Computational protocol: A comprehensive omics analysis and functional survey of cuticular proteins in the brown planthopper

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Protocol publication

[…] Insect CP amino acids and gene sequences were obtained from NCBI (https://www.ncbi.nlm.nih.gov/), EnsemblMetazoa (metazoa.ensembl.org/), CutProtFam (aias.biol.uoa.gr/CutProtFam-Pred/home.php) (), and CuticleDB (bioinformatics2.biol.uoa.gr/cuticleDB/) (). The common motifs of CPs from D. melanogaster, Bombyx mori, A. gambiae, Tribolium castaneum, Apis mellifera, and Locusta migratoria were used as queries against the BPH genome (https://www.ncbi.nlm.nih.gov/, BioProject PRJNA177647; 27,571 coding protein sequences) and transcriptomic databases (https://www.ncbi.nlm.nih.gov/sra, accession no. SRX023419; 21,908 coding protein sequences). The full-length cDNA sequences were obtained from transcriptomic databases, and most of them were confirmed by RT-PCR. The full cDNA sequences of some CP genes were cloned by using RACE core sets (catalog nos. 6107 and 6106; TaKaRa) according to the manufacturer’s instructions. The primers used are shown in Dataset S1. [...] The ORF prediction was performed on the Softberry website. The SMART program (smart.embl-heidelberg.de/) was used for the identification of modular domains. The signal peptide prediction program SignalP 4.1 server (www.cbs.dtu.dk/services/SignalP/) was used to predict N-terminal signal peptides. The multiple sequence alignment of the CPLCP family proteins was carried out by using ClustalX software (). The phylogenetic trees were constructed via the neighbor-joining method by using the MEGA6.06 program (). Homologous relationships were determined by bootstrap analysis based on 1,000 or 5,000 replications, as each legend describes. […]

Pipeline specifications

Software tools SignalP, Clustal W, MEGA
Applications Phylogenetics, Non-coding RNA analysis
Organisms Nilaparvata lugens, Oryza sativa
Diseases Byssinosis, Renal Insufficiency