November 9, 2020 report
Large-scale sequencing of goldfish and carp reveals their origins
A large team of researchers affiliated with multiple institutions in China has sequenced the genomes of a large number of goldfish and carp, revealing much of their shared origin. They've published their results in the Proceedings of the National Academy of Sciences.
As the researchers note, goldfish have been domesticated by humans for over 1,000 years but unlike most other domesticated species, they have not been bred for food or companionship—instead, they serve mostly an ornamental function. Because human tastes vary so widely, goldfish have likewise been bred for a whole host of features, from different coloring to different fin and tail arrangements. Such wide-ranging breeding has led to many changes to the goldfish genome, but until now, these changes have not been very well studied.
The work by the team involved sequencing the genomes of 185 representative goldfish samples and 16 wild crucian carp samples. Prior research has shown that goldfish have 25 chromosomes and that each individual fish has 100 of them—and they have two sets of two copies of each. Prior research had also shown that most of the genetic variants that appear in the goldfish genome are fairly recent, genetically speaking—some so recent that they represent the only variant in a given strain. Such small samples are known as sweeps.
The work by the researchers in this new effort involved studying such sweeps. In so doing, they found that the top 1 percent of all the sweeps they studied had a total of just under 1,000 genes. They noted that most differences they found were related to pigmentation and body shape, though there were a few related to behavior. The researchers also sequenced the genomes of several egg goldfish, a species that has no dorsal fin. This allowed them to identify approximately 400 genes associated with the goldfish dorsal fin.
The team claims to have assembled one of the most contiguous genomes of goldfish to date and to have revealed the genetic architecture of many of the anatomically interesting features of the popular fish.
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