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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETICS AND EVOLUTION OF HOST SPECIFICITY OF INSECT BIOLOGICAL CONTROL AGENTS, EMPHASIZING APHIDS AND MOTHS

Location: Beneficial Insects Introduction Research

Title: Next-generation genome sequencing and assembly provides tools for phylogenetics and identification of closely related species of Spathius, parasitoids of Agrilus planipennis (emerald ash borer)

Authors
item Kuhn, Kristen
item Duan, Jian
item Hopper, Keith

Submitted to: Biological Control
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 26, 2013
Publication Date: May 7, 2013
Citation: Kuhn, K.L., Duan, J.J., Hopper, K.R. 2013. Next-generation genome sequencing and assembly provides tools for phylogenetics and identification of closely related species of Spathius, parasitoids of Agrilus planipennis (emerald ash borer). Biological Control. 66:77-82.

Interpretive Summary: A crucial step in biological control programs is identification of candidates for introduction. This is often difficult when cryptic species are involved. However, recent advances in DNA sequencing allows analysis of whole genomes of non-model species that can provide differences that distinguish populations and species. We used this sort of analysis on four species of parasitic wasps that attack the emerald ash borer, which is an invasive pest of ash trees. Using the DNA sequence data we were able to find differences that identify these species, and we were able to tell which species were most closely related to one another. We describe methods that can rapidly and inexpensively tell these species apart as juveniles and adults. These methods demonstrate the power of new sequencing technology in species identification, and the results will prove useful in determining which of these species is parasitizing the most emerald ash borers and thus which should receive the most attention in biological control of this important pest.

Technical Abstract: A crucial step in biological control programs is identification of candidates for introduction. This is often difficult when cryptic species are involved. However, recent advances in next-generation sequencing allows whole genome sequencing in non-model species for the discovery and genotyping of molecular polymorphisms that provide ample evidence to distinguish populations and species. We sequenced and assembled the genomes of four closely related species in the genus SPATHIUS, that are parasitoids of the invasive emerald ash borer. A sample of 1000 contigs generated from these assembled genomes harbored 150k to 550k single nucleotide polymorphisms (SNPs) or 1-2.8 SNPs per kilobase that were fixed differences between these species. Using these SNPs, we clarified the phylogenetic relationships between two known species, SPATHIUS AGRILI and SPATHIUS FLORIDANUS, and undescribed species of SPATHIUS from Russia and the USA. Taking advantage of insertion/deletions that differed among species, we developed 4 primer pairs that amplified fragments with fixed length differences between these species. These primers can be used in rapid, inexpensive PCR/gel based identification of these SPATHIUS species. Thus next-generation sequencing can provide for a powerful tool for developing markers to identify closely related species without a reference genome.

Last Modified: 12/18/2014
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