Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA, Presidential Initiative in Data Science, University of Oregon, Eugene, OR 97403, USA
Hope Healey
Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
Bernadette Johnson
Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
Elyse Barker
Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA, Presidential Initiative in Data Science, University of Oregon, Eugene, OR 97403, USA
The Gulf pipefish Syngnathus scovelli has emerged as an important species for studying sexual selection, development, and physiology. Comparative evolutionary genomics research involving fishes from Syngnathidae depends on having a high-quality genome assembly and annotation. However, the first S. scovelli genome assembled using short-read sequences and a smaller RNA-sequence dataset has limited contiguity and a relatively poor annotation. Here, using PacBio long-read high-fidelity sequences and a proximity ligation library, we generate an improved assembly to obtain 22 chromosome-level scaffolds. Compared to the first assembly, the gaps in the improved assembly are smaller, the N75 is larger, and our genome is ~95% BUSCO complete. Using a large body of RNA-Seq reads from different tissue types and NCBI's Eukaryotic Annotation Pipeline, we discovered 28,162 genes, of which 8,061 are non-coding genes. Our new genome assembly and annotation are tagged as a RefSeq genome by NCBI and provide enhanced resources for research work involving S. scovelli.
