Abstract
BackgroundPotato 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.ResultsWe 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.ConclusionsTwo 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.
Highlights
Potato cyst nematodes belong to the most harmful pathogens in potato, and durable management of these parasites largely depends on host-plant resistances
Genome Assemblies Two inbred lines of the potato cyst nematode G. rostochiensis were initially derived from crossings between individuals from two populations, Ro1-Mierenbos and Ro5-Harmerz [19]
DNA from these lines, Gr-Line19 and Gr-line22, were sequenced using PacBio sequencing technology with respectively 119X and 132X coverage and assembled into two reference genome sequences (Table 1). Benefitting from this long read technology and the significantly smaller genetic background, the two newly generated G. rostochiensis genome assemblies are less fragmented than the first genome sequence that was published [16] while maintaining a comparable assembly size
Summary
Potato cyst nematodes belong to the most harmful pathogens in potato, and durable management of these parasites largely depends on host-plant resistances. From an economic point of view root-knot and cyst nematodes have the highest impact [2]. Unlike root-knot nematodes, most cyst nematodes have a defined center of origin. Soybean cyst nematodes originate from northeast Asia and have spread as a successful and highly harmful parasite to all major soybean-growing areas. Outside of their centers of origin, cyst nematodes belong to the most harmful pathogens of the crops mentioned above
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
