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viruses may be some of the smallest
borrelia burgdorferi re:users.rcn.com
causes Lyme Disease
It is 1.44 x 10^6, 1738 genes see "Spirochetes"
the smallest genome should be the one owned by an artificial cell whose genes have been deleted one by one until only the ones necessary for survival remained. but it is an artificial organism engeneered by Craig Venter. i wouldn't say viruses own the smallest genomes. i know some of them have genomes big enough to question the traditional view of virus genomes as small and limited to genes coding for proteins indispensible for their life cycle.
The "genome" doesn't only refer to the genes of an organism but also to the non-coding DNA/RNA sequences. Turning to your question, as a biology undergraduate I've heard that Mycoplasma genitalium is currently known to have the smallest genome (580.000bp).
Virus Bacteriophage MS2 3,569 3.5kb 0.000002 First sequenced RNA-genome