The sequence and de novo assembly of Larimichthys crocea genome using PacBio and Hi-C technologies

Larimichthys crocea is an endemic marine fish in East Asia that belongs to Sciaenidae in Perciformes. L. crocea now has been recognized as an "iconic" marine fish species in China not only because it is traditional food fish for people in China, but also because it is the most recognized overfishing victim and still providing high value fish products via large scale mariculture. Here we report a chromosome-level reference genome of L. crocea generated employing the PacBio single molecule sequencing technique (SMRT) and High-through chromosome conformation capture (Hi-C) technologies. The genome sequences were assembled into 1,591 contigs with a total length of 723.86 Mb and a contig N50 length of 2.83 Mb. After chromosome-level scaffolding, 24 scaffolds were constructed with a total length of 668.67 Mb (92.48% of the total length of all contigs). Genome annotation identified 23,657 protein-coding genes, 2,517 ncRNAs. The high accurate, chromosome-level reference genome of L. crocea provides the essential genome resource to develop genome-scale selective breeding and restocking strategies of L. crocea.