In a major breakthrough, scientists from ICAR’s Central Institute of Brackishwater Aquaculture, (ICAR-CIBA), Chennai have sequenced and assembled the whole genome of Indian white shrimp, Penaeus indicus entirely on their own. This is a significant achievement for the country in decoding the whole genome of the native species of shrimp, one of the world’s most important seafood commodities.
Globally, shrimp farming is important contributor of seafood, provides nutritional security, support employment opportunities and export shrimp commodity of high value to many countries. The Indian shrimp industry contributes about 11% share of global production (759,906 tonnes valued at USD 4 billion in 2019) amongst shrimp producing countries.
Shrimps have large number of chromosomes. Other complex factors of shrimp genome which are particularly challenging includes, a high percentage of repetitive sequences, large size of shrimp genome and difficulty in preparation of high quality genomic DNA for long reads sequencing. The complexity associated with the shrimp genome is one of the major hurdles faced by many researchers in sequencing and assembling the genome.
The whole genome sequence of P. indicus is a major landmark and this very high quality genome assembly of P. indicus is of 1.93 Gb size with contig N50 of 1.4 Mb having very high number of 346 un-gapped contigs of over 1 Mb length and scaffold N50 of 34.4 Mb. Considering the large genomes of >1.5 Gb length, the assembly presented for P. indicus is the only crustacean genome and one among the only nine invertebrate genomes sequenced so far, to meet the reference standard of 1 Mb contig N50 and 10 Mb scaffold N50 lengths. The shrimp genome contains 28,720 protein-coding genes. The decoded shrimp genome has applications to genetic improvement programs, stock management & ecology and evolutionary studies in species of commercial significance. To reduce the dependency on exotic species, the Indian native shrimp, P. indicus which has tolerance to wide range of salinity and wide geographical distribution can be developed as a potential species of culture for India. The future genetic improvement programmes with focus on P. indicus would benefit aquaculture with increased productivity and sustainability across Asia and other geographical locations where this shrimp species is predominantly found. The whole genome sequence of shrimp is an invaluable genomic resource to aquaculture science researchers and shrimp breeders and would serve as reference genome for future genetic improvement programmes for developing shrimps with desired economically important traits.
The ICAR-CIBA scientist team involved in shrimp genome assembly were Dr. M.S. Shekhar, Dr. Vinaya Kumar Katneni, Shri Ashok Kumar Jangam and Dr. K.K. Vijayan. The shrimp genome sequencing project was financially supported by ICAR-Consortium Research Platform on Genomics and coordinated by Dr. J.K. Jena, DDG (Fisheries Science), ICAR