Genome Annotation and Comparison of Two Pacific Rockfishes Differing in Longevity

The flag rockfish (Sebastes rubrivinctus) and the tiger rockfish (Sebastes nigrocinctus) are phylogenetic sister species differing in that one species enjoys extreme longevity (>116 yrs) and the other does not (maximum lifespan 10 yrs). To assess the genetic cause of extreme longevity, both genomes were sequenced de Novo using Illumina paired-end sequencing, and were annotated using the Maker2 Annotation Pipeline. The Maker Annotation Pipeline combined gene predictions from intrinsic DNA sequence data and extrinsic evidence including mRNA and protein sequences. Gene and repeat finders were trained on rockfish and used within the Maker pipeline to independently annotate each genome. After each genome was annotated, the quality of each annotation was measured as the distance between each final gene prediction and the extrinsic evidence.  These distances (Annotation Evidence Distant (AED) scores) were of comparable quality to human and mouse genome annotations generated using Maker.  Quality was also assessed by comparing annotations among the two rockfishes and the three-spined stickleback (Gasterosteus aculeatus), with a focus on 200 genes homologous to aging genes in humans.