To build a goldfish, start with a blueprint | NHGRI

To build a goldfish, start with a blueprint | NHGRI

By Teresa L. Carey, M.A. Scientists drafted the blueprint for how to build a common goldfish. Now they'll use it to find out what gives ornamental goldfish their nuanced features, gaining insight into human health. A fish is a fish, right? Not when it comes to comparing its genome to that of humans. Shawn Burgess was out for a drink with a friend when the conversation turned to the utility of studying animal genes to gain insight into human health and evolution. In a field of research called comparative genomics, researchers compare genomes between animals, even humans. When researchers sequence DNA, they figure out the DNA's code. That is the blueprint for life. Dr. Shawn Burgess, a geneticist at the National Human Genome Research Institute, works with zebrafish. He wanted to compare their genome to closely related species to better understand how genes are organized. But most sequenced fish are far distant relatives. Comparing their genomes is not much better than comparing genomes between zebrafish and humans. So, Burgess and his friend honed in on the goldfish, a close cousin to the common carp. The goldfish and common carp diverged into two separate species approximately 60 million years ago, a similar distance as between mice and humans. The common carp's DNA was already sequenced. Together, the common carp and goldfish genomes would be useful in comparative genomics and also add value to the zebrafish genome. So, his friend made an offer: I'll give you the goldfish DNA if you figure out the code. On June 24 Burgess' team published the complete goldfish genome in the journal Science Advances. It took 15 people about a year. That's a small fraction of the time it took for thousands of researchers to complete the decade-long Human Genome Project.

The goldfish Burgess and his team sequenced is known as “Wakin” in Japan.

DNA sequencing has come a long way since the completion of the Human Genome Project in 2003. With new technology, it is faster and more affordable. Burgess' team used a tool called a PacBio RS II sequencer to read the 2 billion chemical letters in goldfish DNA. For comparison, the human genome has 3 billion. When the PacBio sequencer became available in 2011, Burgess knew it was a game-changer. In one pass, it can sequence longer continuous strands of DNA. With fewer, but larger pieces of DNA, the assembly process is more straightforward - like trying to assemble a 50 piece puzzle versus a 50,000 piece puzzle Sequencing the goldfish DNA opens research opportunities for the scientific community at large. The entire sequence is available online. Burgess calls it, "the foundation for the exciting science." On a basic level, DNA codes for proteins. Those proteins function as micro-machines doing all types of work in cells of the body. DNA also codes for when to turn the production of micro-machines on and off. For example, a liver protein is not built in the brain. That production is turned off. If it weren't, then that would be odd and likely problematic.

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