Researchers have identified significant gene activation patterns during the larval development of Malabar groupers, revealing an unexpected early surge in the activation of thyroid and corticoid genes at this stage. Their findings indicate that these genes are activated twice during the developmental process—once in the early larval stage and again during metamorphosis. This early activation is a first for any fish species, marking the unique nature of the Malabar grouper.
Researchers from the Okinawa Institute of Science and Technology (OIST) in both the Marine Climate Change Unit and Marine Eco-Evo-Devo Unit have uncovered distinct patterns of gene activation during the larval development of the Malabar grouper. Their research, published in the journal eLife, reveals that thyroid and corticoid genes are activated on two occasions in the larval development, once early on and again during metamorphosis. This unusual early gene activation has not been documented in any other fish species, highlighting the grouper’s uniqueness.
Groupers are essential meso-predators that help sustain the balance and health of marine ecosystems. The Malabar grouper (Epinephelus malabaricus), referred to as Yaito-hata in Japan, can grow up to 2 meters in length. Due to their popularity and high market value, many grouper species have faced overexploitation and are now at risk of extinction. To address this crisis and satisfy market demand, grouper aquaculture facilities have been established in Okinawa and globally.
Grouper aquaculture in Okinawa
Dr. Roger Huerlimann, the lead author and a molecular biologist in the Marine Climate Change Unit, expressed particular interest in the eco-culture aspect of the study, noting that these fish are bred and sold in Okinawa.
The journey of breeding and raising Malabar groupers began in 1992 at the Ishigaki branch of the Okinawa Prefectural Fisheries and Ocean Research Center, with the first successful breeding achieved in 1996. By 1997, the center celebrated a global milestone by successfully spawning over 200,000 young fish. Today, around ten grouper fish farms operate in Okinawa.
RNA analysis reveals unusual hormone activation
A genome is the total genetic material within an organism. Scientists can investigate genome functionality by studying the RNA produced under certain conditions or within specific cells—referred to as transcriptomic analysis. This approach enables researchers to discover which genes are activated at different developmental stages. In their study, the researchers analyzed the expression levels of genes related to thyroid and corticoid hormones, among other biological functions, in Malabar grouper larvae, particularly focusing on the crucial metamorphosis stage.
After hatching, the larvae float in the open sea for approximately 60 days before approaching coastal habitats. During this impressive journey, they undergo significant hormone-driven metamorphosis, characterized by spine regression and the emergence of adult-like pigmentation.
“Our genomic analysis clearly indicates a high level of thyroid and corticoid gene activation during metamorphosis. In groupers, this metamorphosis aligns with the development of adult-like pigmentation and the loss of spines on the dorsal and pectoral fins,” explained Dr. Huerlimann. “Interestingly, we also observed a rise in these genes right at the onset of larval development, which is not something we’ve seen in other fish species.”
Dr. Natacha Roux, a researcher at the Centre de Recherches Insulaires et Observatoire de l’Environnement (CRIOBE) and a former member of the Computational Neuroethology Unit at OIST, added: “We measured the levels of thyroid and corticoid hormones in the larvae, noting an increase in both at the start of their larval development, further affirming our genomic findings. The reason for this activation remains unknown, but we speculate it may relate to the growth of larval spines, potentially aiding in buoyancy and deterring predators.”
Both researchers underscored that their success in this study was greatly facilitated by the welcoming nature of the Motobu Town community, whose openness to collaboration was crucial. This enabled the team to establish a small lab at the Okinawa Prefectural Sea Farming Center for their sampling and experimental work.
Dr. Huerlimann’s goal is to promote sustainable aquaculture practices in Okinawa and to assist local farmers through his research initiatives: “Initially, our aim was to establish a reference genome sequence for future studies,” he shared. “However, over the past three years, I have engaged with farmers to understand their specific challenges. Disease management is a major concern, and I hope my research can help tackle this issue along with others they might face.”
