How do genetically identical water fleas develop into different sexes?

Researchers from Osaka University have used a novel combination of short-read and long-read RNA sequencing to identify the different isoforms of genes expressed in the crustacean Daphnia magna. Males and females are genetically identical, but using this technique the team revealed genes that switch the predominant isoform in a sex-dependent manner. This study contributes to our understanding of Daphnia’s sexual dimorphism and helps further advance technologies in crustacean aquaculture.

Genetically identical Daphnia magna changes sex in response to environmental stimuli. The female on the right has eggs, while the male on the left does not.


Researchers from Osaka University use a novel combination of long- and short-read RNA sequencing to uncover the mechanism behind this biological mystery

Osaka, Japan – Daphnia are tiny crustaceans, or ‘water fleas’, that are extremely adaptable to their environment. This is owing to their remarkable phenotypic plasticity, i.e., their ability to change their form or behavior despite their genetic makeup remaining unchanged. Even male and female Daphnia are genetically identical!

Now, a group at Osaka University has shed some light on this phenomenon, by combining two different RNA sequencing techniques to reveal that certain genes produce different versions, or isoforms, of the proteins they encode in male and female Daphnia.

Phenotypic plasticity allows a single genome to produce different ‘phenotypes’, meaning Daphnia can physiologically adapt to variations in water salinity, temperature, the presence of predators, and more. A molecule called RNA is produced from a gene in a process called transcription, which provides instructions for the cellular machinery to then make the corresponding protein. Changes to the RNA after transcription can result in multiple isoforms, or slightly different RNA molecules, being produced from a single gene.

Such isoform variants are difficult to study because most RNA sequencing techniques read only very short stretches of RNA molecules, and then rely on computational techniques to piece the sequences back together. This means the fine details of different isoforms are lost.

However, in a novel approach, the team first used a newer, long-read RNA sequencing method called Iso-Seq to precisely identify all the different isoforms present in a species called Daphnia magna, before narrowing down the specific switching of isoforms occurring between males and females using highly accurate short-read RNA sequences.

“Short-read sequencing alone is unable to uncover this information,” explains first author Yasuhiko Kato. “This novel approach, combining long- and short-read sequencing, reveals previously unknown nuances of Daphnia transcription.”

“We identified genes that switch which specific isoforms are expressed in a sex-dependent manner,” adds senior author Hajime Watanabe. “This provides insight into the biological mechanisms that underlie the unique phenotypic plasticity of Daphnia.”

This research reveals the molecular basis for sexual dimorphism in Daphnia, an ecologically important species, and provides a tool for understanding how environmental conditions can determine sex in this species. These findings thus open the way for further advancements in crustacean aquaculture.

The article, “Identification of gene isoforms and their switching events between male and female embryos of the parthenogenetic crustacean Daphnia magna”, was published in Scientific Reports at DOI:

About Osaka University
Osaka University was founded in 1931 as one of the seven imperial universities of Japan and is now one of Japan's leading comprehensive universities with a broad disciplinary spectrum. This strength is coupled with a singular drive for innovation that extends throughout the scientific process, from fundamental research to the creation of applied technology with positive economic impacts. Its commitment to innovation has been recognized in Japan and around the world, being named Japan's most innovative university in 2015 (Reuters 2015 Top 100) and one of the most innovative institutions in the world in 2017 (Innovative Universities and the Nature Index Innovation 2017). Now, Osaka University is leveraging its role as a Designated National University Corporation selected by the Ministry of Education, Culture, Sports, Science and Technology to contribute to innovation for human welfare, sustainable development of society, and social transformation.

Published: 13 May 2024


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Global Strategy Unit

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Japan Society for the Promotion of Science