Limits...
Identification of new genes in Sinorhizobium meliloti using the Genome Sequencer FLX system.

Mao C, Evans C, Jensen RV, Sobral BW - BMC Microbiol. (2008)

Bottom Line: From these data, we identified 20 new genes.These new gene transcripts were confirmed by RT-PCR and their possible functions were analyzed.Our results indicate that high-throughput sequence analysis of bacterial transcriptomes is feasible and next-generation sequencing technologies will greatly facilitate the discovery of new genes and improve genome annotation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. chmao@vt.edu

ABSTRACT

Background: Sinorhizobium meliloti is an agriculturally important model symbiont. There is an ongoing need to update and improve its genome annotation. In this study, we used a high-throughput pyrosequencing approach to sequence the transcriptome of S. meliloti, and search for new bacterial genes missed in the previous genome annotation. This is the first report of sequencing a bacterial transcriptome using the pyrosequencing technology.

Results: Our pilot sequencing run generated 19,005 reads with an average length of 136 nucleotides per read. From these data, we identified 20 new genes. These new gene transcripts were confirmed by RT-PCR and their possible functions were analyzed.

Conclusion: Our results indicate that high-throughput sequence analysis of bacterial transcriptomes is feasible and next-generation sequencing technologies will greatly facilitate the discovery of new genes and improve genome annotation.

Show MeSH
Length distribution of predicted gene candidates.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2396165&req=5

Figure 1: Length distribution of predicted gene candidates.

Mentions: We used an automated gene annotation pipeline provided by PATRIC [19] to predict genes in S. meliloti. This pipeline uses a combination of gene prediction programs, Glimmer [20], GeneMark [21,22], TICO [23] and RBSfinder [24] to predict genes and compares with genes in RefSeq. A total of 512 new protein-coding genes (with length >90 nt) in the intergenic regions of the genome were predicted through this automated pipeline (Additional file 1). The number of predicted genes in different length ranges is shown in Figure 1. Most of the predicted new genes are relatively small (length <400 nt). The average length is about 200 nt. These genes were BLASTed against the NCBI non-redundant (NR) protein database [25,26]. The result showed that 159 candidates had BLAST hits in the NR database with E-values less than 0.01, whereas the remaining 353 of the candidates had no significant hits. Small gene size and lack of BLAST hits may be the reasons that the predicted new gene candidates were missed in the original genome annotation process.


Identification of new genes in Sinorhizobium meliloti using the Genome Sequencer FLX system.

Mao C, Evans C, Jensen RV, Sobral BW - BMC Microbiol. (2008)

Length distribution of predicted gene candidates.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2396165&req=5

Figure 1: Length distribution of predicted gene candidates.
Mentions: We used an automated gene annotation pipeline provided by PATRIC [19] to predict genes in S. meliloti. This pipeline uses a combination of gene prediction programs, Glimmer [20], GeneMark [21,22], TICO [23] and RBSfinder [24] to predict genes and compares with genes in RefSeq. A total of 512 new protein-coding genes (with length >90 nt) in the intergenic regions of the genome were predicted through this automated pipeline (Additional file 1). The number of predicted genes in different length ranges is shown in Figure 1. Most of the predicted new genes are relatively small (length <400 nt). The average length is about 200 nt. These genes were BLASTed against the NCBI non-redundant (NR) protein database [25,26]. The result showed that 159 candidates had BLAST hits in the NR database with E-values less than 0.01, whereas the remaining 353 of the candidates had no significant hits. Small gene size and lack of BLAST hits may be the reasons that the predicted new gene candidates were missed in the original genome annotation process.

Bottom Line: From these data, we identified 20 new genes.These new gene transcripts were confirmed by RT-PCR and their possible functions were analyzed.Our results indicate that high-throughput sequence analysis of bacterial transcriptomes is feasible and next-generation sequencing technologies will greatly facilitate the discovery of new genes and improve genome annotation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. chmao@vt.edu

ABSTRACT

Background: Sinorhizobium meliloti is an agriculturally important model symbiont. There is an ongoing need to update and improve its genome annotation. In this study, we used a high-throughput pyrosequencing approach to sequence the transcriptome of S. meliloti, and search for new bacterial genes missed in the previous genome annotation. This is the first report of sequencing a bacterial transcriptome using the pyrosequencing technology.

Results: Our pilot sequencing run generated 19,005 reads with an average length of 136 nucleotides per read. From these data, we identified 20 new genes. These new gene transcripts were confirmed by RT-PCR and their possible functions were analyzed.

Conclusion: Our results indicate that high-throughput sequence analysis of bacterial transcriptomes is feasible and next-generation sequencing technologies will greatly facilitate the discovery of new genes and improve genome annotation.

Show MeSH