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India earns genome stripes - Delhi unit attempts global feat after sequencing zebrafish

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By G.S. MUDUR in Delhi
  • Published 14.04.09

New Delhi, April 14: A striped fish native to Indian rivers, popular in household aquariums and hailed as an ideal organism to study human genes has become India’s first vertebrate to have its whole genome sequenced.

Scientists at the Institute of Genomics and Integrative Biology, New Delhi, have sequenced about 1.7 billion genetic alphabets that make up the full genome of a zebrafish picked up from a rivulet in Assam.

The researchers who used high-speed sequencers and computers to complete the zebrafish sequence in less than 60 days have now launched the world’s first effort to compare genetic variations in 100 siblings from a single parent zebrafish. Scientists are calling this next phase of the research Project Kaurava — named after the 100 Kaurava brothers in the epic Mahabharata.

Zebrafish grow no bigger than a human little finger, but share biological similarities with humans. Scientists are hoping that studies of zebrafish genes will help them pinpoint genetic mutations involved in a number of human diseases.

“The reproductive habits of zebrafish allow us to study them in a manner we could never study humans,” said Sridhar Sivasubbu, a scientist at the IGIB involved in the project. “A single female can deliver up to 200 embryos per week.”

A large number of genetically related progeny — ideally, siblings — would help in the study of fine variations that may occur within genes. But such studies are hard to do in humans because of the limited number of siblings. “It’s important to understand the natural variations in genes so that we can recognise mutations that may be associated with diseases,” Sivasubbu said.

Scientists at the Wellcome Trust Sanger Institute in Cambridge, UK, had started sequencing zebrafish in February 2001 and have already built a vast and detailed database containing information about zebrafish genes. The zebrafish genome is about half the size of the human genome.

The Sanger Institute work had focused on laboratory-grown strains of zebrafish. The Indian scientists have sequenced a wild type strain of zebrafish caught from a rivulet in Assam.

“After the mouse, the zebrafish is the most favoured animal model for human diseases,” said Vinod Scaria, a research team member at the IGIB. “The zebrafish may be used to study the mechanics of a variety of human diseases — cardiovascular diseases, genetic disorders, blood disorders, muscle and bone diseases,” said Scaria, a medical doctor who has turned his attention to computational biology.

Under an initiative led by the Council of Scientific and Industrial Research, the IGIB will collaborate with the Mayo Clinic in the US to analyse the zebrafish genome and assign functions to its genes. Some of the analysis of the genome at the IGIB is also using algorithms that were originally developed at the Sanger Institute.

“The comparison of genetic variations among the 100 siblings of a single parent (zebrafish) will also help us prepare for an era when hundreds or thousands of genomes of people will be sequenced and compared,” said Scaria.

Two years ago, a team of Indian scientists from Hyderabad and New Delhi had sequenced the full genome of a harmless bacterium that has been named Mycobacterium indicaa pranii .

Over the past decade, international teams of scientists have sequenced the whole genomes of dozens of microbes, animals and plants, including the human, chimp, rat, mosquito, horse, dog, cat, sea urchin, and puffer fish genomes.