Take charge of the slow but unique evolution of sharks

Scientists at the Biosystems Dynamics Research Center (BDR) in Japan, in collaboration with other Japanese institutes and aquariums, decoded for the first time the complete genome of two shark species and improved genomic sequences previously published. By analyzing the genomes and comparing them with those of other vertebrate species, they have constructed a glimpse into their life histories and evolutionary trajectories. This work has been published online in Nature Ecology and Evolution.

Advances in sequencing genomes have made it possible to compare genomes of different species, giving us insight into their evolutionary histories and features. Although data for many organisms are available, shark genome sequencing has been hampered by their huge genomes, which are even larger than the human genome. The notable exception is the elephant shark, although this fish is not properly classified as a true shark.

Sharks have many unique characteristics, including their body structures, reproductive systems, mode of detection and extreme longevity: a shark species is known to live for more than three centuries. Fully decoded shark genomes will be a valuable aid for research to discover the molecular basis of these qualities. In this ultimate goal, a research team led by Shigehiro Kuraku of RIKEN BDR analyzed shark genomes using advanced DNA sequencing and comparative bioinformatics technologies capable of processing large sequences. They chose two main species – bamboo shark with brown band and cloudy chakhark – because they can be bred in aquariums, which makes it relatively easy to obtain live specimens. They also carried out an improved assembly of the whale shark genome, which had already been made public.

One of the riddles about sharks is why their genome is so big. The team found that the large genome size is due to massive insertions of repetitive elements. At the same time, shark genomes are evolving slowly, which means that they have retained many ancestral gene repertoires and can be considered as "living fossils" in the genomic sense.

The team discovered that sharks have human gene counterparts that regulate growth, reproduction, and homeostasis, such as obesity, appetite, and sleep, suggesting that elements of our molecular mechanism for Basic physiology have existed for more than 450 million years, before sharks separate our common ancestors.

The newly decoded shark genomes have already provided a number of information, especially those related to visual function. The researchers analyzed the light absorption of visual pigments in whale sharks and found that their rhodopsin pigment was set to detect relatively short wavelengths, close to 480 nm, that could penetrate into the whale shark. deep waters. This is not the case in bamboo sharks, and researchers believe that the altered function of rhodopsin is related to the unique lifestyle of the whale shark, which dives to about 2000 m when it does not feed. near the surface. This discovery was achieved by combining DNA sequence analysis and laboratory work using synthesized materials, but without animal experimentation.

The team also showed that the three species of sharks analyzed have relatively few olfactory receptor genes, which implies that they depend on other systems, such as the detection of electromagnetic fields, for the navigation.

"Our results will fill a long-standing gap in animal genomic biology and will also help us better understand the metabolism, reproductive cycle and health surveillance of sharks," said Keiichi Sato, author and associate director of 39; Okinawa. Churaumi Aquarium. "Such an understanding should contribute to the conservation of marine environments as well as to sustainable livestock farming and aquarium displays that allow everyone to experience biodiversity closely."

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More information:
Yuichiro Hara et al., Shark genomes provide information on the evolution of elasmobranchs and on the origin of vertebrates, Nature Ecology & Evolution (2018). DOI: 10.1038 / s41559-018-0673-5