Complex Sex Determination in the Grey Mullet Mugil cephalus Suggested by Individual Whole Genome Sequence Data

<i>Mugil cephalus</i> is a cosmopolitan marine fish highly relevant from ecological and economic perspectives. Previous studies identified sex-associated variants in the follicle-stimulating hormone receptor (<i>fshr</i>) gene following an XX/XY sex determination (SD) system. However, these variants could not be fully associated with sex in all samples. This suggests other genes and/or environmental factors may be involved in the SD of this species, denoting intraspecific variation. In this study, we constructed a new high-quality genome assembly of <i>M. cephalus</i>. We then re-sequenced the whole genome in males and females from two divergent Mediterranean populations to ascertain whether other genetic variants could also be involved in SD. <i>fshr</i> gene variants showed to only partially explain SD, while a new intronic variant in the <i>sestd1</i> gene appeared to be associated with SD following a ZZ/ZW system. The presence of other putative candidate SD variants showing significant differences between the two populations suggested a regional pattern of variation in SD in the Mediterranean Sea. The incomplete association of all the identified variants also pointed to a potential role for environmental factors.