Long-Read De Novo Genome Assembly of Gulf toadfish Opsanus beta.

Abstract

The Gulf toadfish, Opsanus beta, within the family Batrachoididae, plays an important role ecologically and as a comparative research model. Only 4 genome assemblies are available for Batrachoids, with three being highly fragmentary and not up to current assembly standards. Here we present a new, de novo genome and transcriptome assemblies for the Gulf toadfish using PacBio long read technology. The final assembly is among the largest teleost genomes at 2.1 gigabases. This new assembly improves significantly upon the currently available reference for Opsanus beta with a final scaffold count of 62, of which 23 are chromosome scale, an N50 of 98,402,768, and a BUSCO completeness score of 97.3%. Annotation with ab intio and transcriptome-based methods generated 41,076 gene models. Modeling of gene orthogroup change indicated expansion of many immune associated orthogroups and contraction of olfactory receptor orthogroups. The genome is highly repetitive, with ~ 70% of the genome composed of simple repeats and transposable elements. Satellite DNA analysis identified potential telomeric and centromeric regions. This improved assembly represents a valuable resource for future research using this important model organism and to teleost genomics more broadly.