Meeting Abstract
We sequenced the genome of the intertidal, herbivorous fish, Cebidichthys violaceus (Teleostei: Stichaeidae), to elucidate the genetic underpinnings of dietary specialization and intertidal existence in this species. C. violaceus is part of a phylogeny that showed independent intertidal invasion and evolution of herbivory in comparison to other herbivorous stichaeids (e.g., Xiphister mucosus). A juvenile individual collected from San Simeon, California was used to sequence the C. violaceus genome, and the genome was generated with Illumina and Pacific Biosciences (PacBio) datasets with 107X and 9X coverage, respectively. From our genomic datasets, we conducted a de novo assembly of the Illumina reads and then a hybrid assembly with both Illumina and PacBio datasets. With bioinformatic tools, we estimated the genome to be 526,436,767 base pairs with a N50 scaffold size of 542 kilobases. The C. violaceus genome provides a multitude of opportunities to link genomic information to ecological and nutritional physiology. We are using this data set to better understand the multitude of processes that allow a fish to be herbivorous and to tolerate the vagaries of intertidal existence (e.g., temperature fluxes, and breathing water and air). Moreover, what we learn from C. violaceus will be used to inform analyses of other fishes in the family Stichaeidae, which features dietary diversity, ontogenetic dietary shifts (including a shift from carnivory to herbivory in C. violaceus and other taxa), and large biogeographic ranges spanning the eastern and western Pacific Ocean. This will be one of the most robust non-model system, vertebrate genomes available to date and will expand our understanding of the biology of fishes and beyond.
