DOI: 10.5061/dryad.x0k6djhfj
title: Identifying diagnostic genetic markers for a cryptic invasive agricultural pest: a test case using the apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae)

description: Insect pests destroy ~15% of all USA crops, resulting in losses of $15
 billion annually. Thus, developing cheap, quick and reliable methods for
 detecting harmful species is critical to curtail insect damage and lessen
 economic impact. The apple maggot fly, Rhagoletis pomonella (Diptera:
 Tephritidae), is a major invasive pest threatening the multibillion-dollar
 apple industry in the Pacific Northwest USA. The fly is also sympatric
 with a benign but morphologically similar and genetically closely related
 species, R. zephyria, which attacks non-commercial snowberry. Unambiguous
 species identification is essential due to a zero-infestation policy of
 apple maggot for fruit export. Mistaking R. zephyria for R. pomonella
 triggers unnecessary and costly quarantines, diverting valuable control
 resources. Here we develop and apply a relatively simple and
 cost-effective diagnostic approach using Illumina sequencing of double
 digest restriction-site associated DNA markers. We identified five
 informative single nucleotide polymorphisms (SNPs) and designed a
 diagnostic test based on agarose gel electrophoresis of restriction enzyme
 digested polymerase chain reaction amplification products (RFLPs) to
 distinguish fly species. We demonstrated the utility of this approach for
 immediate, one day species identification by scoring apple- and
 snowberry-infesting flies of known host plant identity, reared directly
 from 11 sites throughout Washington. However, if immediate diagnosis is
 not required, or hundreds to thousands of specimens must be assessed, then
 a direct Illumina-based sequencing strategy, similar to that used here for
 diagnostic SNP identification can be powerful and cost-effective. The
 genomic strategy we present is effective for R. pomonella and also
 transferable to many cryptic pests.
description: Filtered vcf file with genotype
 probabilities: DoellmanHoodRzephSNPs.vcf.gz This is a
 vcf file generated using the GATK unified genotyper, then filtered as
 describe in the paper. The PL field provides the phred-scaled and
 normalized genotype probabilities produced using the GATK model.
 File mapping individual IDs to host
 associations: DoellmanHoodRzeph_popIDs.txt column 1 =
 sample id (sample id in the vcf file), column 2 = host
 association Raw Illumina sequencing data and barcodes
 for demultiplexing, Lane 1
 DoellmanHoodRzephL1_1.fq.gz Illumina forward
 reads DoellmanHoodRzephL1_2.fq.gz
 Illumina paired reads
 DoellmanHoodRzephL1_barcodes.txt column 1 =
 inline barcode (5' end of the forward read), column 2 = sample id
 (sample id in the vcf file) Raw Illumina sequencing
 data and barcodes for demultiplexing, Lane 2
 DoellmanHoodRzephL2_1.fq.gz Illumina forward
 reads DoellmanHoodRzephL2_2.fq.gz
 Illumina paired reads
 DoellmanHoodRzephL2_barcodes.txt column 1 =
 inline barcode (5' end of the forward read), column 2 = sample id
 (sample id in the vcf file) Raw Illumina sequencing
 data and barcodes for demultiplexing, Lane 3
 DoellmanHoodRzephL3_1.fq.gz Illumina forward
 reads DoellmanHoodRzephL3_2.fq.gz
 Illumina paired reads
 DoellmanHoodRzephL3_barcodes.txt column 1 =
 inline barcode (5' end of the forward read), column 2 = sample id
 (sample id in the vcf file) Raw Illumina sequencing
 data and barcodes for demultiplexing, Lane 4
 DoellmanHoodRzephL4_1.fq.gz Illumina forward
 reads DoellmanHoodRzephL4_2.fq.gz
 Illumina paired reads
 DoellmanHoodRzephL4_barcodes.txt column 1 =
 inline barcode (5' end of the forward read), column 2 = sample id
 (sample id in the vcf file)