Deep in the Dating Pool

Studies into Sex Differentiation of Marine Species to Aid Aquaculture

Photo by Hanson Lu on Unsplash

Whoever quipped about plenty of other fish in the sea never waded through the New York City dating pool, nor the wild waters of our warming world.

Aquaculture has become an increasingly important source of sustainable seafood. And similar to the city singles scene, its viability has a lot to do with sex.

Sex is a surprisingly important trait at commercial fish farms. In tilapia — the second most farmed fishes in the world — males grow to market-size earlier than females. Females also start to reproduce at a smaller size, filling production ponds with small fish. It is therefore advantageous to grow out only male fish.

This used to be achieved by producing all-male populations through interspecific crosses, but those strains have been lost or contaminated. Many fisheries now use hormonal masculinization, in which synthetic steroid hormones are administered to young tilapia before sexual differentiation. But the practice is banned in several major producing countries, and scientists and fish farmers alike have been seeking alternatives.

The first step to finding a genetic solution is to figure out the basis of sex determination in the genomes of commercial tilapia stocks, which are dominated by the Nile tilapia (Oreochromis niloticus). What causes the fish to become male or female, and when exactly does it happen?

Work so far has been hampered by incomplete maps of these sex determination genes, many of which are believed to be located in areas of highly differentiated, repetitive DNA sequences. Previous genome assemblies were pieced together using many sequences of small stretches of the tilapia DNA. Believing that more contiguous sequences based on longer stretches of DNA would capture more detail, a team of scientists from the University of Maryland created a new assembly using PacBio long-read sequencing technology.

According to Thomas Kocher and Matthew Conte, lead author and first author of a paper in BMC Genomics, some of the most interesting and evolutionarily important regions of the genome may be the most difficult to assemble accurately, and the repetitive “dark-matter” part of the genome is vastly underrepresented in the majority of current genome assemblies.

“Attempts to assemble these regions using only short read sequencing are futile. Only long sequencing reads will produce more contiguous and complete assemblies of complex vertebrate genomes,” they wrote. “The importance of such high-quality assemblies for downstream applications cannot be overemphasized.”

With the new PacBio genome map, which contained nearly a third more genes than previous draft assemblies, the team were able to better characterize tilapia sex determining genes, data they predict will be a big boon to the aquaculture industry. It could also benefit the wider scientific community, as tilapias and related species of other cichlid fishes are a promising model system for understanding the gene network controlling sex determination in vertebrates, they report.

Not Alone: Abalone

Another sea organism of significant economic interest is the abalone, a marine snail with mother-of-pearl shells that are attractive to jewelry lovers and delicate flesh that is attractive to gastronomes.

Once widely distributed throughout temperate and tropical coastal regions, most abalone consumed today has been farmed from commercial fisheries in China, Korea and Japan. Of approximately 20 species used in commercial aquaculture, the Haliotis discus hannai variety is particularly popular, and scientists are keen to better understand its physiology, molecular adaptation, genetic selection, disease, defense mechanisms, and ecological genetic diversity in order to support the growing industry.

In response to this need, a group of Korean scientists led by Young Chang Sohn of Gangneung-Wonju National University, set out to trace sex-preferential gene expression in H. discus hannai abalone.

Their study started in a fish market, where they obtained sexually mature male and female abalone. Back in the lab at Seoul National University’s National Instrumentation Center for Environmental Management, they constructed full-length complementary DNA (cDNA) libraries and sequencing with the PacBio RS II platform.

They then used the Iso-Seq method to sequence RNA, capturing transcriptome information for 15,110 and 12,145 genes that coded for proteins in female and male abalones, respectively.

“We found that the number of isoforms and their alternatively spliced patterns are variable and sex-dependent,” the authors wrote in a paper in Genes.

The researchers investigated differentially expressed isoforms involved in numerous signaling pathways and physiological metabolisms, and created a library of isoform information to assist further research — “the first significant contribution to sex-preferential genomic resources of the Pacific abalone,” they wrote.

“The availability of whole female and male transcriptome database and their isoform information will be useful to improve our understanding of molecular responses and also for the analysis of population dynamics in the Pacific abalone.”