Highway to Heaven: Sequencing the Genome of the Waterfall Climbing Hawaiian Goby (Sicyopterus stimpsoni)

Certain animals have evolved unique characteristics necessary for survival in extreme environments. For example, closely related species of gobies have developed very different strategies to overcome extreme conditions such as climbing high waterfalls using repurposed mouthparts or walking out of water using modified fins. However, we lack information on how such novel adaptations arose. These species share a close ancestor and may have adapted preexisting structures to new uses. Therefore, in order to explore how the Hawaiian goby (or O’opu nopili, “the fish that clings”) Sicyopterus stimpsoni evolved to being able to climb waterfalls, we decided to sequence its genome. We will then compare and contrast with other goby genomes to identify specific regions of change and relate these to regions known to control physiology. Here, we extracted DNA from muscle tissue from two climbing gobies and performed two genomic libraries using the Bioo PCR Free kit. We sequenced these two libraries using one lane of the Illumina HiSeq 1x100bp and two lanes of 2x100 bp, which yielded 860 million reads total. We then used FASTQC for quality checking, Trimmomatic 0.32 for trimming and filtering, Abyss 1.5.1 for assembly, and SSPACE 3.0 for scaffolding. The resulting assembly contained 196,045 scaffolds with lengths greater than 500 nucleotides. The sum of lengths of these scaffolds is 812.4 MB, approximately 81% of the estimated genome size (1 Gb). This discrepancy is believed to be due to the more highly repetitive genomic regions being compressed during the assembly process to their shortest common sequences. The N50 statistic, the sequence length at which all sequences greater than or equal to it contain 50% of the sum of the lengths of all assembled sequences, is 7,078. The genome is now being annotated and further analysis will be performed to try to elucidate why the Hawaiian goby evolved to be a waterfall climbing species. Furthermore, samples have been taken for RNAseq from successful and unsuccessful climbers. Analysis is in process.