Abstract
BackgroundCampylobacter jejuni is the leading bacterial cause of human gastroenteritis in the developed world. To improve our understanding of this important human pathogen, the C. jejuni NCTC11168 genome was sequenced and published in 2000. The original annotation was a milestone in Campylobacter research, but is outdated. We now describe the complete re-annotation and re-analysis of the C. jejuni NCTC11168 genome using current database information, novel tools and annotation techniques not used during the original annotation.ResultsRe-annotation was carried out using sequence database searches such as FASTA, along with programs such as TMHMM for additional support. The re-annotation also utilises sequence data from additional Campylobacter strains and species not available during the original annotation. Re-annotation was accompanied by a full literature search that was incorporated into the updated EMBL file [EMBL: AL111168]. The C. jejuni NCTC11168 re-annotation reduced the total number of coding sequences from 1654 to 1643, of which 90.0% have additional information regarding the identification of new motifs and/or relevant literature. Re-annotation has led to 18.2% of coding sequence product functions being revised.ConclusionsMajor updates were made to genes involved in the biosynthesis of important surface structures such as lipooligosaccharide, capsule and both O- and N-linked glycosylation. This re-annotation will be a key resource for Campylobacter research and will also provide a prototype for the re-annotation and re-interpretation of other bacterial genomes.
Highlights
Campylobacter jejuni is the leading bacterial cause of human gastroenteritis in the developed world
Gene number adjustment A complete re-annotation of the C. jejuni NCTC11168 genome was performed resulting in the reduction of the total number of coding sequences (CDSs) from 1654 to 1643
Three CDSs originally designated as pseudogenes were removed as a result of merging with adjacent pseudogenes
Summary
Campylobacter jejuni is the leading bacterial cause of human gastroenteritis in the developed world. To improve our understanding of this important human pathogen, the C. jejuni NCTC11168 genome was sequenced and published in 2000. Since the publication of the C. jejuni NCTC11168 genome sequence in 2000, there has been a spectacular increase in research on this important human pathogen. One result of this has been significant revisions of the genetic loci that code for important surface structures on C. jejuni strains. The Nlinked glycosylation pathway has been identified in C. jejuni (Cj1119 – Cj1130) [9,12,13,14] This N-linked general glycosylation system was initially thought to only be present in eukaryotes. Research over the last 7 years on C. jejuni, coupled with the publication of a further 2 C. jejuni genome sequences [15,16] and another 3 Campylobacter species [15], has heightened the need for re-analysis of the original NCTC11168 genome sequence
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