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Int. J. Mol. Sci. 2017, 18(10), 2100; doi:10.3390/ijms18102100

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

1
Department of Entomology and Nematology, Mid-Florida Research and Education Center, University of Florida, Apopka, FL 32703, USA
2
U.S. Horticultural Research Laboratory, USDA-ARS, Fort Pierce, FL 34945, USA
3
Department of Entomology and Nematology, Tropical Research and Education Center, University of Florida, Homestead, FL 33031, USA
4
Present Address: U.S. Meat Animal Research Center, USDA-ARS, Clay Center, NE 68933, USA
*
Author to whom correspondence should be addressed.
Received: 31 August 2017 / Revised: 28 September 2017 / Accepted: 30 September 2017 / Published: 6 October 2017
(This article belongs to the Special Issue Molecular Entomology of Insects of Economic Importance)
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Abstract

The mitochondrial cytochrome oxidase I gene (mtCO1) and the ribosomal internal transcribed spacer 2 region (ITS2) 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 variation within these two marker regions in the family Thripidae, and determine if this variation would affect the utility of markers in thrips molecular diagnostics. For each species, intragenomic (within individual) variation and intergenomic (among individuals) variation was assessed by cloning and sequencing PCR-amplified copies. Intergenomic variation was generally higher than intragenomic variation except in cases where intergenomic variation was very low, as in mtCO1 from S. dorsalis and F. occidentalis. Intragenomic variation was detected in both markers in all three of the thrips species, however, 2–3 times more intragenomic variation was observed for ITS2 than mtCO1 in both S. dorsalis and T. palmi. Furthermore, levels of intragenomic variation were low for both of the genes in F. occidentalis. In all of the three thrips species, no sex-based clustering of haplotypes was observed in either marker. Unexpected high intragenomic variation in ITS2 for two of three thrips species did not interfere with thrips diagnostics. However, caution should be taken in applying ITS2 to certain studies of S. dorsalis and T. palmi when high levels of intragenomic variation could be problematic or confounding. In such studies, mtCO1 may be a preferable marker. Possible reasons for discrepancies in intragenomic variation among genomic regions are discussed. View Full-Text
Keywords: cytochrome oxidase 1 (CO1); internal transcribed spacer (ITS2); intergenomic variation; genetic diversity; chilli thrips; melon thrips; western flower thrips cytochrome oxidase 1 (CO1); internal transcribed spacer (ITS2); intergenomic variation; genetic diversity; chilli thrips; melon thrips; western flower thrips
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MDPI and ACS Style

Kumar, V.; Dickey, A.M.; Seal, D.R.; Shatters, R.G.; Osborne, L.S.; McKenzie, C.L. 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. Int. J. Mol. Sci. 2017, 18, 2100.

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