A colorful mandarinfish on a reef
A colorful mandarinfish on a reef

Genome Spotlight: Mandarinfish (Synchiropus splendidus)

The high-quality genome sequence sheds light on the colorful nature of these popular aquarium fish.

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Christie Wilcox

Christie was a well-established science blogger and writer when she was awarded a PhD from the University of Hawaii in 2014 for her research on the genetics of lionfishes. A...

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Oct 28, 2021

ABOVE: A colorful mandarinfish perches on a piece of coral.
© ISTOCK.COM, VOJCE

If any fish deserves the name spendidus, it is the mandarinfish. Its magnificent colors have made this fish popular in the aquarium industry despite the fact that it’s covered in poison, has notoriously picky eating habits, and smells terrible. The secrets of how it produces its vibrant hues and foul mucus have remained shrouded in mystery, but may soon be revealed thanks to a genome sequence for the species published this month (October 18) in G3 Genes|Genomes|Genetics. The assembly will also put the animal in prime position to aid in learning more about the strange and varied order to which it belongs. 

University of Oregon researchers Martin Stervander and William Cresko built the genome using linked-read sequencing, a process which generates synthetic long reads from much shorter ones. Long DNA molecules are extracted from cells but then broken up for rapid, cost-efficient sequencing; the key is that each chunk is given a special barcode so that its genomic context isn’t lost. The tagged short reads can then be readily reassembled, ultimately generating long sequences using less DNA and at a much lower cost than true long-read sequencing. The final 483-Mbp assembly the team generated boasts 59x coverage of an estimated 92.6 percent of the genome—robust enough to provide insights into the biology and ecology of these roughly thumb-sized dragonets that inhabit the shallow, protected lagoons and reefs of a wide swath of the western Pacific. 

One distinctive feature of mandarinfish that this genome may shed light on is their toxic, foul-smelling mucus. Despite being bite-sized for many of the ocean’s smaller predators, these fish lack the protective scales many of their kin have. Instead, they are armed with sharp spines and poisonous mucus that makes them both smell and taste horrible. Little is known about the composition of this mucus, though the animals have at least two types of secretory cells in their epidermis that generate it. The new genome could prove useful for annotating transcriptomes of these cells, helping researchers better understand the animals’ defensive goo and elucidate its composition. 

Given the distasteful nature of the animals’ mucus (at least to humans, though reportedly to predators as well), it’s hypothesized that the fish’s incredible colors function as a warning, although some researchers have suggested other possible functions, such as reproduction-related signaling. The fish produce their vivid colors via at least two pigmentation cell types: vibrant blue cyanophores and blue-and-red cyano-erythrophores. These discoveries represent two of the nine total pigment cell types known in fish, and armed with a genome, researchers can finally begin to unpack how these cells develop and function.   

Finally, though mandarinfish might look like extra-colorful gobies, they and the rest of the family Callionymidae have most recently been identified as members of the Syngnathiformes, a quirky order of fishes that includes the family Syngnathidae (seahorses and pipefish). The authors note they expect the new genome will be a resource for comparative genomics, allowing deeper probing of the evolution of the Sygnathids’ most prominent traits, including male pregnancy and elongate, highly camouflaged bodies. 

Note to readers: This post is the first in a monthly column we’re calling Genome Spotlight, which will highlight recently-published genome sequences and the mysteries of life they may reveal.

Runners Up:

Brown Anole (Anolis sagrei)

The brown anole has emerged as a major model organism in ecology; it was even the first reptile to be edited with CRISPR. So the species’ complete genome sequence, uploaded as a bioRxiv preprint on September 30, is a big step forward for the field, and will likely help reveal the genetic underpinnings of ecologically important traits.

Green Bottle Fly (Lucilia sericata)

Usually, green bottle flies lay their eggs on carcasses, and the maggots consume dead flesh. That’s why they were chosen for maggot debridement therapy: in people, they don’t damage healthy tissues. But in Northern Europe, New Zealand, and Australia, they’ll lay eggs in the wounds of live sheep, and can kill the animals. The animal’s genome, published in Genomics on October 5, could shed light on why maggot debridement therapy is so effective and, conversely, why the animals sometimes cause such harm.