A draft genome assembly of spotted scat (Scatophagus argus): the first
reference genome for Scatophagidae fish.
Abstract
Spotted scat (Scatophagus argus) is an economically important marine
cultured fish species in Asia, especially in Southeast China. As an XY
sex-determining type fish species, spotted scat can be used as a model
for understanding the mechanism of novel sex determination system
evolution in vertebrates. However, genomic resources of spotted scat are
lacking, and no highly contiguous reference genome has been released. In
this study, the first chromosome-level genome of spotted scat was
constructed using PacBio’s single-molecule real-time (SMRT) sequencing
and high-throughput chromosome conformation capture (Hi-C) sequencing
technologies. The genome comprised 572.42 Mb, with the contig N50 of
19.60 Mb. A total of 24,256 protein-coding genes were predicted in the
genome, and 96.30% of the predicted genes were functionally annotated.
Evolutionary analysis showed that spotted scat diverged from the common
ancestor of Japanese puffer (Takifugu rubripes) approximately 114.8
million years ago. In addition, doublesex and mab-3 related
transcription factor 1 (dmrt1), a gene associated with sex determination
process, was not found in the high-quality female genome, while it
existed in the re-sequencing data of three XY genotype male fish. The
conserved dmrt1 locus of vertebrates was substituted by its truncated
homologue (dmrt1b), which derives from dmrt1 via allelic diversification
and munitions. The genomic resources offer a strong foundation for
further research on the sex determination of spotted scat and facilitate
the understanding of the evolution of sex chromosomes in teleost
species.