With the decoding of complete draft genome and tissue-specific transcriptomes (functional genes) of three Important Indian Fish Species, Hilsa, Rohu and Magur, ICAR institutes have demonstrated their capabilities in this frontier area of research. The genomes are analysed to identify the genes and their assignment to functions. The capability is demonstrated, as the complete work has been done within India. The first drafts of these fish genomes are accomplished under different programs. In addition, genome of two important pathogens, namely Aphaynomyces invadans and White Spot Syndrome Virus (Indian strain), has also been sequenced.
The Indian Council of Agricultural Research has given a strong push to develop capability in this field of research through a program Consortium Research Platform on Genomics (CRP Genomics) during 2015, led by ICAR-National Bureau of Fish Genetic Resources, Lucknow, involves institutes on several commodities including Crops, Livestock, Fish, Microbes and Pathogens.
- Rohu and Magur
- EUS Pathogen
Hilsa First draft genome of Hilsa, an iconic fish of Indo-Pacific, was completed under CRP Genomics by ICAR-NBFGR which was presented during the conference, PAG ASIA 2017 at Seoul, South Korea. The long read dominated strategy implemented through third generation sequencing technology, assembled a high-quality draft of Hilsa genome, which covered about 95% of the genomic region. Nearly 32000 protein coding genes have been identified, which include genes for growth, lipid metabolism and immune function. Researchers at ICAR-NBFGR have identified important osmoregulatory genes, important for enduring extreme environmental stress conditions, faced during spawning migration of hilsa.
Rohu and Magur:
The Indian major carp, rohu genome was predicted to have over 40,000 genes and functional role of around 25000 genes have been annotated. The results are based on the 95% coverage achieved for the whole genome through multiple platforms. Similarly, Indian catfish, magur genome assembly with 93% coverage was find to have over 51000 genes and near 35000 genes have been analysed to assign biological function. This program on two cultivable fish species, rohu and magur was supported by Department of Biotechnology, Government of India and accomplished by ICAR-NBFGR in collaboration with ICAR-Central Institute of Freshwater Aquaculture, Bhubaneshwar; Anand Agricultural University, Anand and ICAR-Indian Agricultural Statistical Research Institute, New Delhi. The program generated important genomic information for rohu and magur for the first time and would pave the way for finding genes for aquaculture important traits such as growth, disease resistance etc.
Under another program me, ICAR-NBFGR has established high quality draft genome of oomycete, Aphanomyces invadans, known to cause epizootic ulcerative syndrome (EUS), with 87% coverage. With a total of nearly 18000 genes predicted, 636 genes were identified to be secretory in nature. EUS is one of the most destructive diseases of fresh and brackishwater fishes, which has been reported from 28 countries. Currently, more than 120 species of fishes are naturally infected and the disease causes substantial losses particularly in Asia and Africa. In the Indian strain of WSSV, responsible for losses in shrimp industry, the surprising finding of reduction of genome by ICAR-Central institute of Brackishwater Aquaculture (CIBA) Chennai is also recorded by another independent study done at CAH College, Vellore. The results will help in further studies on the pathogenic mechanisms and identification of virulence factors, thereby, useful to develop novel strategies in disease management.