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. 2023 Apr 6;14(4):363.
doi: 10.3390/insects14040363.

Combined PacBio Iso-Seq and Illumina RNA-Seq Analysis of the Tuta absoluta (Meyrick) Transcriptome and Cytochrome P450 Genes

Min Liu  1 , Feng Xiao  1 , Jiayun Zhu  1 , Di Fu  1 , Zonglin Wang  1 , Rong Xiao  1
Affiliations

Combined PacBio Iso-Seq and Illumina RNA-Seq Analysis of the Tuta absoluta (Meyrick) Transcriptome and Cytochrome P450 Genes

Min Liu et al. Insects. .

Abstract

Tuta absoluta (Meyrick) is a devastating invasive pest worldwide. The abamectin and chlorantraniliprole complex have become an alternative option for chemical control because they can enhance insecticidal activity and delay increased drug resistance. Notably, pests are inevitably resistant to various types of insecticides, and compound insecticides are no exception. To identify potential genes involved in the detoxification of abamectin and chlorantraniliprole complex in T. absoluta, PacBio SMRT-seq transcriptome sequencing and Illumina RNA-seq analysis of abamectin and chlorantraniliprole complex-treated T. absoluta were performed. We obtained 80,492 non-redundant transcripts, 62,762 (77.97%) transcripts that were successfully annotated, and 15,524 differentially expressed transcripts (DETs). GO annotation results showed that most of these DETs were involved in the biological processes of life-sustaining activities, such as cellular, metabolic, and single-organism processes. The KEGG pathway enrichment results showed that the pathways related to glutathione metabolism, fatty acid and amino acid synthesis, and metabolism were related to the response to abamectin and chlorantraniliprole complex in T. absoluta. Among these, 21 P450s were differentially expressed (11 upregulated and 10 downregulated). The qRT-PCR results for the eight upregulated P450 genes after abamectin and chlorantraniliprole complex treatment were consistent with the RNA-Seq data. Our findings provide new full-length transcriptional data and information for further studies on detoxification-related genes in T. absoluta.

Keywords: Illumina RNA-seq analysis; PacBio Iso-Seq analysis; Tuta absoluta; cytochrome P450.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Venn diagram of lncRNA transcripts identified from PLEK, CNCI, CPC, and Pfam. The values in the figure represent the common and non-common parts of each subset.
Figure 2
Figure 2
Homologous species distribution of T. absoluta annotated in NR.
Figure 3
Figure 3
KEGG enrichment analysis of DETs compared between different concentrations. Subfigure (A) represents the enrichment results between CK and each treatment group, and subfigure (B) represents the enrichment results between the treatment group and the treatment group. The round dot indicates down-regulated genes, the triangle indicates up-regulated genes, and the square indicates both up-regulated and down-regulated genes. The abscissa represents the enrichment factor; the larger the enrichment factor, the more significant the enrichment level of the differentially expressed transcripts in this pathway. The q-value is the p value after correction for multiple hypothesis testing. The smaller the q-value, the more reliable the enrichment significance of the differentially expressed transcripts in this pathway.
Figure 4
Figure 4
Phylogenetic analysis of 21 P450 genes of T. absoluta and related species’ P450s.
Figure 5
Figure 5
Validation of P450 genes expressions by RT-qPCR.
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