Wild type Zebrafish: Whole Genome Sequence

Till date, the main genomics work has been focused on lab grown Zebrafish strains that functionally represent genetic clones; little or no true genetic diversity was captured in these initial genome studies. Therefore to address questions related to genomic variations, IGIB sequenced a Wild type Strain of Zebrafish caught directly from the water bodies in India.

Institute of Genomics and Integrative Biology (IGIB), which is a constituent laboratory of the Council of Scientific and Industrial Research (CSIR) has completed the whole genome sequencing of a Wild type Strain of Zebrafish (Danio rerio). This work marked India’s entry into the arena of whole genome sequencing of animals.

The Zebrafish genome is about half the size of the human genome, containing about 1700 million DNA base pairs. The research team at IGIB generated over 89 Gigabases of DNA sequences in two months time resulting in over 20X coverage of the Zebrafish genome. The Solexa / Illumina sequencing technology was employed for sequencing the Zebrafish Wildtype strain. This next-generation sequencing technology enables massively parallel sequencing of millions of genomic fragments ranging from 36 to 76 base pairs, which are then mapped back to the reference genome. This humongous exercise was made possible with the CSIR Supercomputing facility at IGIB. Mayo Clinic, Rochester, USA will join this CSIR led project for genome annotation.

Zebrafish, a four centimeter-long fish native to Indian rivers, has attracted considerable scientific interest worldwide primarily as a non-mammalian vertebrate model organism. Zebrafish  share many features of the human system. Using the new advancements in sequencing technologies alongside cutting-edge bioinformatics capabilities, Indian scientists explored genetic variation through comparing the genomes of single Wild type Strain Zebrafish parent and approximately 100 of its offsprings, which were bred and phenotyped at IGIB. The whole genome sequencing of approximately 100 of the offspring is expected to complete by 2012.