Reannotation Of The Protein-Coding Genes In Shewanella Loihica PV-4 Genome

The prediction of protein coding genes in microbial genomes has lasted for nearly thirty years. Due to lack of intron, it was thought that gene prediction is relatively simple in microbial genomes. However, more and more researches showed that there are extensive annotation errors of protein-coding genes in microbial genomes. The accumulations of such errors in public databases may have the potential for propagation effect, which will decrease greatly the value of public databases and even cause false researching conclusions. Therefore, the reannotation method was proposed by combining RPGM(a program designed for filtering the over annotated protein-coding genes in microbial genome) program and four ab initio gene finding programs(Prodigal, GeneMark.hmm, Glimmer 3.02, and Rast). In the present study,Shewanella loihica PV-4, as an excellent exoelectrogen in microbial fuel cell, were firstly reannotated based on the hybrid method. As a result, one over-annotated protein coding genes was identified and 30 missing protein coding genes were predicted. Based on the function of known protein coding genes, the Ac, MCC, and AUC were 99.93%, 0.9986 and 0.9999 respectively. Six of 30 missing protein coding genes are assigned biological functions based on BLAST and COG method, including two phosphoribosyl glycinamide formyltransferase 2, two glucose-1-phosphate thymidylyl transferase, one membrane protein and one transposase. These genes may play an important role in ion exchange and protein modification. The further analysis shows that the proposed algorithm is accurate and reliable. This reannotating algorithm was applied to the other 9 Shewanella genomes, as a result, 64over-annotated genes and 1036 missing genes were filtered. Further functional analysis showed that 261 missing genes had specific biological function, and 259 missing genes had COG classification. In 261 function known missing genes, "transposase" has 123, accounting for about 47% of the total number of definite gene function. There are 16 "Integrase", 5 "dehydrogenase", 3 " Cytochrome C " and so on.These genes may play an indispensable role in ion exchange and signal transduction.In 259 missing genes with COG classification, 182 new genes are associated with the cytochrome C, suggesting that these genes are related to ion transport and protein modification; 30 new genes are associated with the flagellar gene, which suggest that these genes are closely related to cell movement; 48 new genes are related to the chemokines, indicating that these genes are closely related to cell movement and signal transduction. Therefore, these works are much reliable, and also provide alternative method in microbial genomes.