Discoveryof Insect Specificsequences And Noncoding Rna From Transcriptome Data

Disappearance of old genes and emergence of new genesare important evolutional phenomna, which is the result of natural selection. The ogransims gain strong ability of adapting to environment pressure. A huge amount of sequences have been produced by the next-generation sequencing technique. Exploring insect-specific sequences would be great helpful to find target genes for pest control via gene silecneing strategies. Moreover, it can provide a new understanding of emergence mechanism of new gene in evolution.In this paper, a bioinformatics pipeline was established to find the insect specific sequences from four Lepidoptera species, Chilo supressalis, Scirpophaga incertulas, Cnaphalocrocis medinalis, Spodoptera exigua and four Homoptera species, Laodelphax striatellus, Nilaparvata lugens, Sogatella furcifera, Bemisia tabaci.. First, the transcriptome data were annotated by Blastx. Then, we downloaded the gene dataset of fifteen species, Bos Taurus, Caenorhabditis elegans, Canis familiaris, Danio rerio, Gallus gallus, Homo sapiens, Mus musculus, Saccharomyces cerevisiae, Sus scrofa, Bombyx mori, Drosophila melanogaster, Nopheles gambiae, Acyrthosiphon pisum Harris, Tribolium caslaneum, Apis mellifera, form the GenBank database. Last, the insect specific sequences were obtained by comparative genomic analysis using these dataasets. Gene ontology (GO) anaysis were performed for the insect specific sequences.Noncoding RNA genes have been found to play important roles.We predictednoncoding RNAswith the software PORTRAIT. The predicted noncoding RNA genes were used to search the well known database of NONCODE, RFAM, RNADB. As results, only a limited number of noncoding RNA genes were found. An exception was that many noncoding RNA genes were found in S. furcifera. We reasoned that the seqeunces of noncoding RNA are not conserved, which can not be found by homology searching. Another reason is that the sequences of noncoding RNA might be lost in the sequencing procedures of Solexa, which need be further investigated.