Chromosome-level reference genome of the jellyfish Rhopilema esculentum

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.

Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny

“…This stands in stark contrast to the genome of the jelly sh Rhopilema esculentum. In Rhopilema, recent Hi-C analysis suggested the existence of 21 chromosomes, in line with the earlier analyses of chromosome spreads 11,36 . We observed that all Rhopilema and Nematostella chromosomes show a clear 1-to-1, 1-to-2 or, in a single case, a 1-to-3 correspondence (Figure 5a).…”

Combined QTL and GWAS Analysis to Identify the Growth-Related Gene in Rhopilema Esculentum with the Help of 2b-RAD Sequencing

“…Nevertheless, the function of EGF_CA domains has not been well understood in aquaculture animals. With the release of genomic information of R. esculentum 14 and the development of biotechnology, the gene function studies of R. esculentum will be improved and more genes will be investigated for genetic breeding.…”

“…The genes located on the up-and down-stream 500 Kb distance of the associated genomic region of body weight and umbrella diameter were detected 14,50…”

“…Although the genomic information of R. esculentum has been released 14 , the high-resolution linkage map of R. esculentum is still lacking and the growth-related genes have not been reported yet. For R. esculentum, body weight and umbrella diameter are the main growth traits.…”

Proteomic Analysis of the Venom of Jellyfishes Rhopilema esculentum and Sanderia malayensis

“…Most of the toxins in this family share sequence similarity with ryncolins, a group of hemostasis-impairing toxins originally described from C. rynchops [ 21 ]. Ryncolin genes [ 22 ], transcripts, and proteins [ 23 , 24 , 25 , 26 ] have also been found in other species of jellyfish, but their functions are not well-characterized. C-type lectins, another major group of hemostasis-impairing toxins, are commonly found in the venoms of a wide variety of animals [ 27 , 28 , 29 , 30 ], including several jellyfish species: Pacific sea nettle Chrysaora fuscescens [ 31 ], Lion’s mane jellyfish Cyanea capillata, Nomura’s jellyfish N. nomurai [ 26 ], and cannonball jellyfish Stomolophus meleagris [ 23 ].…”