表現序列標幟(EST)功能註解分析的新流程

Abstract

Expressed sequence tag (EST) is the fragment of cDNA sequence. Direct study of EST is therefore helpful to obtain the gene expression information. A complete and rapid procedure including EST functional annotation, classification and representation statistics was established as the followings. The first step was to use unique sequences of high quality from removing redundancy after clustering and assembling by CAP3 software to homology search TC (tentative consensus sequence) database of TIGR (The Institute of Genomic Research). The second step was to link the functional catalogs of GO (Gene Ontology) and MIPS (Munich Information Center for Protein Sequences) from tentative annotation of the selected TC sequences. Finally the statistics of gene functional representation was calculated. Brown planthopper [Nilaparvata lugens (Stal.)] is the major pest of rice (Oryza sativa L.) in Asia. In order to know the mechanisms of rice genes resistant to brown planthopper, we used rice EST sequences induced by brown planthopper from NCBI-dbEST database as materials to compare the gene expression differences between the resistant and sensitive varieties. Using our procedure of EST functional annotation and analysis, the results showed that the dominant gene function of rice ESTs induced by brown planthopper was biological process based on GO functional category. According to minute classification of MIPS functional category system, the genes of resistant rice variety expressed richer metabolism function than that of sensitive rice variety. The resistant rice variety switched on the gene functions related to cell rescue/defense and virulence, transcription, and cell growth/morphogenesis, but sensitive variety did not.