABSTRACT: In African cacao-producing countries, control of cacao black pod disease caused by Phytophthora megakarya is a priority. Introducing biological control agents as part of a P. megakarya control strategy is highly desirable, especially in a perspective of pesticide reduction. Trichoderma species are among the most used biological control agents. In Cameroon, Trichoderma asperellum formulated in wettable powder has produced positive effects against this disease. However, with this type of formulation, shelf-life and persistence of conidia on pods are limited. Our study therefore sought to develop a new T. asperellum formulation that would be more effective and better suited to the conditions of field application by small-scale producers in Cameroon. We selected a soybean oil-based oil dispersion, in which the half-life of the conidia reached 22.5 weeks, versus 5 weeks in aqueous suspension. Tested on detached pods, the formulation completely inhibited the development of the disease. When sprayed in the field on cacao clones highly sensitive to P. megakarya, the formulation resulted in 90% protection of treated pods after 1 week, and 50% after 3.2 weeks. The formulations exercised a measurable effect for up to 7 weeks, versus 2 weeks in the case of an aqueous conidial suspension and 5 weeks for that of a conventional fungicide (Kocide). Trichoderma asperellum formulated in oil dispersion has therefore great potential for the control of cacao black pod disease with less recourse to synthetic fungicides. Moreover, this formulation is well adapted to the types of sprayers used by small-scale cacao producers in Cameroon.
    Biological Control 10/2014; 77. DOI:10.1016/j.biocontrol.2014.06.004 · 1.64 Impact Factor
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    • "Over half (51%) of proteins considered to be effector-like (small, cysteine-rich, secreted proteins) belong to gene families. This is comparable to results found in the hemibiotrophic pathogens Phytophthora ramorum and P. sojae where 77% of their secretomes are found in multigene families (Tyler et al., 2006). These findings demonstrate the value of an evolutionary perspective for highlighting families harboring putative Cqf effectors. "
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    ABSTRACT: 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.
    Frontiers in Plant Science 06/2014; 5:299. DOI:10.3389/fpls.2014.00299 · 3.95 Impact Factor
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