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Title: Unexpected high intragenomic variation in two of three major pest thrips species does not affect ribosomal internal transcribed spacer 2 (ITS2)utility for thrips identification

item KUMAR, VIVEK - University Of Florida
item Dickey, Aaron
item SEAL, DAKSHINA - University Of Florida
item Shatters, Robert - Bob
item OSBORNE, LANCE - University Of Florida
item McKenzie, Cindy

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/30/2017
Publication Date: 10/6/2017
Citation: Kumar, V., Dickey, A.M., Seal, D.R., Shatters, R.G., Osborne, L.S., McKenzie, C.L. 2017. Unexpected high intragenomic variation in two of three major pest thrips species does not affect ribosomal transcribed spacer 2(ITS2) utility for thrips identification. International Journal of Molecular Sciences. 18(10):2100.

Interpretive Summary: Correct identification is a fundamental step in the development of sound management practices against a pest. The traditional morphological identification of various species in the order Thysanoptera can be difficult because of their small size (< 1.5 mm), high degree of polymorphism within species and the similarity of larvae belonging to different species. Considering the importance of correct identification, in this study we examine the suitability of two widely used genes, mtCO1 and ITS2, for the identification of three major thrips species, Frankliniella occidentalis, Scirtothrips dorsalis, and Thrips palmi. Our study showed the existence of intragenomic and intergenomic variations in both markers in three thrips species. The significantly lower intragenomic variation in mtCO1 for two of the three thrips species suggests that this gene is more suitable for the taxonomic characterization of Scirtothrips dorsalis and Thrips palmi, whereas both the markers appear equally suitable for Frankliniella occidentalis. Given equivalent primer-template binding efficiencies, a researcher is >3X more likely to obtain the dominant haplotype of mtCO1 than ITS2 in two out of these three species. Role of pseudogenes and molecular process such as nuclear heteroplasmy and concentric evolution affecting these variations has been discussed.

Technical Abstract: The mitochondrial gene mtCO1 and the internal transcribed spacer (ITS) region of the ribosomal DNA are among the most widely used molecular markers for insect taxonomic characterization. Three economically important species of thrips, Scirtothrips dorsalis, Thrips palmi, and Frankliniella occidentalis were selected to examine the extent of intragenomic and intergenomic variation within these two marker regions in the family Thripidae. The within species intragenomic and intergenomic variation were assessed by cloning and sequencing Polymerase chain reaction-amplified copies of these two genes. Intragenomic and intergenomic variation were detected in both markers in three thrips species and intergenomic variation was significantly higher than intragenomic variation for both genes in all three species. For ITS2,intragenomic variation ranged between 0.20 - 3.82 percent, 0.18 - 2.84 percent, 0.44 - 1.10 percent for Scirtothrips dorsalis, Thrips palmi and Frankliniella occidentalis, respectively and intergenomic variation ranged between 0.0 - 3.82 percent, 0.0 - 3.01 percent, 0.0 - 1.77 percent for Scirtothrips dorsalis, Thrips palmi and Frankliniella occidentalis, respectively. Significantly higher amounts of intragenomic variation were observed for ITS2 than mtCO1 in Scirtothrips dorsalis and Thrips palmi. In all the three thrips species no sex-based clustering of haplotypes was observed in ITS2 and mtCO1. While our results validate the utility of ITS2 for Frankliniella occidentalis, extreme caution should be used in applying this marker to taxonomic characterization of other thrips species. The mitochondrial gene mtCO1 should be considered a preferable marker for diagnostics over Internal transcribed spacer (ITS) in two out of three thrips species due to significantly lower levels of potentially problematic intragenomic variation. Possible reasons for discrepancies in intragenomic variation among genes are discussed.