Development And Application Of Analysis System For EST Of Major Crops

With the development of plant genomics, a great deal of valuable data is generated, of which EST (expressed sequence tag) is an important part. It has been an emphasis part of nowadays research to mine valuable information from these huge number EST data by bioinformatics technique. The research involves the following two parts.To analyze EST of major crops on a large scale, automatic analysis system with integrating functions is developed. At the same time, for facilitating other studies in our lab, the system can also supply bioinformatic service. Therefore, the developed system for analyzing EST of major crops includes two parts: data mining and bioinformatic service. Data mining of the system is the core, which includes standalone blast (blast basic local alignment search tool) system, EST clustering system, cSNP (single nucleotide polymorphism) and EST-SSR (simple sequence repeat) mining system, and EST silico-cloning system. Using in-house and free bioinformatic softwares, we developed the system. Standalone blast system was built by integrating the blast package of NCBI (The National Center for Biotechnology Information), ours databases and some programs analyzing blast results such as homology analysis and auto-annotation. Two EST clustering systems were generated by integrating Cap3 and Phrap respectively. cSNP mining system included two programs, one could mine SNP from abundant EST; the other could find EST homologous to a query EST from EST database and then detects i ts c andidate SNP. The core of EST-SSR m ining s ystems, S SRFinder c ould find perfect and compound SSR, and also give exactly statistical analysis about all kinds of SSR. The program was developed for EST silico-cloning with Cap3 and Phrap. The bioinformatic service part was involved web bioinformatic analysis system and all kinds of data or results MIS (Manage Information System) for data analysis and query on line.By using the system and softwares, EST of wheat, barley etc. were analyzed on a large scale. The contents involved five aspects:1. Orthology comparisons of major crops. Orthologies of major crops were screened by E value (le-6) and homology analysis program (similarity of the whole sequence more than 50%) respectively. The orthology of wheat and barley was the highest followed by wheat with rice and maize respectively.2. Analysis of SSR in major crops. Public available EST of wheat, rice, maize and soybean were used to search for the types and frequencies of SSR with motif length of l-6bp long. The frequency of EST-SSR was one every 11.81kb in rice, 17.42 kb in wheat, 23.80kb in soybean, and 28.32kb in maize respectively. Trinucleotide repeat was the most abundant SSR types. Compared with the dicot, the monocots preferred GC-rich tri- and hexa- motifs very much, especially in rice.3. Comparative analysis of EST and SSR-EST of major crops. Comparing orthologies between EST, SSR-containing EST (SSR-EST) of wheat, maize, and soybean with rice BAC/PAC, the number of SSR-EST from wheat or maize orthologious to rice was significantly less than that of wheat or maize EST orthologious to rice. Moreover, only 1707 SSR-EST were mined from 101299 wheat FST orthologious to rice, maize and barley.4. Comparative analysis of wheat genetic maps with rice physical maps. By comparing 164 genetic markers of wheat with 3 281 o rdered B AC/PAC clones of rice, 94 markers orthologous to rice were located on the physical map of rice. And it would facilitate comparative relationship of wheat and rice.5. Prediction of the number of expressed genes of major crops. The number of expressed genes of wheat, rice and corn were predicted using EST clustering system. There were more than forty thousand genes obtained from 160000 wheat EST.