Unravelling the Black Tiger Prawn Transcriptome
/
AGRF is a proud partner of The Australian Research Council Industrial Transformation Research Hub (ARC ITRH) for Advanced Prawn Breeding, which is applying cutting-edge genetic and genomic selection methodologies in the most advanced and industry-transformative improvement program for any prawn/shrimp species globally.
Working with Hub host James Cook University, along with research and industry partners including the CSIRO, University of Sydney, Vlaams Instituut voor Biotechnologie and Seafarms, Australia, our scientists are helping to improve and polish the transcriptome assembly of the Black Tiger Prawn using state-of-the-art long-read sequencing technologies.
Knowledge on genome structure of the black tiger prawn can provide information essential to the downstream development of advanced genomic breeding programs, along with providing the capacity to better understand gene function through detailed comparative genomic studies.
A sub-program of the ITRH for Advanced Prawn Breeding, Elucidation of the Black Tiger Prawn Transcriptome, was identified as a key genomic resource required for an advanced genomically-guided breeding program for the aquaculture industry. The sub-program utilised the Pacific Biosciences Sequel platform to generate Iso-Seq reads to map an improved version of the transcriptome.
The experiment was designed and executed through close collaboration between AGRF wet lab scientists and bioinformaticians, and other Hub partners, and culminated in the publication of the assembled transcriptome in the paper De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome, in Nature’s Scientific Reports.[1]
The main objective of the program was to reconstruct the black tiger prawn transcriptome to help understand the genes driving key developmental events and commercially important traits during farming. The transcriptome will also be useful in annotating the full draft of the genome, needed for advanced genetic mapping of traits and breeding.
The ARC ITRH brings together world-leading animal geneticists, research and service providers, and Australia's largest prawn farm. The goal of the Hub is to develop and transfer to the farmed black tiger prawn industry the capacity to benefit from advanced genomic-informed breeding programs.
JCU’s Head of Aquaculture and Fisheries and Director of the Hub, Professor Dean Jerry, said ‘our focus is on developing the world’s most advanced breeding program for the farmed black tiger prawn. At the moment the tiger prawn is farmed but the full productivity potential locked in the species’ genes hasn’t been exploited.
‘The aim of the Hub is to achieve the same high efficiency in farming the tiger prawn as has been achieved for livestock such as pigs and chickens. The end result being prawns that grow faster, are more disease-tolerant and that will retain outstanding eating qualities. Ultimately this will enable increased productivity and international competitiveness for the Australian industry.’[2]
The ARC ITRH for Advanced Prawn Breeding received $4.9 million from the Federal Government in 2015 to undertake research leading to a significant boost in the productivity of the Australian prawn industry.
References:
[1] De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome. Huerlimann et al., 10th September 2018, Scientific Reports, volume 8, Article number: 13553.
[2] JCU unleash the Australian tiger prawn, Media release, 1st January 2015, https://www.jcu.edu.au/news/releases/2015/may/news-and-media11111111112
