Scientists generated a karyotype, chromosome-scale genome assembly, and manual genome annotation for a common ctenophore.

Ctenophores—beautiful marine invertebrates also known as “comb jellies”—have long fascinated and perplexed biologists. Phylogeneticists believe that either ctenophores or sponges were the first organisms to branch off from the tree of life, making them the “sister clade” to all other animals. However, debate is ongoing about which group can claim this title.

A study published in G3: Genes|Genomes|Genetics provides researchers with new tools to address these questions. The paper describes the first-ever published ctenophore karyotype and the first full annotated genome assembly for Hormiphora californensis, a small, globular ctenophore that is found off the shores of California and elsewhere in the Pacific Ocean.

The chromosome-scale H. californensis genome will allow whole-genome comparisons that weren’t possible with previous assemblies, says lead author Darrin Schultz. “The applications go beyond studying ctenophores—we can compare this genome to that of any other species to look for differences and understand more about the history of evolution.”

Going Over the Genome with a Fine-Toothed Comb

Schultz and his fellow researchers started with karyotyping, using a simple DNA staining protocol on ctenophore embryos to determine that H. californensis has 13 chromosomes. Then, after successfully isolating DNA samples suitable for long-read sequencing—a feat in and of itself—the team used PacBio Iso-Seq and Illumina RNA-seq technologies to sequence and annotate the full 110-Mb genome, manually determining at high resolution how genes were arranged on each chromosome.

“We spent hundreds of hours going through the entire genome by hand and making sure that every single gene annotation was correct,” says Schultz. “We did this because we saw evidence that previous ctenophore genome assemblies contained incorrect fusions or splits in genes. We wanted it to be right this time.”

As the researchers sifted through the genome, they found that H. californensis has an unusually high degree of heterozygosity—up to eight or nine percent in some areas of the genome. This presented bioinformatic challenges.

“The copies of the genome from the maternal side and the paternal side are so different from each other that it was like I had to assemble two separate genomes and try to come up with one assembly to represent both of those unions at the same time,” says Schultz.

As they got further into the annotation process, the team realized that two to three percent of the protein-coding genes occur completely within the bounds of another gene—not just one inside another, but multiple genes nested like Russian dolls. This architectural quirk has been observed in other species, especially eukaryotes with smaller genomes, but scientists are not yet sure whether the transposition processes that likely cause this “nesting” have any implications for the overall biology of an organism.

Comparative and Evolutionary Studies in Store

The new annotated ctenophore genome assembly will likely be used for comparative studies to address the phylogenetic “sister clade” debate between ctenophores and sponges in the coming years. Other applications of this study include addressing even broader questions about life on Earth. Some researchers are studying the genetic underpinnings of symbiosis using marine models like corals, ctenophores, and other cnidarians that have symbiotic algae. Others are interested in using comparative genomic studies to examine the evolution of specific traits that separate animals from all other organisms.

“This genome is just another step toward understanding how neurons and muscle cells—these things that made all of us uniquely animals—evolved over 600 million years ago,” says Schultz.

Schultz also notes that H. californensis may eventually be able to become a model species. It has a short life cycle, clear embryos ideal for developmental observation, and is more easily maintained in culture than many other related organisms. And now, it has a complete annotated genome available for study.

CITATION:

A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis
Darrin T Schultz, Warren R Francis, Jakob D McBroome, Lynne M Christianson, Steven H D Haddock, Richard E Green
G3 Genes|Genomes|Genetics 2021: jkab302
https://doi.org/10.1093/g3journal/jkab302

, ,

Grace Niewijk is a freelance science writer and editor from Chicago. Her writing has appeared in Genetic Engineering & Biotechnology News, Clinical OMICs, Proto Magazine, and elsewhere. She holds a degree in molecular biophysics and biochemistry from Yale.

View all posts by Grace Niewijk »

Read more in

  • Ed Grell at his dissecting microscope using ether to anesthetize his flies.

    In Memoriam: Ellsworth Herman Grell (1932–2023), a pioneer of Drosophila genome engineering and annotation

    Ellsworth (Ed) Grell blessed the Drosophila community through three enduring legacies: as a pioneer of chromosome mechanics, as a primary organizer and synthesizer of genetic knowledge in Drosophila, and as a graceful mentor to those fortunate to have known him personally. Ed grew up in rural Nebraska, completed his undergraduate studies at Iowa State, and…

  • Congratulations to the #Fungal24 Poster Award winners!

    We are pleased to announce the recipients of the GSA Poster Awards for posters presented at the 32nd Fungal Genetics Conference! Undergraduate and graduate student members of GSA were eligible for the awards, and a hard-working team of judges made the determinations. Congratulations to all! Felicia Ebot Ojong, The University of Georgia My research is focused…

  • Poster presentation tips for TAGC 2024

    You’ve been selected to present a poster at The Allied Genetics Conference 2024 in March—you’ve celebrated, made plans to attend, now what? This is an exciting opportunity to showcase your research and engage with fellow members of the genetics community, so you want to make sure you’re prepared. We wanted to offer you some tips…

  • Maximize your TAGC 2024 experience 

    A guide to all that National Harbor & DC have to offer Are you joining us for The Allied Genetics Conference 2024 in March? Make the most of your #TAGC24 experience in National Harbor! We know the science will keep you busy, but you deserve to unwind and have some fun, so we’ve curated a…

  • Early Career Leadership Spotlight: Sarah Petrosky

    We’re taking time to get to know the members of the GSA’s Early Career Scientist Committees. Join us to learn more about our early career scientist advocates. Sarah PetroskyMultimedia SubcommitteeUniversity of Pittsburgh Research Interest I am interested in understanding adaptation that has been happening recently in populations by dissecting the ways that genes underlying an adaptation…

  • TAGC 2024 Early Career Award Winners

    GSA is pleased to announce the winners of the early career awards presented at The Allied Genetics Conference 2024. These awards are specific to particular TAGC communities and recognize early career scientists’ outstanding work on their respective research organisms. The awardees will present their talks in keynote sessions at TAGC 2024.  Don’t miss the opportunity…

  • Preeminent geneticists recognized with revamped GSA Awards

    In 2022, GSA’s Board of Directors launched an audit to review the five major awards conferred by the Society. Today, we are thrilled to announce the recipients of the reimagined GSA Awards, including the new Genetics Society of America Early Career Medal. The scientists honored this year are recognized by their peers for their outstanding…

  • Fly Board funds outreach programs to spread the word about Drosophila research

    In 2020, the Fly Board voted to use part of its reserve fund to support efforts to increase trainee participation as well as equity and diversity in the Drosophila community. An awards committee decides how the money will be spent each year, and from 2020–2022, the committee posted a very broad call for applications from…

  • New members of the GSA Board of Directors: 2024–2026

    We are pleased to announce the election of four new leaders to the GSA Board of Directors: 2024 Vice President/2025 President Brenda Andrews Professor, University of Toronto It’s an honor to continue my association with the Society by serving as Vice President of the Board of Directors. I have broad knowledge of the ongoing activities…

  • A rose-ringed parakeet, one of three parrot species used in the study.

    Parrot plumage study aids breeders and endangered natural populations

    Yellow coloration is maladaptive in the wild but prized by breeders. People have long been fascinated with birds, which exhibit one of the widest ranges of coloration among vertebrates. Parrots, in particular, have captivated humans by their ability to mimic human speech and spectacular plumage. Brightly colored feathers are used primarily to attract mates, intimidate…

  • Early Career Leadership Spotlight: Sarah Gilmour

    We’re taking time to get to know the members of the GSA’s Early Career Scientist Committees. Join us to learn more about our early career scientist advocates. Sarah GilmourMultimedia SubcommitteeStowers Institute for Medical Research Research Interest Questions of evolution have always fascinated me. I am extremely fortunate to be starting out my research career in a…