This study has been carried out to give some scientific reasons for genome annotation, shorten the annotating time, and improve the results of gene prediction. Taking the sequence of the 6th chromosome, which has more length sequences than others, of Oryza sativa L. ssp. japonica cv. Nipponbare as analysis data in this research, the gene prediction of monocots module, rice, has been done by using Fgenesh ver. 2.0, and the predicting results have been explored particularly by bioinformatics methods. Results showed that the number of predicted genes for this chromosome was very close to the number of TIGR annotated genes. The majority of the predicted genes were multi-exon genes which had a percentage of 77.52. Length range was very big in the predicted genes. According to the significant match number, multi-exon genes can be predicted more veracity than single exon genes and the support can be reached up to 100% by TIGR annotation and up to 78% by cDNA. From the angle of predicted exons location of multi-exon genes, the internal exons and last exons had a high support of cDNA. The length of internal exons was relatively short in high (> 95% length, > 78% similarity) cDNA and/or TIGR annotation support multi-exon genes, but the first exons and last exons were on the reverse. The majority of single exon genes which had more than 95% in length, and 78% in similarity support by cDNA and/or TIGR annotation was relatively short in length. From the angle of exon number, the majority of the multi-exon genes of high (> 95% length, > 78% similarity) cDNA and/or TIGR annotation support had no more than 5 exon number. It was concluded that the rice gene prediction by Fgenesh was very good but needed modification manually to some extent according to cDNA support after aligning the predicting sequence of genes with cDNA database of rice.
ZHANG Sheng-liLI Dong-fangZHANG Gai-shengWANG Jun-weiNIU Na
To investigate the CMS mechanism of wheat on proteomic level and find the crucial proteins which related to fertility,mitochondria was isolated from young spike of wheat by differential centrifugation and Percoll density-gradient methods.Determined by marker enzyme assays and chlorophyll content,the mainly contaminants in the spike mitochondrial fraction were caused by peroxisomes,plastids and chloroplasts after the first discontinuous Percoll density gradient centrifugation.In order to improve the purity of spike mitochondria,a second 28% Percoll self-forming density gradient centrifugation was further carried out,the result showed that the contaminants were decreased to negligible amount,meanwhile the integrity of mitochondria (88%) was improved to 90%.The spike mitochondria proteins extracted from uninucleate stage of (S)-1376A and (A)-1376B were separated by two-dimensional electrophoresis (2-DE),and the silver stained gels were analyzed by PDQuest 2-DE software,about 326 protein spots could be visualized on the 2-DE maps,and also revealed a similar pattern between the male sterile line and its maintainer line,except 11 spots were differentially expressed.A total of five differentially expressed proteins were analyzed by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS),three of them were identified as manganese superoxide dismutase and T5E216 following NCBInr database by the Mascot software.These results may contribute to further understanding of the mechanisms of CMS in wheat.
