Species composition and virus detection of thrips (Thysanoptera: Thripidae) in Iraqi cucumber greenhouses, with insights into insecticide susceptibility

Abstract

The objective of this study was to characterize thrips populations associated with greenhouse-grown cucumber (Cucumis sativus L.) in northern and central Iraq.The study identified the predominant thrips species, detected associated plant viruses, and investigated molecular mechanisms potentially involved in insecticide resistance through transcriptome-based analysis of resistance-related genes. The findings provide insights into thrips diversity, virus associations, and regional resistance patterns to support sustainable integrated pest management (IPM).Whole-transcriptome RNA sequencing (RNA-Seq) was performed using the DNBSEQ platform with paired-end 100 bp (PE100) reads. High-quality transcriptomic datasets were obtained for the Ath-North and Ath-Middle populations, with Q20 values exceeding 98.86%. Molecular identification based on the mitochondrial cytochrome c oxidase subunit I (COX1) gene revealed that Thrips palmi Karny was the predominant species, representing 67% and 64% of the populations in northern and central Iraq, respectively, whereas Thrips tabaci Lindeman accounted for 33% and 36%. COX1 sequences were deposited in GenBank (PZ169500–PZ169509), and phylogenetic analysis showed 98–100% similarity with global isolates. Transcriptomic analysis detected three plant viruses: Arabidopsis latent virus 1 (ArLV1), Cucumber green mottle mosaic virus (CGMMV), and Cucurbit aphid-borne yellows virus (CABYV). ArLV1 and CGMMV are reported for the first time in Iraq. Differential gene expression analysis showed reduced expression of the Cytochrome P450 gene in the central population (log₂FC = −2.15) and increased expression of the Voltage-Gated Sodium Channel (VGSC) gene in the northern population (log₂FC = +0.91), indicating regional variation in insecticide resistance mechanisms. These findings provide a molecular basis for developing region-specific, environmentally sustainable IPM strategies for greenhouse cucumber production in Iraq.