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The Characteristics and Functions of SSRs and SNPs Based on the Transcriptome of Tuta absoluta Exposed to Different Concentrations of Abamectin and Chlorantraniliprole
Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Institute of Entomology, Guizhou University, Guiyang 550025, China
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Insects 2025, 16(5), 446; https://doi.org/10.3390/insects16050446
Submission received: 7 March 2025
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Revised: 15 April 2025
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Accepted: 18 April 2025
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Published: 24 April 2025
(This article belongs to the Special Issue Women’s Special Issue Series: Insects)
Simple Summary
Tuta absoluta (Meyrick) is a globally distributed invasive pest. Its larvae form tunnels in leaves when feeding on the leaf mesophyll. In the research based on full-length transcriptome and comparative transcriptome data for T. absoluta by using the combined sequencing technology, a total of 25,123 SSR loci and 332,537 SNP loci were identified. Through the analysis of GO, COG annotations, and the KEGG pathway database, it was revealed that the majority of SSR-transcripts and SNP-transcripts were involved in fundamental cellular metabolic functions. These findings might help us understand how T. absoluta adapts to or resists the abamectin and chlorantraniliprole.
Abstract
Tuta absoluta (Meyrick) is an important invasive pest that seriously affects the yield and quality of tomatoes. In this study, based on the previously obtained transcriptome data, a total of 25,123 SSR loci and 332,537 SNP loci were identified. The identified SSRs had occurrence and appearance frequencies of 28.62% and 40.60%, respectively. SSRs with a length equal to or greater than 12 bp constituted 58.25% of the total SSR loci. Through the analysis of GO, COG annotations, and the KEGG pathway database, it was revealed that the majority of SSR-transcripts were involved in fundamental cellular metabolic functions. In addition, the frequency of SNP occurrence was approximately one SNP locus per 175 base pairs (bp), and the transition type was the main variant type. The functional annotations of SNP-transcripts were primarily concentrated in biological synthesis pathways such as peroxisome, RNA transport, carbon metabolism, and protein processing in the endoplasmic reticulum. These synthesis pathways are involved in the detoxification mechanism of T. absoluta and contribute to its enhanced survival under pesticide susceptibility. These findings provide valuable data for constructing genetic maps, assessing genetic diversity, and determining functional orientation in insects, and they also provide basic data for the molecular mechanism of T. absoluta ‘s response to pesticide susceptibility.
Keywords:
Tuta absoluta; transcriptome analysis; molecular marker; SSR; SNP
