Comparative genomics of two inbred lines of the potato cyst nematode Globodera rostochiensis reveals disparate effector family-specific diversification patterns

This work was funded as part of a grant by the Netherlands Organization for Scientific Research (NWO) as part of the Applied and Technical Science domain (TTW) under grant no. 14708. PT: bioinformatics and computational biology analyses were supported by the University of St Andrews Bioinformatics Unit (AMD3BIOINF), funded by Wellcome Trust ISSF award 105621/Z/14/Z.Background: Potato cyst nematodes belong to the most harmful pathogens in potato, and durable management of these parasites largely depends on host-plant resistances. These resistances are pathotype specific. The current Globodera rostochiensis pathotype scheme that defines five pathotypes (Ro1 - Ro5) is both fundamentally and practically of limited value. Hence, resistant potato varieties are used worldwide in a poorly informed manner. Results : We generated two novel reference genomes of G. rostochiensis inbred lines derived from a Ro1 and a Ro5 population. These genome sequences comprise 173 and 189 scaffolds respectively, marking a ≈ 24-fold reduction in fragmentation as compared to the current reference genome. We provide copy number variations for 19 effector families. Four dorsal gland effector families were investigated in more detail. SPRYSECs, known to be implicated in plant defence suppression, constitute by far the most diversified family studied herein with 60 and 99 variants in Ro1 and Ro5 distributed over 18 and 26 scaffolds. In contrast, CLEs, effectors involved in feeding site induction, show strong physical clustering. The 10 and 16 variants cluster on respectively 2 and 1 scaffolds. Given that pathotypes are defined by their effectoromes, we pinpoint the disparate nature of the contributing effector families in terms of sequence diversification and loss and gain of variants. Conclusions : Two novel reference genomes allow for nearly complete inventories of effector diversification and physical organisation within and between pathotypes. Combined with insights we provide on effector family-specific diversification patterns, this constitutes a basis for an effectorome-based virulence scheme for this notorious pathogen.Publisher PDFPeer reviewe

Effects of microplastics on common bean rhizosphere bacterial communities

Microplastic pollution in terrestrial ecosystems is a growing concern due to its potential influences on soil properties and crop growth. Little is known about the effects of microplastics on the microbiome in the rhizosphere. Here, we studied the effects of two types of microplastics (MPs), low density polyethylene (LDPE-MPs) and biodegradable microplastic (Bio-MPs) of poly-butylene-adipate-co-terephthalate (PBAT) mixed with polylactic acid (PLA), on rhizosphere bacterial communities of Phaseolus vulgaris at doses of 0.5 %, 1.0 % and 2.5 % (w/w, dry weight ratio between MPs and soil). Bio-MPs and LDPE-MPs showed significant higher α-diversity (Chao 1, ACE, Shannon and Simpson) than control. For each type of microplastic material, 2.5 % of LDPE-MPs and Bio-MPs showed lowest α-diversity as compared to doses of 0.5 % and 1.0 %, indicating 2.5 % dose of MPs might pose selective effect on rhizosphere bacterial communities. β-Diversity of 1.0 % and 2.5 % Bio-MPs were distinctive from the control and other treatments. Microplastics also affected the relative abundance at family level, i.e. as compared to control, Comamonadaceae was higher in all the MPs treatments, Rhizobiaceae was highest in 2.5 % LDPE-MPs and lowest in 2.5 % Bio-MPs. LefSe results showed, as compared to control, Bio-MPs induced more indictive taxa than LDPE-MPs. Our findings evidenced that LDPE-MPs and Bio-MPs exerted profound effects on rhizosphere bacterial communities, and these effects might have far-reaching effects on soil nutrient cycling and plant health in agroecosystems

Globodera rostochiensis genome sequencing

This data was used for the creation of two high quality reference genomes

Characterization of the habitat-and season-independent increase in fungal biomass induced by the invasive giant goldenrod and its impact on the fungivorous nematode community

Outside its native range, the invasive plant species giant goldenrod (Solidago gigantea) has been shown to increase belowground fungal biomass. This non-obvious effect is poorly character-ized; we don’t know whether it is plant developmental stage-dependent, which fractions of the fungal community are affected, and whether it is reflected in the next trophic level. To address these questions, fungal assemblages in soil samples collected from invaded and uninvaded plots in two soil types were compared. Although using ergosterol as a marker for fungal biomass demonstrated a significant increase in fungal biomass, specific quantitative PCR (qPCR) assays did not point at a quantitative shift. MiSeq-based characterization of the belowground effects of giant goldenrod revealed a local increase of mainly Cladosporiaceae and Glomeraceae. This asymmetric boost in the fungal community was reflected in a specific shift in the fungivorous nematode community. Our findings provide insight into the potential impact of invasive plants on local fungal communities