Archived Comments for:
Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains
David Ussery, Center for Biological Sequence analysis, Technical Uni. Denmark
13 June 2007
What is the difference between the "Supra-genome" mentioned in this article, and the "pangenome" first used to describe several sequenced Streptococcus agalactiae genomes, back in 2005? I can find the phrase "pan-genome" 16 times in PubMed, but "Supra-genome" is found only 3 times - once in this paper, and twice other by papers from the same group. Can't we reach an agreement on what to call all the combined genes in a set of sequenced genomes from the same species?
Why should it be called "pan-genome" for Burkholderia, Campylobacter, E. coli, Streptococcus, and Vibrio, but for Haemophilus it is the "supra-genome"?
Competing interests
Along with Tim Read, I wrote an editorial overview with the title "Opening the PanGenomics Box" in 2006 for Current Opinion in Microbiology.
Supra-genome vs. pangenome
13 June 2007
What is the difference between the "Supra-genome" mentioned in this article, and the "pangenome" first used to describe several sequenced Streptococcus agalactiae genomes, back in 2005? I can find the phrase "pan-genome" 16 times in PubMed, but "Supra-genome" is found only 3 times - once in this paper, and twice other by papers from the same group. Can't we reach an agreement on what to call all the combined genes in a set of sequenced genomes from the same species?
Why should it be called "pan-genome" for Burkholderia, Campylobacter, E. coli, Streptococcus, and Vibrio, but for Haemophilus it is the "supra-genome"?
Competing interests
Along with Tim Read, I wrote an editorial overview with the title "Opening the PanGenomics Box" in 2006 for Current Opinion in Microbiology.