We’ve sequenced the genome of the largest venomous snake with short reads and published that in 2015 in PNAS. This genome showed that long reads are vital to resolve the most complex (and interesting) regions of this genome and it was the main reason to join the Oxford Nanopore Technologies MAP program in 2014.
Eels are a very old species. We sequenced the genome of the European eel with both short reads (published in PLoS One) and did that again as one of the first vertebrate genomes assembled with nanopore reads (published in Scientific Reports). A improved version of this genome contributed to resolve the early diversification of teleost fishes (published in Science).