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Using comparative genomics to develop a molecular diagnostic for the identification of an emerging pest Drosophila suzukii

Published online by Cambridge University Press:  25 March 2015

K.A. Murphy ,
T.R. Unruh ,
L.M. Zhou ,
F.G. Zalom ,
P.W. Shearer ,
E.H. Beers ,
V.M. Walton ,
B. Miller  and
J.C. Chiu
K.A. Murphy
Affiliation:
Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, CA 95616, USA
T.R. Unruh
Affiliation:
USDA-ARS, Wapato, WA 98951, USA
L.M. Zhou
Affiliation:
Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, CA 95616, USA
F.G. Zalom
Affiliation:
Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, CA 95616, USA
P.W. Shearer
Affiliation:
Mid-Columbia Agricultural and Extension Center, Oregon State University, Hood River, OR 97031, USA
E.H. Beers
Affiliation:
Tree Fruit Research and Extension Center, Washington State University, Wenatchee, WA 98801, USA
V.M. Walton
Affiliation:
Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA
B. Miller
Affiliation:
Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA
J.C. Chiu*
Affiliation:
Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, CA 95616, USA
*
*Author for correspondence Phone: (530) 752-1839 Fax: (530) 754-9077 E-mail: jcchiu@ucdavis.edu
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Abstract

Drosophila suzukii (Spotted Wing Drosophila) has recently become a serious invasive pest of fruit crops in the USA, Canada, and Europe, leading to substantial economic losses. D. suzukii is a direct pest, ovipositing directly into ripe or ripening fruits; in contrast, other Drosophilids utilize decaying or blemished fruits and are nuisance pests at worst. Immature stages of D. suzukii are difficult to differentiate from other Drosophilids, posing problems for research and for meeting quarantine restrictions designed to prevent the spread of this pest in fruit exports. Here we used a combined phylogenetic and bioinformatic approach to discover genetic markers suitable for a species diagnostic protocol of this agricultural pest. We describe a molecular diagnostic for rapid identification of single D. suzukii larva using multiplex polymerase chain reaction. Our molecular diagnostic was validated using nine different species of Drosophila for specificity and 19 populations of D. suzukii from different geographical regions to ensure utility within species.

Keywords

spotted wing drosophilaDrosophila suzukiispecies-specific PCRinvasive pestcomparative genomics
Type
Research Papers
Information
Bulletin of Entomological Research , Volume 105 , Issue 3 , June 2015 , pp. 364 - 372
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Copyright
Copyright © Cambridge University Press 2015 

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References

Atallah, J., Teixeira, L., Salazar, R., Zaragoza, G. & Kopp, A. (2014) The making of a pest: the evolution of a fruit-penetrating ovipositor in Drosophila suzukii and related species. Proceedings of the Royal Society B: Biological Sciences 281(1781), 20132840.Google Scholar
Behura, S.K. (2006) Molecular marker systems in insects: current trends and future avenues. Molecular Ecology 15, 3087–3113.Google Scholar
Calabria, G., Maca, J., Bachli, G., Serra, L. & Pascual, M. (2012) First records of the potential pest species Drosophila suzukii (Diptera: Drosophilidae) in Europe. Journal of Applied Entomology 136, 139–147.Google Scholar
Chiu, J.C., Lee, E.K., Egan, M.G., Sakar, I.N., Coruzzi, G.M., DeSalle, R. (2006) OrthologID: automation of genome-scale ortholog identification within a parsimony framework. Bioinformatics 22(6), 699–707.CrossRefGoogle ScholarPubMed
Chiu, J.C., Jiang, X., Zhao, L., Hamm, C.A., Cridland, J.M., Saelao, P., Hamby, K.A., Lee, E.K., Kwok, R.S., Zhang, G., Zalom, F.G., Walton, V.M., Begun, D.J. (2013) Genome of Drosophila suzukii, the Spotted Wing Drosophila. G3: Genes, Genomics, Genetics 3(12), 2257–2271.Google Scholar
Cini, A., Ioraitti, C. & Anfora, G. (2012) A review of the invasion of Drosophila suzukii in Europe and a draft research agenda for integrated pest management. Bulletin of Insectology 65, 149–160.Google Scholar
Dhami, M.K. & Kumarasinghe, L. (2014) A HRM real-time PCR assay for rapid and specific identification of the emerging pest Spotted-Wing Drosophila (Drosophila suzukii). PLoS ONE 9(6), e98934.Google Scholar
Gariepy, T.D., Kuhlmann, U., Gillott, C. & Erlandson, M. (2007) Parasitoids, predators and PCR: the use of diagnostic molecular markers in biological control of Arthropods. Journal of Applied Entomology 131(4), 225–240.Google Scholar
Hauser, M. (2011) A historic account of the invasion of Drosophila suzukii (Matsumura) (Diptera-Drosophilidae) in the continental United States, with remarks on their identification. Pest Management Science 67, 1352–1357.Google Scholar
Hebert, P.D.N., Cywinska, A., Ball, S.L. & deWaard, J.R. (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences 270(1512), 313–321.Google Scholar
Heid, C.A., Stevens, J., Livak, K.J. & Williams, P.M. (1996) Real time quantitative PCR. Genome Research 6, 986–994.Google Scholar
Katoh, K. & Standley, D.M. (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30(4), 772–780.Google Scholar
Kim, S.S., Tripodi, A.D., Johnson, D.T. & Szalanski, A.L. (2014) Molecular diagnostics of Drosophila suzukii (Diptera: Drosophilidae) using PCR-RFLP. Journal of Economic Entomology 107(3), 1292–1294.CrossRefGoogle ScholarPubMed
Lee, J.C., Bruck, D.J., Curry, H., Edwards, D., Haviland, D.R., Van Steenwyk, R.A., Yorgey, B.M. (2011) The susceptibility of small fruits and cherries to the spotted-wing drosophila, Drosophila suzukii . Pest Management Science 67, 1358–1367.Google Scholar
Marygold, S.J., Leyland, P.C., Seal, R.L., Goodman, J.L., Thurmond, J.R., Strelets, V.B., Wilson, R.J. FlyBase consortium. (2013) FlyBase: improvements to the bibliography. Nucleic Acids Research 41(D1), D751–D757.CrossRefGoogle Scholar
modENCODE Consortium , Roy, S., Ernst, J., Kharchenko, P.V., Kheradpour, P., Negre, N., Eaton, M.L., Landolin, J.M., Bristow, C.A., Ma, L., Lin, M.F., Washietl, S., Arshinoff, B.I., Ay, F., Meyer, P.E., Robine, N., Washington, N.L., Di Stefano, L., Berezikov, E., Brown, C.D., Candeias, R., Carlson, J.W., Carr, A., Jungreis, I., Marbach, D., Sealfon, R., Tolstorukov, M.Y., Will, S., Alekseyenko, A.A., Artieri, C., Booth, B.W., Brooks, A.N., Dai, Q., Davis, C.A., Duff, M.O., Feng, X., Gorchakov, A.A., Gu, T., Henikoff, J.G., Kapranov, P., Li, R., MacAlpine, H.K., Malone, J., Minoda, A., Nordman, J., Okamura, K., Perry, M., Powell, S.K., Riddle, N.C., Sakai, A., Samsonova, A., Sandler, J.E., Schwartz, Y.B., Sher, N., Spokony, R., Sturgill, D., van Baren, M., Wan, K.H., Yang, L., Yu, C., Feingold, E., Good, P., Guyer, M., Lowdon, R., Ahmad, K., Andrews, J., Berger, B., Brenner, S.E., Brent, M.R., Cherbas, L., Elgin, S.C., Gingeras, T.R., Grossman, R., Hoskins, R.A., Kaufman, T.C., Kent, W., Kuroda, M.I., Orr-Weaver, T., Perrimon, N., Pirrotta, V., Posakony, J.W., Ren, B., Russell, S., Cherbas, P., Graveley, B.R., Lewis, S., Micklem, G., Oliver, B., Park, P.J., Celniker, S.E., Henikoff, S., Karpen, G.H., Lai, E.C., MacAlpine, D.M., Stein, L.D., White, K.P., Kellis, M. (2010) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330(6012), 1787–1797.Google Scholar
Stamatakis, A. (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688–2690.Google Scholar
Stamatakis, A. (2012) RAxML GitHub repository. https://githubcom/stamatak/standard-RAxML/.Google Scholar
Walsh, K., Boonham, N., Barker, I. & Collins, D.W. (2005) Development of a sequence-specific real-time PCR to the melon thrips Thrips palmi (Thysan., Thripidae). Journal of Applied Entomology 129, 272–279.Google Scholar
Walsh, D.B., Bolda, M.P., Goodhue, R.E., Dreves, A.J., Lee, J., Bruck, D., Walton, V.M., O'Neal, S.D., Zalom, F.G. (2011) Drosophila suzukii (Diptera: Drosophilidae): invasive pest of ripening soft fruit expanding its geographic range and damage potential. Journal of Integrated Pest Management 2, 1–7.CrossRefGoogle Scholar
Williams, J.G., Kybelik, A.R. & Livak, K.J. (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research 18, 6531–6535.Google Scholar
Wyman, A.R. & White, R. (1980) A highly polymorphic locus in human DNA. Proceedings for National Academy of Science of the United States of America 77(11), 6754–6758.Google Scholar
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