Genome Spotlight: Freshwater Angelfish (Pterophyllum scalare)

ABOVE: A tropical angelfish (Pterophyllum scalare) © ISTOCK.COM, 13THREEPHOTOGRAPY

When 17-year-old Indeever Madireddy’s pet angelfish Calvin died, he could have unceremoniously flushed it down the toilet like so many dearly departed fish companions had been before. Instead, he sequenced the animal’s genome. “I wanted to preserve it forever,” he tells New Scientist. “I decided to sequence the genome of the angelfish with the hopes that I could contribute that information to the scientific community, while also paying a small tribute to my pet!”

Although Madireddy is an adept fishkeeper, he is a high school student in California and didn’t exactly have the resources necessary for genomic work. So, he spent about a month researching the methodology, then bought reagents and paid the modest member fee to gain access to BioCurious, a community laboratory with abundant equipment—including, most importantly for Madireddy, a -80 °C freezer and an Oxford Nanopore MinION long-read sequencer. The bulk of the sequencing costs were paid by funds raised through a campaign on the scientific crowdfunding site Experiment.

With the help of scientists he met at BioCurious and University of North Carolina’s Yuanyu Lin, Madireddy assembled and annotated the fish’s nearly 735 Mb genome. The sequence, detailed in an October 18 paper in microPublication Biology, is roughly 86.5 percent complete. The reads also revealed the presence of Pseudomonas aeruginosa, a common opportunistic aquatic pathogen—which could explain how Calvin met his demise.

Despite Pterophyllum scalare’s popularity in the aquarium trade, Madireddy’s assembly is a first for the species. In the paper, he suggests that the sequence could enable the fish to become a model organism, like other members of the cichlid family.

See “Can These Fish Do Math?”

Runners Up:

Tricolored blackbird (Agelaius tricolor)

         

Tricolored blackbirds once darkened the skies of central California with enormous flocks numbering in the tens of thousands. Indeed, the species is known for having the largest colonies of any extant North American land bird. But habitat loss in the 20th century led to a precipitous 63 percent decline in the passerine’s populations over just 40 years, landing the species on the IUCN’s Red List of Threatened Species. Conservation efforts could be bolstered by genetic characterizations of the species, so a research team led by University of California, Santa Cruz, biologists used a combination of PacBio HiFi long reads and Dovetail Omni-C chromatic capture to produce a highly contiguous 1.15 Gb assembly, which is estimated to be 97.2 percent complete. “This genome adds a valuable resource for important evolutionary and conservation research on tricolored blackbirds and related species,” the researchers conclude in their September 13 paper in Journal of Heredity.

Paracyclopina nana

         

The copepod Paracyclopina nana doesn’t have a common name. Its claim to fame, albeit limited, is that it’s easy to breed and grow in the lab, leading researchers to suggest it could be a great model organism, especially for ecotoxicology research. But researchers from Sungkyunkwan University in South Korea weren’t interested so much in pollutants as in climate change—they wanted to understand how increasing levels of dissolved CO₂ (and the acidification of seawater that accompanies them) impact species whose calcified tissues are affected by changes in pH. They were specifically interested in epigenetic changes, but such research requires a genome sequence. So the team first assembled the animal’s 186 Gb genome. The methylomic and transcriptomic analyses that followed revealed that P. nana exhibits transgenerational epigenetic plasticity in response to acidic conditions, and “indicated that P. nana can acclimate to multigenerational exposure to elevated CO₂ through epigenetic plasticity in the absence of genetic diversity,” the authors write in a September 29 paper in Nature Climate Change, adding that “understanding the responses and adaptability of copepods to [acidification] not only is important for assessing the impact on biodiversity, biogeochemical cycles and trophodynamics in the marine environment, but also provides critical insights into marine ecology.”

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.