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twoday.net AGB

The microbial pan-genome

Genomic sequencing of prokaryotes is now in a stage where it's no longer sufficient just to sequence the genome of a prokaryote with some relevance for publication in a good journal. You will have to come up with novel insights and either an interesting bug (getting rarer...) or sequence a bunch of related genomes. The latter was performed by a group at TIGR on Group B Streptococci, reporting that sequencing a few strains are not sufficient to represent all strains in the species.

From the abstract:
Analysis of these genomes and those available in databases showed that the S. agalactiae species can be described by a pan-genome consisting of a core genome shared by all isolates, accounting for approximately 80% of any single genome, plus a dispensable genome consisting of partially shared and strain-specific genes. Mathematical extrapolation of the data suggests that the gene reservoir available for inclusion in the S. agalactiae pan-genome is vast and that unique genes will continue to be identified even after sequencing hundreds of genomes.


Dr Ferfried Gutfind from the Barbara Cartland Center for Positivistic Genomics says: "The massive sequencing of six strains is a beautifully analyzed, yielding the surprising conclusion that species diversity in some niches will not be covered ever by traditional sequencing approaches. Even "classical" meta-genomics won't help to cover the sequence space in these organisms."
However, Noland Works, chairman of "Bioinformatics students against basically everything" concludes: "Yeah, roight, after sequencing six strains theses guys say that they need to sequence way more species to ever reach their goal in a contributed paper to PNAS. Sounds like setting up publications for references if you ask me." (I won't.)

See also the note in The Scientist.

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