Genetic resource could be used to protectfarm-raised kuruma shrimp from disease13 September 2021

Kuruma shrimp are considered a delicacy in Japan.Credit: OIST

New research from the Okinawa Institute ofScience and Technology Graduate University(OIST) and Tokyo University of Marine Scienceand Technology has resulted in a useful geneticresource on the kuruma shrimp. These are one ofthe largest species of prawn (females can reach27cm in length) and are found throughout theIndian and Pacific Oceans. In Japan, they'reconsidered a delicacy and have been a majorfisheries and aquaculture product (especially inOkinawa) since the early 20th century. But a bigproblem with the shrimp farms is that the highdensity of the animal means that diseases spreadquickly.

One concerning disease is a viral infection calledwhite spot disease, which is one of the mostthreatening pathogens to shrimp aquacultureworldwide. It is lethal and highly contagious;outbreaks have wiped out entire farms in just a fewdays.

"We're interested in the relationship between

aquaculture animals and disease-related bacteriaand viruses," explained Dr. Eiichi Shoguchi, aGroup Leader in the Marine Genomics Unit atOIST. "Having this genetic resource on hand couldbe useful for producing a disease-resistant line ofthe shrimp or vaccines."

Supported by OIST's DNA Sequencing Section, theresearchers used two differenttechniques—genome sequencing andtranscriptome sequencing—to produce this geneticresource. Their work was published in G3: Genes lGenomes l Genetics.

A genome is the full set of genetic informationfound in every cell. It is subdivided into genes.These genes are made up of DNA base pairs andeach gene contains the instructions needed tocreate a protein, and thus leads to the proper careand maintenance of a cell. For the instructions tobe carried out, the DNA must first be transcribedinto RNA. A transcriptome is a collection of allthese gene readouts. In some ways, thetranscriptome can be considered a reflection of thegenome. Some genes might be related to diseaseresistance, and some individuals may containvariations of these gene that leads to strongerresistance. If these genes can be identified, then itcould be possible to establish a disease-resistantline of shrimp.

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Kuruma Shrimp are an important aquaculture product inOkinawa, second only to mozuku seaweed. Credit: OIST

Firstly, the researchers focused on deciphering thegenome. They took one kuruma shrimp from acommercial farm in Okinawa and generated theinitial sequences. This produced many short DNAsequences which, although useful, didn't providethe researchers with enough clues to string themtogether. Essentially, they had all the pieces of apuzzle but no way of assembling it. They then useda second technology to produce longer, but lessprecise, DNA sequences–the scaffolding of thegenome. By bringing the two sequences togetherthey were able to assemble a draft of the genome.

Following this, the researchers analyzed 49 RNAsamples of different shrimp individuals (includingboth adults and larvae). This provided them with66,406 high-quality gene readouts—the draft of thetranscriptome.

"The kuruma shrimp genome provides us with acomprehensive catalog of immune-related genes,"explained Mr. Satoshi Kawato, lead author of thepaper and Ph.D. student at the Laboratory ofGenome Science, Tokyo University of MarineScience and Technology. "This will allow us tobetter understand how shrimp respond topathogens and will aid in developing strategies forpreventing disease outbreaks. The genomicresources will also help address various otheraspects of shrimp biology, such as growth andreproduction."

When their work was compared to that of thekuruma shrimp's relatives—the giant tiger prawn andthe whiteleg shrimp—nearly 70% genes was foundto be the same across all three species, meaningthat a high number of genes have been preserved.

"We think that this will serve as a useful resourcefor future research to understand the shrimp's basicbiology," concluded Dr. Shoguchi. "But it could alsobe used for fishery management and to establish abreeding program."

More information: Satoshi Kawato et al, Genome

and transcriptome assemblies of the kurumashrimp, Marsupenaeus japonicus, G3Genes|Genomes|Genetics (2021). DOI:10.1093/g3journal/jkab268

Provided by Okinawa Institute of Science andTechnology

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APA citation: Genetic resource could be used to protect farm-raised kuruma shrimp from disease (2021,September 13) retrieved 24 May 2022 from https://phys.org/news/2021-09-genetic-resource-farm-raised-kuruma-shrimp.html

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