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Cited by 31Marine Invertebrate Physiology and EcologyGenomics and Phylogenetic StudiesChromosomal and Genetic Variations

Chromosome-level reference genome of the jellyfish Rhopilema esculentum

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Li, Yunfeng, Gao, Lei, Pan, Yongjia, Tian, Meilin, Li, Yulong, He, Chongbo, Dong, Ying, Sun, Yamin +1 more·2020·GigaScience
DOI 10.1093/gigascience/giaa036PMC PMC7172023
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Abstract

Background: Jellyfish belong to the phylum Cnidaria, which occupies an important phylogenetic location in the early-branching Metazoa lineages. The jellyfish Rhopilema esculentum is an important fishery resource in China. However, the genome resource of R. esculentum has not been reported to date. Findings: In this study, we constructed a chromosome-level genome assembly of R. esculentum using Pacific Biosciences, Illumina, and Hi-C sequencing technologies. The final genome assembly was ~275.42 Mb, with a contig N50 length of 1.13 Mb. Using Hi-C technology to identify the contacts among contigs, 260.17 Mb (94.46%) of the assembled genome were anchored onto 21 pseudochromosomes with a scaffold N50 of 12.97 Mb. We identified 17,219 protein-coding genes, with an average CDS length of 1,575 bp. The genome-wide phylogenetic analysis indicated that R. esculentum might have evolved more slowly than the other scyphozoan species used in this study. In addition, 127 toxin-like genes were identified, and 1 toxin-related “hub” was found by a genomic survey. Conclusions: We have generated a chromosome-level genome assembly of R. esculentum that could provide a valuable genomic background for studying the biology and pharmacology of jellyfish, as well as the evolutionary history of Cnidaria.

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  • By 2020 and 2021, technological and algorithmic advances culminated in publication of the first complete, chromosome-scale genomes of non-bilaterian animals, including jellyfish Rhopilema esculentum, sponge Ephydatia muelleri, and ctenophore Hormiphora californiensis.

    “By 2020 and 2021, these technological and algorithmic advances culminated in the publication of the first complete, chromosome-scale genomes of non-bilaterian animals, including the jellyfish Rhopilema esculentum (92), the sponge Ephydatia muelleri (93), and the ctenophore Hormiphora californiensis (57).”

    From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [92]

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Cited by

Sorted by citations

Authors
Li, Y., Gao, L., Pan, Y., Tian, M., Li, Y., He, C., Dong, Y., Sun, Y., & Zhou, Z.
Affiliations
  • Liaoning Ocean and Fisheries Research Institute (CN)
  • Tianjin Biochip Corporation , 23 Hongda St., Tianjin 300457,
Corresponding author
  • Sun, Yamin
  • Zhou, Zunchun
ORCID
Venue
GigaScience
Publisher
Oxford University Press (OUP)
Published
2020-04-01
Volume
9
Issue
4
ISSN
2047-217X (ISSN-L)
DOI
10.1093/gigascience/giaa036
PMC
PMC7172023
OpenAlex
W3017091274
Cited by
31
References
2
Citations by year
2026: 2 · 2025: 7 · 2024: 5 · 2023: 7 · 2022: 6 · 2021: 3 · 2020: 1
FWCI
2.36
Type
journal article
Language
en
Open access
Licence
Locations
  • GigaScience (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • National Natural Science Foundation of China (31,302,173, 31,602,156, 31,602,155)
  • Natural Science Foundation of Liaoning Province (20,180,551,158)
Topics
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Marine Invertebrate Physiology and Ecology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
Keywords
Rhopilema esculentum, chromosome-level genome assembly, Cnidaria, Scyphozoa, pseudochromosomes, protein-coding genes, genome-wide phylogeny, evolutionary rates, genome assembly
MeSH terms
Animals, China, Chromosomes, Cnidaria, Reference Standards, Genome, Genomics, Molecular Sequence Annotation, High-Throughput Nucleotide Sequencing

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