A tubifer cardinalfish
A tubifer cardinalfish

Genome Spotlight: Tubifer cardinalfish (Siphamia tubifer)

These tiny reef fish harbor luminous bacteria, and the chromosome-level assembly of the species’ genome may facilitate the duo’s use as a vertebrate model for symbiosis.

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Christie Wilcox

Christie joined The Scientist's team as Newsletter Editor in 2021, after more than a decade of science writing. She has a PhD in cell and molecular biology, and her debut book Venomous: How Earth’s Deadliest Creatures Mastered Biochemistry, received widespread acclaim.

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Apr 28, 2022

ABOVE: A tubifer cardinalfish (Siphamia tubifer) in captivity at the California Academy of Sciences’ Steinhart Aquarium Tim Wong, California Academy of Sciences

During the day, tubifer cardinalfishes (Siphamia tubifer) can be found darting among the needly spines of urchins on reefs across the Indian and Pacific Oceans. At night, they become bolder, perhaps because of their partnership with luminous Photobacterium mandapamensis bacteria. Thanks to the microbes, in the dark, these fish gently glow—light that scientists suspect creates predator-confusing countershading.

Tubifer cardinalfish inside the spines of an urchin surrounded by yellow coral
Tubifer cardinalfish hide amongst urchin spines during the day, a behavior that has led some to call them sea urchin cardinalfish.
Alison Gould, California Academy of Sciences

This partnership has made the fish and bacteria an emerging model for symbioses between microbes and vertebrates. Because the bacteria are housed in an organ that’s connected to the fish’s intestines, the mutualism shares similarities with gut microbiome symbioses. Research to date has been hampered by a lack of genomic resources for the fish, but that changed March 29 with the publication of a chromosome-level genome assembly for the cardinalfish in Genome Biology and Evolution.

To put together the fish’s 23-chromosome, 1.2 Gb genome, California Academy of Sciences evolutionary ecologist Alison Gould and her colleagues combined PacBio HiFi long-read sequencing with Hi–C, a technology that reveals the 3D structure of the genome by gluing together regions of chromatin that are in close physical proximity prior to sequencing. The result was a high-quality nuclear genome with a 99 percent BUSCO score, a measure that indicates completeness based on the extent to which an assembly contains single-copy genes found in related species (in this case, ray-finned fishes). The team was also able to sequence the fish’s roughly 18 kb mitochondrial genome.

Initial comparisons with the only other cardinalfish genome sequenced to date—the nonbioluminescent Sphaeramia orbicularis—and those of other fishes revealed a chromosome fusion that occurred sometime before the split of the two cardinalfishes, as well as significant overlap in the positioning of genes in both cardinalfishes despite an estimated 50 million years of divergence between the two species. The authors note that the early divergence of the tubifer cardinalfish “raises the possibility that the bioluminescent symbiosis played a role in the host’s initial divergence and speciation from a common ancestor”—a hypothesis that could be investigated by future studies now that this assembly has enabled deeper research on symbiosis-related genes.

Runners Up:

Townsend’s least gecko (Sphaerodactylus townsendi)

The vast majority of knowledge about sex determination in vertebrates comes from birds and mammals, whose sex determination systems tend to be evolutionarily stable. In contrast, squamate reptiles—and especially geckos—exhibit a wide diversity of sex determination systems, including what are considered rapid changes from one system to another on an evolutionary timescale. To accelerate insights into the genetic basis for such flexibility, researchers published the genome of the Towsend’s least gecko April 1 in Journal of Heredity.

False clownfish (Amphiprion ocellaris)

False clownfish were rocketed to international stardom by Pixar’s 2003 film Finding Nemo. They’ve been gaining popularity in scientific circles, too, as an emerging model organism for studying evolution, ecology, and developmental biology in reef fishes. A high-quality genome for the species, published March 30 in G3 Genes|Genomes|Genetics, will bolster research involving the species, and serve as “a valuable resource for understanding the ecology and evolution of reef fishes,” the authors write.

Tasmanian tiger (Thylacinus cynocephalus)

The Tasmanian tiger, also known as the thylacine, is one of the most famous examples of a human-caused extinction. Although not the first genome assembly for the beloved marsupials, the genome published March 29 in Genome Biology and Evolution takes advantage of rapidly improving sequencing technologies to generate the first chromosome-scale genome, which despite relying on ancient DNA, is about as contiguous and complete as recent extant marsupial genomes. “Future whole-genome resequencing studies, empowered by this assembly, have the potential to provide population-level insights into the thylacine’s demography and level of genetic load prior to its extinction,” the authors conclude.


Genome Spotlight is a monthly column for The Scientist’s Genetics & Genomics newsletter that highlights recently published genome sequences and the mysteries of life they may reveal.