Background

Kuruma shrimp are one of the largest species of prawn (females can reach 27cm in length!) and are found throughout the Indian and Pacific Oceans. In Japan, they’re considered a delicacy and have been a major fisheries and aquaculture product (especially in Okinawa) since the early 20th century. However, shrimp farms have experienced issues related to white spot disease – a viral infection which is one of the most threatening pathogens to shrimp aquaculture worldwide.

“We’re interested in the relationship between
aquaculture animals and disease-related bacteria and viruses,” explained Dr
Eiichi Shoguchi, a group leader in the marine genomics unit at OIST, in a press
release. “Having this genetic resource on hand could be useful for producing a
disease-resistant line of the shrimp or vaccines.”

Genetic research

Supported
by OIST’s DNA Sequencing Section, the researchers used two different
techniques—genome sequencing and transcriptome sequencing—to produce this
genetic resource. Their
work
was published in G3: Genes l Genomes l Genetics.

Firstly,
the researchers focused on deciphering the genome. They took one kuruma shrimp
from a commercial farm in Okinawa and generated the initial sequences. This
produced many short DNA sequences which, although useful, didn’t provide the
researchers with enough clues to string them together. Essentially, they had
all the pieces of a puzzle but no way of assembling it. They then used a second
technology to produce longer, but less precise, DNA sequences–the scaffolding
of the genome. By bringing the two sequences together they were able to
assemble a draft of the genome.

Following
this, the researchers analyzed 49 RNA samples of different shrimp individuals
(including both adults and larvae). This provided them with 66,406 high-quality
gene readouts—the draft of the transcriptome.

“The kuruma shrimp
genome provides us with a comprehensive catalogue of
immune-related genes,” explained Satoshi Kawato, lead author of the paper and
PhD student at the Laboratory of Genome Science, Tokyo University of Marine
Science and Technology. “This will allow us to better understand how shrimp
respond to pathogens and will aid in developing strategies for preventing
disease outbreaks. The genomic resources will also help address various other
aspects of shrimp biology, such as growth and reproduction.”

When their
work was compared to that of the kuruma shrimp’s relatives—the giant tiger
prawn and the whiteleg shrimp—nearly 70 percent genes was found to be the same
across all three species, meaning that a high number of genes have been
preserved.

“We think
that this will serve as a useful resource for future research to understand the
shrimp’s basic biology,” concluded Dr Shoguchi. “But it could also be used for
fishery management and to establish a breeding program.”

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