Deep versus wide genomes

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Remember Genome 10K? Well, here’s a new study by Michel Milinkovitch and colleagues, that points out the deficiencies of comparative data from 1X genomes:

2 genomes - depth does matter
Here, using recently-developed comparative genomic application systems, we evaluate the impact of low-coverage genomes on inferences pertaining to gene gains and losses when analyzing eukaryote genome evolution through gene duplication. We demonstrate that, when performing inference of genome content evolution, low-coverage genomes generate not only a massive number of false gene losses, but also striking artifacts in gene duplication inference, especially at the most recent common ancestor of low-coverage genomes. We show that the artifactual gains are caused by the low coverage of genome sequence per se rather than by the increased taxon sampling in a biased portion of the species tree.

They conclude that a diversity of 1X genomes may not be as useful as a smaller number of genomes at higher coverage. Wide coverage is good for testing conserved loci, but deep coverage will be necessary for many other kinds of comparisons.


Milinkovitch MC, Helaers R, Depiereux E, Tzika AC, Gabaldón T. 2010. 2X genomes -- depth does matter. Genome Biology 2010, 11:R16 doi:10.1186/gb-2010-11-2-r16