How many "finished" or permanent draft complete genome sequences have been published?
How many of them are eukaryotes?
Here are the answers from: GOLD
(Apologies for the Three Domain influence.)
Why are there so few eukaryotes? Because many eukaryotic genomes are very large and it takes a lot more work to sequence that much DNA. Furthermore, many eukaryotic genomes are full of junk DNA and it's difficult to sequence and assemble repetitive regions in order to get a complete chromosome. The bottom line is money—for most labs it's too expensive to sequence the genome of their favorite eukaryote but it can be quite cheap these days to sequence a bacterial genome.
[Hat Tip: Jonathan Eisen]