A recent article in Scientific American by Jennifer Ackerman entitled “The Ultimate Social Network”, highlights a particular problem when trying to sequence the genomes of eukaryotic organisms. The problem is that the organism in question, whether it is an ant, butterfly, a polar bear, frog or Blue whale is not a singular organism at all.
In fact the organism in question plays host to many millions of other prokaryotic organisms, mainly bacteria, viruses, fungi or parasites. In humans for example the genetic material from the microbiome outnumbers the human genome by at least 10 to 1. This is also expected to be true of all other eukaryotic species which harbour and maintain a symbiotic relationship with their microbiome.
The genes from the microbiome help process beneficial compounds and act to temper host immune defences for example. Therefore, when taking and extracting DNA from a eukaryotic organism it has to be considered what other genomes you may be preparing and sequencing alongside the desired genome of interest. For example it cannot be simply a case of freeze drying an insect crushing into a powder then extracting the DNA, as the resultant samples will contain a highly mixed and diverse set of genomes, whereby the genome of interest may be present only in the lowest possible ratio. So, be warned! When assembling genomes be sure you know what your starting material actually contains.