Data from: A metagenetics approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual

Distinct populations of the potato cyst nematode (PCN) Globodera pallida exist in the UK that differ in their ability to overcome various sources of resistance. An efficient method for distinguishing between populations would enable pathogen-informed cultivar choice in the field. Science and Advice for Scottish Agriculture (SASA) annually undertake national DNA diagnostic tests to determine the presence of PCN in potato seed and ware land by extracting DNA from soil floats. These DNA samples provide a unique resource for monitoring the distribution of PCN and further interrogation of the diversity within species. We identify a region of mitochondrial DNA descriptive of three main groups of G. pallida present in the UK, and adopt a metagenetics approach to the sequencing and analysis of all SASA samples simultaneously. Using this approach we describe the distribution of G. pallida mitotypes across Scotland with field-scale resolution. Most fields contain a single mitotype, one fifth contain a mix of mitotypes, and less than 3 % contain all three mitotypes. Within mixed fields we were able to quantify the relative abundance of each mitotype across an order of magnitude. Local areas within mixed fields are dominated by certain mitotypes and indicate towards a complex underlying "pathoscape". Finally, we assess mitotype distribution at the level of the individual cyst, and provide evidence of "hybrids". This study provides a method for accurate, quantitative and high throughput typing of up to one thousand fields simultaneously, while revealing novel insights into the national genetic variability of an economically important plant-parasite.

top_50_most_common_refine
50 most common amplicons aligned and refined.
top_50_midrr
Mid point re-routed bayesian phylogeny of top 50 most common amplicons with 2 million iterations
Consensus_types_align
Consensus of each mito type alignment
Consensus_types_with_4_align
consensus of each mito type alignment with addition of "type 4"
Barcode_and_type
tab separated table of location and relative type percentage with barcodes.
CYTB_sequences_used_to_identify_groups
CYTB_sequences_used_to_identify_groups

Eves-van den Akker, Sebastian; Lilley, Catherine; Reid, Alex et al. (2015). Data from: A metagenetics approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual [Dataset]. Dryad. https://doi.org/10.5061/dryad.pd7r6