Globodera rostochiensis genome sequencing
This data was used for the creation of two high quality reference genomes.
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Wageningen University & Research
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| Subjects: | Genome sequencing and assembly, Globodera rostochiensis, Multispecies, |
| Online Access: | https://research.wur.nl/en/datasets/globodera-rostochiensis-genome-sequencing |
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dig-wur-nl-wurpubs-5976202024-09-23 van Steenbrugge, Joris J.M. van den Elsen, Sven Holterman, Martijn Sterken, Mark G. Thorpe, Peter Goverse, Aska Smant, Geert Helder, Johannes Dataset Globodera rostochiensis genome sequencing 2021 This data was used for the creation of two high quality reference genomes. Abstract 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. Wageningen University & Research text/html https://research.wur.nl/en/datasets/globodera-rostochiensis-genome-sequencing https://edepot.wur.nl/570321 Genome sequencing and assembly Globodera rostochiensis Multispecies Wageningen University & Research |
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biblioteca |
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WUR Library Netherlands |
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Genome sequencing and assembly Globodera rostochiensis Multispecies Genome sequencing and assembly Globodera rostochiensis Multispecies |
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Genome sequencing and assembly Globodera rostochiensis Multispecies Genome sequencing and assembly Globodera rostochiensis Multispecies van Steenbrugge, Joris J.M. van den Elsen, Sven Holterman, Martijn Sterken, Mark G. Thorpe, Peter Goverse, Aska Smant, Geert Helder, Johannes Globodera rostochiensis genome sequencing |
| description |
This data was used for the creation of two high quality reference genomes. |
| format |
Dataset |
| topic_facet |
Genome sequencing and assembly Globodera rostochiensis Multispecies |
| author |
van Steenbrugge, Joris J.M. van den Elsen, Sven Holterman, Martijn Sterken, Mark G. Thorpe, Peter Goverse, Aska Smant, Geert Helder, Johannes |
| author_facet |
van Steenbrugge, Joris J.M. van den Elsen, Sven Holterman, Martijn Sterken, Mark G. Thorpe, Peter Goverse, Aska Smant, Geert Helder, Johannes |
| author_sort |
van Steenbrugge, Joris J.M. |
| title |
Globodera rostochiensis genome sequencing |
| title_short |
Globodera rostochiensis genome sequencing |
| title_full |
Globodera rostochiensis genome sequencing |
| title_fullStr |
Globodera rostochiensis genome sequencing |
| title_full_unstemmed |
Globodera rostochiensis genome sequencing |
| title_sort |
globodera rostochiensis genome sequencing |
| publisher |
Wageningen University & Research |
| url |
https://research.wur.nl/en/datasets/globodera-rostochiensis-genome-sequencing |
| work_keys_str_mv |
AT vansteenbruggejorisjm globoderarostochiensisgenomesequencing AT vandenelsensven globoderarostochiensisgenomesequencing AT holtermanmartijn globoderarostochiensisgenomesequencing AT sterkenmarkg globoderarostochiensisgenomesequencing AT thorpepeter globoderarostochiensisgenomesequencing AT goverseaska globoderarostochiensisgenomesequencing AT smantgeert globoderarostochiensisgenomesequencing AT helderjohannes globoderarostochiensisgenomesequencing |
| _version_ |
1813194916235313152 |