| The transcriptome is the set of all RNA molecules, including mRNA, rRNA, tRNA, and other non-coding RNA produced in one or a population of cells under a specific developmental stage or physiological condition. In the study of agricultural pests, the transcriptome data researching is conducive to understand some important biological processes and molecular mechanisms, such as growth, metabolic regulation and resistant mechanism. With the development of high-throughput sequencing and information technology, data volume of transcriptome is increasing rapidly. So far, there are more than 100 insects’ transcriptome that have been sequenced and published, and how to mining the biological significances appears especially important. Previously, data analyzing and information mining of transcriptome is mainly directed against the protein-coding genes, but more than 50 percentage of the transcriptome which is non-coding genes have few studies. With the improvement of the knowledge and research of non-coding genes, the study of non-coding genes has recently become a hot spot. MicroRNA is one of the non-coding genes which plays an important role in gene expression, cell cycle, timing and other aspects of the development.In this article, all the research is focused around the microRNA. Firstly, a pipeline to identify microRNAs from insect transcriptome sequenced data was developed and used to predict microRNAs from four tissues of diamondback moth (Plutella xylostella). Then, we studied the interaction between microRNA and its targets in order to reveal the important mechanism of gene regulation. Finally, from the practical application of prevention and controlling of agricultural pests resistance, we predicted microRNA and resistance genes from transcriptome data in five agricultural pests and explored how the microRNAs regulate resistant gene in insect to develop resistance.1. MicroRNA identification from transcriptome data of P. xylostellaThe transcriptome data of egg, larva, pupa, and adult from P. xylostella moth was downloaded from SRA database. We predicted microRNAs according to the conservation, stable hairpin structures and other characteristics combining the result of triplet-SVM. Finally 185 microRNAs were found which is 103,51,92,115 distributed in egg, larva, pupae and adult respectively. It shows that most of the microRNAs were expressed in specific development stages and the maximum number of specifically expressed microRNAs is in the adult, minimum in the larva.2. MicroRNA and target interactions in P. xylostellaThe targets of the microRNAs were predicted by the Miranda software and the result shows that 179 of front predicted microRNA have 13,954 site at 4,674 genes. A mount of microRNAs in adult indicate the highest level of regulation by microRNA, followed by eggs and pupa, larvae. According to the annotation by KEGG, in adult the most genes regulated by the microRNA are mainly distributed in the pathways related with metabolize, and others genes also regulated most in adult and lowest in larva associated with cell processing, digestive system, excretory system and development pathway and etc.3. Resistant genes and microRNAs in insect transcriptomeIn this paper, we gained genes and microRNAs related to resistant from transcriptome data of 12 agricultural pests, and analyzed evolutionary relationships to reveal the difference and connection between these genes from perspective of multi-species and multi-gene. Then we predicted microRNAs in five Lepidoptera insects to research their targets and discovered the development of resistance is related with some microRNAs. We discovered that most of these genes exist microRNA target sites in their 3’UTR region, such as p450, ryanodine receptor, γ-aminobutyric acid, carboxylesterase, acetylcholine receptor, glutathione S-transferase, cadherin, glycosyltransferase. It appeared that the genes related to resistant may be controlled by microRNAs. |
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