A long-read–based <i>de novo</i> assembly of <i>Magallana bilineata</i> for improved tropical oyster aquaculture

True oysters, molluscs in the family Ostreidae, are important species in fisheries and aquaculture. As such, genome-enabled research can improve these industries and the conservation of these species. The tropical rock oyster Magallana bilineata (known as the black scar oyster or Indian backwater oyster) is naturally distributed in the tropical Indo-Pacific Ocean excluding Australia and is intensively cultured in India and the Philippines. It is also an aquaculture species in Sri Lanka with potential for much greater cultivation. We present the first reference genome for M. bilineata sourced from a Sri Lankan individual along with genetic variants that can be used in tool development for questions of molecular ecology and evolution as well as in breeding and commercial applications. Long-read PacBio data from a single M. bilineata were assembled following the Vertebrate Genomes Project workflow on the Galaxy Australia platform. A primary assembly composed of 105 contigs that is 551.94 Mbp in size was produced. The assembly N50 is 13.42 Mb and has a BUSCO completeness score of 98.1%. As collection and transport conditions challenged transcriptomic as well as scaffolding data generation, these approaches were undertaken computationally. Genetic variants in the form of SNPs from 90 individuals representing three naturally occurring populations in Sri Lanka and a fourth introduced population in Fiji was generated through DArTseq and a set of 3,115 SNPs produced after filtering. Combined, we present the first known genome assembly and the first genome-wide SNP data from M. bilineata, both of which have diverse applications for conservation and aquaculture.