Tetranychus urticae is an important agricultural pest that feeds on more than 1100 plant species. To investigate gene expression network in development process of deutonymph, a comprehensive transcriptome analysis of different developmental time points of deutonymph in T. urticae was performed. Comparing with expression profile of 7 h, 309, 876, 2736, and 3432 differential expression genes were detected at time points 14 h, 21 h, 28 h, and 35 h, respectively. The expression dynamic analysis indicated that genes in hormone- (ecdysteroid and juvenile hormone) and cuticle- (chitin and cuticle proteins) related pathways were indispensable for development process in deutonymph. Among hormone related pathway genes, the ecdysteroid biosynthesis pathway genes were highly expressed at the growth period of development process, which is opposite to the expression patterns of juvenile hormone biosynthesis pathway genes. For cuticle related pathway genes, 13 chitinase genes were identified in the genome of T. urticae, and 8 chitinase genes were highly expressed in different time points of developmental process in the deutonymph of T. urticae. Additionally, 59 cuticle protein genes were identified from genome, and most of the cuticle protein genes were expressed in the molting period of developmental process in deutonymph. This study reveals critical genes involved in the development process of deutonymph and also provides comprehensive development transcriptome information for finding more molecular targets to control this pest.

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.

MicroRNA-mediated post-transcriptional regulations are involved in many physiological processes in insects, such as development, reproduction, metamorphosis, immunity, and insecticide resistance. In this study, the transcript profile of miRNAs over the developmental transitions of the citrus red mite Panonychus citri (McGregor) including egg hatching and three molting processes from egg to adult were analyzed. A total of 142 miRNAs, including 74 known, 64 novel miRNAs, 14 isomiRNAs and 12 duplicate miRNAs, were identified. Meanwhile, 21 differentially expressed miRNAs (DEMs) over the developmental transitions were analyzed, including 14 and 8 DEMs in egg hatching and molting process from mite deutonymph to adult. Amongst these DEMs, there were 2 and 2 in the developmental transitions from larva to protonymph and the protonymph to deutonymph, respectively, suggesting a complicated role of miRNAs in the regulation of developmental transitions. Additionally, two miRNAs were identified as reference miRNAs for mites from 7 candidate reference miRNAs after a systematic evaluation about their relative expression patterns at different developmental stages of both Panonychus citri and Tetranychus urticae. Furthermore, feeding miR-34-5p mimic in the deutonymph of P. citri resulted in a significant decrease in adult eclosion rate, and miR-92c and miR-305-5p also had similar functions in the emergence process from deutonymph to adult. Moreover, over expression of miR-315 and let-7a significantly inhibited egg hatching by dripping miRNA mimic on the back of mites with a microinjector. This study identified critical miRNAs involved in the developmental transitions of this important agricultural pest P. citri from egg hatching to adult eclosion, and thus provided a useful resource for exploring the application of miRNAs in mite pest control.