Resequencing: important, but hardly rewarded

17 Jan 2012

With the advances in sequencing technology and analysis, the sequencing of genomes has become a routine activity. Even so, re-doing the whole exercise to improve your original sequence and annotation is much less common. The lactic acid bacterium Lactobacillus plantarum WCFS1 is one of the few organisms that have been 'honoured' with a complete resequencing and gene re-annotation.

Legacy
In 2001, a group of researchers from TI Food and Nutrition, Centre for Molecular and Biomolecular Informatics, NBIC and NIZO food published a sequence of L. plantarum WCFS1. Recently, they published the results of a complete resequencing and annotation efforts. Why go through all the motions again? "First of all, it is very important that a sequence and the annotation are as accurate as possible, because they are the starting materials for all subsequent research and analyses", says Sacha van Hijum, one of the contributors. "L. plantarum is one of the workhorses of the fermentation industry and it is a popular model system for research. There are so many researchers working with this bacterium that over the years an enormous amount of new knowledge and data on L. plantarum has been generated. But only the original authors of a sequence are allowed to make adjustments in the sequence and the annotation in the popular NCBI database. We wanted to do justice to this community effort and we also see the sequence and annotation as a legacy, which allows incorporating new insights and correcting inconsistencies."   

Publication
Now that sequencing has become a lot faster and cheaper, does that mean we can expect a lot of re-sequencing efforts? Van Hijum: "Yes, I do think so, but it remains to be seen to what extent the results will be made public. I foresee that many labs will resequence the genomes of their 'own' strains, but will keep the results in-house. Unless you're an original author, it is very difficult to get this type of work accepted for publication. And that is a real shame because it is a common interest to update and improve sequencing information. With no 'reward' for this type of work, I think that many researchers will not bother to communicate their results to the broader community."

Siezen RJ, Francke C, Renckens B, Boekhorst J, Wels M, Kleerebezem M, van Hijum SAFT
Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome
Journal of Bacteriology 2012 (194:1), 195-196

By: Esther Thole

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