Deep versus wide genomes

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.

References:

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