Towards a Reference Genome and Reference Transcriptome for the Calanoid Copepod Acartia tonsa

Copepods are thought to be the most abundant of any animals on earth on earth, and they are highly valuable for the aquaculture industry for use as live feed for fish larvae. Most historical and contemporary scientific efforts focus on ecology rather than genetic aspects of copepod biology, and despite several attempts, no highly contiguous genome sequence has been published for the subclass copepoda. All previous attempts to produce a high quality copepod genome have failed, likely as a result of highly repetitive genomes, chromatin diminution and inexplicably huge genome sizes within Copepoda. Here, we present our approach to obtaining a high quality genome from the numerous and cosmopolitan calanoid copepod species Acartia tonsa Dana, and compare several approaches to the genome sequencing of this species. Further, we present and validate a reference transcriptome and compare it with similar efforts on other non-model organisms.