The key facts
- The rice field eel genome has been assembled in full for the first time: 838 million nucleotides across 12 chromosomes, with telomeres and centromeres described
- The rice field eel is the first vertebrate with discovered sex change: all juveniles are born female and turn into males after spawning
- In 2023, China raised 355,000 tons of eel worth 23 billion yuan, but juveniles are still caught in the wild
Gap-free genome assembly
The Institute of Hydrobiology of the Chinese Academy of Sciences has for the first time read and assembled the genome of the rice field eel in full, from telomere to telomere, without a single gap. The work is published in the journal Scientific Data. The rice field eel lives in flooded fields of East and Southeast Asia and became the first vertebrate in which science discovered sex change.
Biological features and economic importance
All eel juveniles are female: only after laying eggs do they gradually turn into males. For science, this is a model of how sex in vertebrates is determined and re-determined, and for fish farmers it is a problem: females and males mature at different times, which complicates breeding in captivity. In 2023, in China, where eel meat is considered a delicacy, 355,000 tons of this fish were raised, worth 23 billion yuan. At the same time, juveniles are still caught in the wild, and wild populations are being depleted.
How the sequencing was carried out
Reading the genome to the end was made possible by combining three technologies: long PacBio HiFi reads, ultra-long Oxford Nanopore strands, and a map of spatial proximity of DNA segments. The result was 838 million nucleotides arranged across 12 chromosomes; for each chromosome, telomeres and a centromere were described for the first time. More than 25 thousand protein-coding genes were found in the genome.
How the new assembly differs from the previous one
The previous version of the genome, assembled in 2018, was a set of fragments: contiguous DNA pieces were five times shorter — 14.5 million letters versus 70.7 million. Complex repeats occupying almost half of the eel genome remained undeciphered: telomeres and centromeres consist precisely of them, and sequencers confused them. The new assembly closed these regions as well.
Significance for science and aquaculture
Biologists now have a precise foundation for searching for the genes that control the transformation of a female into a male. Understanding how they work would make it possible to learn to regulate the sex of offspring and create breeds adapted to life on farms, which would solve the problem of depletion of wild populations. The assembly has been deposited in open databases available to laboratories around the world. The rice field eel will remain the main model organism for studying how vertebrates choose and change sex.
