Evaluating the annotation of protein-coding genes in bacterial genomes: Chloroflexus aurantiacus strain J-10-fl and Natrinema sp J7-2 as case studies

Gene annotation plays a key role in subsequent biochemical and molecular biological studies of various organisms. There are some errors in the original annotation of sequenced genomes because of the lack of sufficient data, and these errors may propagate into other genomes. Therefore, genome annotation must be checked from time to time to evaluate newly accumulated data. In this study, we evaluated the gene density of 2606 bacteria or archaea, and identified 2 with extreme values, the minimum value (Chloroflexus aurantiacus strain J-10-fl) and maximum value (Natrinema sp J7-2), to conduct genome re-annotation. In the genome of C. aurantiacus strain J-10-fl, we identified 17 new genes with definite functions and eliminated 34 non-coding open-reading frames; in the genome of Natrinema sp J7-2, we eliminated 118 non-coding open reading frames. Our re-annotation procedure may provide a reference for improving the annotation of other bacterial genomes.