Time-resolved dual transcriptomics reveal early induced Nicotiana benthamiana root genes and conserved infection-promoting Phytophthora palmivora effectors

BACKGROUND: Plant-pathogenic oomycetes are responsible for economically important losses in crops worldwide. Phytophthora palmivora, a tropical relative of the potato late blight pathogen, causes rotting diseases in many tropical crops including papaya, cocoa, oil palm, black pepper, rubber, coconut, durian, mango, cassava and citrus. Transcriptomics have helped to identify repertoires of host-translocated microbial effector proteins which counteract defenses and reprogram the host in support of infection. As such, these studies have helped in understanding how pathogens cause diseases. Despite the importance of P. palmivora diseases, genetic resources to allow for disease resistance breeding and identification of microbial effectors are scarce. RESULTS: We employed the model plant Nicotiana benthamiana to study the P. palmivora root infections at the cellular and molecular levels. Time-resolved dual transcriptomics revealed different pathogen and host transcriptome dynamics. De novo assembly of P. palmivora transcriptome and semi-automated prediction and annotation of the secretome enabled robust identification of conserved infection-promoting effectors. We show that one of them, REX3, suppresses plant secretion processes. In a survey for early transcriptionally activated plant genes we identified a N. benthamiana gene specifically induced at infected root tips that encodes a peptide with danger-associated molecular features. CONCLUSIONS: These results constitute a major advance in our understanding of P. palmivora diseases and establish extensive resources for P. palmivora pathogenomics, effector-aided resistance breeding and the generation of induced resistance to Phytophthora root infections. Furthermore, our approach to find infection-relevant secreted genes is transferable to other pathogen-host interactions and not restricted to plants.This work was supported by the Gatsby Charitable Foundation (RG62472), by the Royal Society (RG69135) and by the European Research Council (ERC-2014-STG, H2020, 637537)

Panicum streak virus diversity is similar to that observed for maize streak virus

Panicum streak virus (PanSV; genus Mastrevirus, family Geminiviridae) is, together with maize streak virus (MSV), sugarcane streak virus (SSV), sugarcane streak Reunion virus (SSRV) and sugarcane streak Egypt virus (SSEV), one of the currently described "African streak virus" (AfSV) species [6]. As with all the other AfSV species other than MSV, very little is known about PanSV genomic sequence diversity across Africa. Only two PanSV full genome sequences have ever been reported: one from Kenya [2], and the other from South Africa [17]. Both these genomes were isolated from Panicum maximum plants, but share only approximately 90% sequence identity. The reason this is noteworthy is that throughout mainland Africa all MSV genomes ever sampled from maize have been found to share > 97% sequence identity. Although other MSV strains sharing between 78 and 90% identity with the maize-adapted strain (MSV-A) have been described, these have all been isolated from different host species, indicating that host adaptation is probably the main force driving MSV diversification. MSV and PanSV share common vector species (leafhoppers in the genus Cicadulina) and probably also share some host species. Although the host range of PanSV is currently unknown, the MSV host range is extensive and includes P. maximum [3]. One might therefore expect that similar evolutionary forces acting on both species might result in their sharing similar patterns of both geographical and host-associated diversity. Here we describe the full genome sequences of five new PanSV isolates (including two new strains) sampled from southern and western Africa, and report that PanSV and MSV do indeed have similar patterns of diversity. We find, however, that unlike with MSV, geographical separation rather than host adaptation is possibly the dominant force driving PanSV diversification

Novel sugarcane streak and sugarcane streak Reunion mastreviruses from southern Africa and La Réunion

The sugarcane infecting streak viruses (SISVs) are mastreviruses (Family Geminiviridae) belonging to a group of "African streak viruses" (AfSVs) that includes the economically devastating Maize streak virus (MSV). Although there are three currently described SISV species (Sugarcane streak virus [SSV], Sugarcane streak Egypt virus [SSEV] and Sugarcane streak Reunion virus [SSRV]), only one strain variant has been fully sequenced for each of these species and as a result very little is known about the diversity and evolutionary origins of the SCISVs. Here we present annotated full genome sequences of four new SISV isolates, including a new strain of both SSRV and SSV, and one potentially new SISV species, sampled from wild grasses in La Reunion and Zimbabwe. For the first time, we report the finding of SSRV isolates in Zimbabwe and SSV isolates on the island of La Reunion. Phylogenetic and recombination analyses indicate continent-wide SSRV strain diversity and that our isolate potentially representing a new SISV species is a recombinant