A Zebrafish Can’t Change Its Stripes

But NCBI can—and did—produce an updated zebrafish (Danio rerio) genome annotation.

The annotation used NCBI’s Eukaryotic Genome Annotation Pipeline and the new and improved zebrafish genome assembly (GRCz11).

A zebrafish (danio rerio)

Characteristics of the zebrafish make it important to scientific research.

In releasing the genome annotation, the National Center for Biotechnology Information is making it possible for researchers and scientists all over the world to download more genetic information than ever before about the zebrafish. (Genome annotation is the process of finding and designating locations of individual genes and other features of raw DNA sequences or assemblies.) A total of 39,989 genes were annotated, including 26,522 that code for proteins.

There’s much more to this tropical freshwater fish than its stripes. The zebrafish, which is a member of the minnow family, is particularly important to scientific research. A few qualities that make this minnow appealing include its cost—much cheaper than mice—the ability to produce hundreds of offspring every week, its quick growth rate, and its transparency. Surprisingly, zebrafish share about 70 percent of their genes with us, and about 84 percent of genes known to be associated with human disease have a zebrafish counterpart.

Scientists funded by NIH have used the zebrafish to study many conditions, including arrhythmia, a heart condition; spinal cord injuries; and scoliosis, a medical condition in which a person’s spine has a sideways curve.

One fish, two fish. . .

The zebrafish wasn’t the only sea creature to have new annotations in RefSeq. NCBI also announced the addition of genome annotation for the rainbow trout (Oncorhynchus mykiss) and the yesso scallop (Mizuhopecten yessoensis).

Nothing fishy about these guys. . .

NCBI posted genome annotations for more than animals that live in the water. A couple of them have common names that might make you chuckle. New annotations were also released for the following plants and animals:

Domestic silkworm (Bombyx mori)
Helmeted guineafowl (Numida meleagris)
Eudicot (Herrania umbratica)
Sorghum (Sorghum bicolor)
Bengalese finch (Lonchura striata domestica)
Ma’s night monkey (Aotus nancymaae)
Mongolian gerbil (Meriones unguiculatus)
Hawaiian monk seal (Neomonachus schauinsland)
Thirteen-lined ground squirrel (Ictidomys tridecemlineatus)

Fine print on the fish and more

The latest zebrafish (Danio rerio) genome annotation produced by the NCBI Eukaryotic Genome Annotation Pipeline is now in RefSeq, NCBI’s Reference Sequence Database. The data are available for download and can be explored in the Genome Data Viewer, with BLAST, and in the Gene database.

In Annotation Release 106, a total of 39,989 genes were annotated, including 26,522 that code for proteins. This annotation was done on an improved assembly (GRCz11), which has an increased scaffold N50 and includes alternate loci scaffolds. (See the release page for more information.)