Non-coding RNAs (ncRNAs) comprise a set of abundant and functionally diverse RNA molecules. Since the discovery of the first ncRNA in the 1960s, ncRNAs have been shown to be involved in nearly all steps of the central dogma of molecular biology. In recent years, the pace of discovery of novel ncRNAs and their cellular roles has been greatly accelerated by high-throughput sequencing. Advances in sequencing technology, library preparation protocols as well as computational biology helped to greatly expand our knowledge of which ncRNAs exist throughout the kingdoms of life. Moreover, RNA sequencing revealed crucial roles of many ncRNAs in human health and disease. In this review, we discuss the most recent methodological advancements in the rapidly evolving field of high-throughput sequencing and how it has greatly expanded our understanding of ncRNA biology across a large number of different organisms.

Advances in Non-Coding RNA Sequencing.

A new opening for the tricky untargeted investigation of natural and modified short peptides.

Abstract Insect general odorant-binding proteins (GOBPs) play irreplaceable roles in filtering, binding, and transporting host odorants to olfactory receptors. Grapholita funebrana (Treitscheke) (Lepidoptera: Tortricidae), an economically important pest of fruit crops, uses fruit volatiles as cues to locate host plants. However, the functions of GOBPs in G. funebrana are still unknown. Three GOBP genes, namely, GfunGOBP1, GfunGOBP2, and GfunGOBP3, were cloned, and their expression profiles in different tissues were detected by the method of real-time quantitative PCR (RT-qPCR). The binding properties of recombinant GfunGOBPs (rGfunGOBPs) to various ligands were investigated via fluorescence binding assays. The three GfunGOBPs were mainly expressed in the antennae of both male and female moths. All these three rGfunGOBPs could bind to sex pheromones, while having varying affinities toward these pheromones. The three rGfunGOBPs also displayed a wide range of ligand-binding spectrums with tested host odorants. The rGfunGOBP1, rGfunGOBP2, and rGfunGOBP3 bound to 34, 33, and 30 out of the 41 tested odorants, respectively. Three rGfunGOBPs had overlapping binding activities to β-myrcene, (-)-α-phellandrene, and ethyl isovalerate with the Ki less than 3.0 μM. The rGfunGOBP1 and rGfunGOBP3 could selectively bind to several insecticides, whereas rGfunGOBP2 could not. Three rGfunGOBPs had the dual functions of selectively binding to sex pheromones and host odorants. Moreover, the rGfunGOBP1 and rGfunGOBP3 can also serve as ‘signal proteins’ and bind to different insecticides. This study contributed to elucidating the potential molecular mechanism of the olfaction for G. funebrana, and thereby promotes the development of effective botanical attractants or pheromone synergists to control G. funebrana. 

https://academic.oup.com/jee/advance-article-pdf/doi/10.1093/jee/toac055/43532369/toac055.pdf

OUP accepted manuscript

Long non-coding RNA (lncRNA) research has emerged as an independent scientific field in recent years. Despite their association with critical cellular and metabolic processes in plenty of organisms, lncRNAs are still a largely unexplored area in mosquito research. We propose that they could serve as exceptional tools for pest management due to unique features they possess. These include low inter-species sequence conservation and high tissue specificity. In the present study, we investigated the role of ovary-specific lncRNAs in the reproductive ability of the Asian tiger mosquito, Aedes albopictus. Through the analysis of transcriptomic data, we identified several lncRNAs that were differentially expressed upon blood feeding; we called these genes Norma (NOn-coding RNA in Mosquito ovAries). We observed that silencing some of these Normas resulted in significant impact on mosquito fecundity and fertility. We further focused on Norma3 whose silencing resulted in 43% oviposition reduction, in smaller ovaries and 53% hatching reduction of the laid eggs, compared to anti-GFP controls. Moreover, a significant downregulation of 2 mucins withing a neighboring (∼100 Kb) mucin cluster was observed in smaller anti-Norma3 ovaries, indicating a potential mechanism of in-cis regulation between Norma3 and the mucins. Our work constitutes the first experimental proof-of-evidence connecting lncRNAs with mosquito reproduction and opens a novel path for pest management. 

/pdf/a-species-specific-lncrna-modulates-the-reproductive-ability-3bqqfxnl.pdf

A species-specific lncRNA modulates the reproductive ability of the asian tiger mosquito

Full-length codling moth transcriptome atlas revealed by single-molecule real-time sequencing.

Long noncoding RNAs (lncRNAs) have emerged as an important class of transcriptional regulators in cellular processes. The past decades have witnessed great progress in lncRNA studies in a variety of organisms. The codling moth (Cydia pomonella L.) is an important invasive insect in China. However, the functional impact of lncRNAs in this insect remains unclear. In this study, an atlas of codling moth lncRNAs was constructed based on publicly available RNA-seq datasets. In total, 9875 lncRNA transcripts encoded by 9161 loci were identified in the codling moth. As expected, the lncRNAs exhibited shorter transcript lengths, lower GC contents, and lower expression levels than protein-coding genes (PCGs). Additionally, the lncRNAs were more likely to show tissue-specific expression patterns than PCGs. Interestingly, a substantial fraction of the lncRNAs showed a testis-biased expression pattern. Additionally, conservation analysis indicated that lncRNA sequences were weakly conserved across insect species, though additional lncRNAs with homologous relationships could be identified based on synteny, suggesting that synteny could be a more reliable approach for the cross-species comparison of lncRNAs. Furthermore, the correlation analysis of lncRNAs with neighbouring PCGs indicated a stronger correlation between them, suggesting potential cis-acting roles of these lncRNAs in the regulation of gene expression. Taken together, our work provides a valuable resource for the comparative and functional study of lncRNAs, which will facilitate the understanding of their mechanistic roles in transcriptional regulation.

/pdf/the-landscape-of-lncrnas-in-cydia-pomonella-provides-19uyhhxca2.pdf

The landscape of lncRNAs in Cydia pomonella provides insights into their signatures and potential roles in transcriptional regulation

Insect olfaction is vital for foraging, mating, host-seeking, and avoidance of predators/pathogens. In insects, odorant binding proteins (OBPs) are involved in transporting hydrophobic odor molecules from the external environment to receptor neurons. The codling moth, Cydia pomonella, one of the most destructive insect fruit pests, causes enormous economic losses. However, little is known about the number, variety, gains and losses, and evolution of OBP genes in C. pomonella. Here we report the identification of 40 OBPs in C. pomonella, most (75%) of which are classic OBPs, using genomic and transcriptomic analyses. Two OBP genes were lost in C. pomonella relative to possible distant ancestor in Lepidoptera lineage based on an analysis of gene gains and losses. The phylogenetic tree and chromosome location showed that the expansion of OBP genes mainly resulted from tandem duplications, as the CpomGOBP2 gene was duplicated twice along with loss of CpomPBPB. Two positive selection sites of the CpomGOBP1 gene were identified while other OBP genes evolved under purifying selection. Our results provide fundamental knowledge of OBP genes allowing further study of their function in C. pomonella.

/pdf/comparative-genomics-provide-insights-into-function-and-4l2xf2sjop.pdf

Comparative Genomics Provide Insights Into Function and Evolution of Odorant Binding Proteins in Cydia pomonella

A comprehensive atlas of lysine acetylome in onion thrips (Thrips tabaci Lind.) revealed by proteomics analysis

Gene expression patterns of Cydia pomonella granulovirus in codling moth larvae revealed by RNAseq analysis.

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Papers

The landscape of lncRNAs in Cydia pomonella provides insights into their signatures and potential roles in transcriptional regulation

Comparative Genomics Provide Insights Into Function and Evolution of Odorant Binding Proteins in Cydia pomonella

A comprehensive atlas of lysine acetylome in onion thrips (Thrips tabaci Lind.) revealed by proteomics analysis

Gene expression patterns of Cydia pomonella granulovirus in codling moth larvae revealed by RNAseq analysis.