The reader comments contain many good nominees (whales, naked mole rats, potato blight, and more), but I’m afraid I was not selfless. I wrote in the comments:
Coelacanth is an excellent choice. It could be difficult to get enough tissue, given that they are such elusive creatures.
I want to argue for a crayfish genome.
Crayfish (and their relatives, lobsters and other decapod crustaceans) are commercially important. They are harvested for food and cause ecological and economic damages as invasive species to name just two reasons.
Crayfish are important model organisms for research, particularly neurobiology. Discoveries made in crayfish include electrical synapses, presynaptic inhibition, and neuromodulation of aggression.
Crayfish are the current record holder for highest number of chromosomes in an animal (Pacifastacus leniusculus: 2n=376).
There is only one crustacean genome (a small freshwater one, Daphnia pulex). In comparison, about a dozen insect genomes are complete and more are on the way.
Probably the best choice of species would be Louisiana red swamp crayfish (Procambarus clarkii), because it is common, spread across the globe, and well studied.
The mysterious crayfish Marmorkrebs could be an interesting second choice, because their origins are unknown, and they are the only known decapod crustacean where all the individuals are female.