Abstract
Molting is essential for arthropods to grow. As one of the important arthropod pests in agriculture, key spider mite species (Tetranychus and Panonychus) can normally molt three times from the larva to adult stage within a week. This physiological strategy results in the short lifecycle of spider mites and difficulties in their control in the field. Long non-coding RNAs (lncRNAs) regulate transcriptional editing, cellular function, and biological processes. Thus, analysis of the lncRNAs in the spider mite molting process may provide new insights into their roles in the molting mechanism. For this purpose, we used high-throughput RNA-seq to examine the expression dynamics of lncRNAs and mRNAs in the molting process of different development stages in Panonychus citri. We identified 9199 lncRNAs from 18 transcriptomes. Analysis of the lncRNAs suggested that they were shorter and had fewer exons and transcripts than mRNAs. Among these, 356 lncRNAs were differentially expressed during three molting processes: late larva to early protonymph, late protonymph to early deutonymph, and late deutonymph to early adult. A time series profile analysis of differentially expressed lncRNAs showed that 77 lncRNAs were clustered into two dynamic expression profiles (Pattern a and Pattern c), implying that lncRNAs were involved in the molting process of spider mites. Furthermore, the lncRNA–mRNA co-expression networks showed that several differentially expressed hub lncRNAs were predicted to be functionally associated with typical molting-related proteins, such as cuticle protein and chitin biosynthesis. These data reveal the potential regulatory function of lncRNAs in the molting process and provide datasets for further analysis of lncRNAs and mRNAs in spider mites.
Highlights
Long non-coding RNAs are more than 200 bp in length and lack coding capability [1]
To systematically identify the Long non-coding RNAs (lncRNAs) involved in molting process in P. citri, 18 RNA
12,955 known mRNAs were obtained from the transcripts based on the spider mite genome sequences, and 9199 highly reliable putative lncRNAs were identified from the unknown transcripts (Figure 2F)
Summary
Long non-coding RNAs (lncRNAs) are more than 200 bp in length and lack coding capability [1]. As with mRNAs, lncRNAs are transcribed by RNA polymerase II through splicing, capping, and polyadenylation [2]. Compared with mRNAs, lncRNAs have lower expression and sequence conservation, so lncRNAs are hard to identify and annotate based on the conserved sequences [3,4]. The lncRNAs are divided into four categories (sense, antisense, intronic, and intergenic) based on their position and direction of transcription about the protein-coding genes [5]. Sequencing technology has identified abundant lncRNAs in some species and verified lncRNAs to be important regulators of biological processes rather than transcription byproducts [6,7,8,9,10]. LncRNAs could regulate the expression of protein-coding genes by cis-regulation of near genes and trans-regulation of terminal 4.0/). The functional annotation of lncRNAs in insect species has revealed that they can regulate immunity, behavioral plasticity, development, fecundity, and resistance [18,19,20,21,22]
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