Genomic Classification: A(nother) novel attempt

Hello Phylobabblers

Recently I came across this paper: Marakeby et al 2014 - A System to Automatically Classify and Name Any Individual Genome-Sequenced Organism Independently of Current Biological Classification and Nomenclature

Here the authors propose “a classification and naming system that is exclusively based on genome similarity and that is suitable for automatic assignment of codes to any genome-sequenced organism without requiring any phenotypic or phylogenetic analysis”

Did any of you fellows had the chance to read? If so, what are your opinions about it?

I gave the paper a quick read. It’s an interesting idea to give each genome a unique ID using genome similarity that is expected to be related to phylogenetic similarity. One issue I see is that the naming might be misunderstood as actually being based on phylogenetics. It is not a replacement for scientific naming (and the authors do not claim it is).

I think the biggest issue with such a naming scheme is that you need a centralized group in charge of names. Names are only unique within a single system so there would have to be a single server that every biologist submitted genomes to. If any part of the system is lost then naming conflicts could result. Private genomes could not be named. I’m also not sure how well this would work with metagenomic data.

I think their Table 2 shows some of the trade-offs. Creating a naming system is not trivial; desired functions should be analyzed, alternatives tested. http://plato.stanford.edu/entries/reference/