Dissertation > Agricultural Sciences > Plant Protection > Pest and Disease Control > Plant pest and its control

Gene Prediction and Sequence Analysis of Insect Odorant Binding Protein, Chemosensory Protein and Ryanoding Receptor in Eight Transcriptome Data

Author ZhangZuo
Tutor LiFei
School Nanjing Agricultural College
Course Agricultural Entomology and Pest Control
Keywords Odorant binding proteins (OBPs) Chemosensory proteins (CSPs) Ryanodine receptor ( RyRS ) Bioinformatics Transcriptome Evolutionary Analysis
CLC S433
Type Master's thesis
Year 2011
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Gene cloning is an important task in insect molecular biology. The traditional strategy to amplify a gene relies on using degenerate primers and RACE. However, this strategy is time-consuming with low efficiency. As rapid decreasing of sequencing cost in recent years, transcriptome and expressed sequence tags (EST) provide an efficient method to obtain gene sequences.In agriculture, rice leaffolder (Cnaphalocrocis medinalis), beet armyworm (Spodoptera exigua),Diamondback moth (Plutella xylostella) striped riceborer (Chilo suppressalis),yellow rice borer (Tryporyza incertulas),whiteflies (Bemisia tabaci),small brown planthopper (Laodelphax striatellus) and Colorado potato beetle (Leptinotarsa decemlineata) cause damage to crops and lead to economic loss. In this work, we conducted homology searching of Odorant binding protein (OBP), chemosensory proteins (CSPs) and Ryanodine receptor (RyR) genes from the transcriptome data of above mentioned pests. The gene structural characteristic and molecular evolution were also performed.1) Insect odorant-related genesInsect binding proteins (OBPs) and chemosensory proteins (CSPs) play an important role in chemical communication of insects. Studying of OBP and CSP helps us to further understand olfactory protein of agricultural pests. Uncovering the co-evolution and interaction between insects and their environment can be exploited to in controlling agricultural pests.We predicted 7,7 and 6 candidate OBPs from diamondback moth, whiteflies and small brown planthopper respectively. After the process of sequence assembling and removing the duplication sequences, we found 5,4 and 4 full-length OBP sequences from the above mentioned three species, respectively.For the genes of CSP,14 pupative CSPs were predicted in rice leaffolder,21 in beet armyworm,8 in diamondback moth,10 in striped rice borer,12 in yellow rice borer,7 in whiteflies,11 in small brown planthopper, and 9 in Colorado potato beetle. In total, there were 92 putative CSP sequences found in 8 species. After sequence assembling, full-length sequences filtering and removing duplication sequences, we finally found 52 CSP full-length sequences in the 8 insects.We also performed evolutional analsyis of OBP and CSP genes. We found that the C-pattern of CSPs were more conserved than that of OBPs. In the evolution tree of OBP, the genes were mainly clustered by insect Orders, indicating that most genes appeared after diversification of Orders. However, the situation is different for CSPs. In the evolution tree of CSPs, only one clade is clustered of CSP in Hemiptera. Some CSPs are clustered of CSPs in Lepidoptera and others are clustered of CSPs in both insects. These results indicated that some CSPs are ancient, whereas others appeared after the diversification of Orders.2) Ryanodine receptor genesRyanodine receptor (RyR) is the target of diamide insecticides and has been exploited to control Lepidoptera rice pests. By using the data of transcriptome, we predicted RyR genes from agricultural pests.For the RyR genes,34,9,20,48,14,19,14 and 22 sequences were predicted respectively in rice leaffolder, beet armyworm, diamondback moth, striped rice borer, yellow rice borer, whiteflies, small brown planthopper and Colorado potato beetle. After assembling,33,9,10,18,9,18,9 and 22 candidate genes were obtained. The known sequences of RyR genes in 8 insects were analyzed. Though the full length of Ryr gene is about 15Kb and is difficult to be amplified, the results showed that the assembled RyR partial sequences covered more than 85 percent of full-length RyR genes in beet armyworm, striped rice borer, whiteflies and small brown planthopper.

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