The genome of the giant Nomura’s jellyfish sheds light on the early evolution of active predation

Abstract

Background Unique among cnidarians, jellyfish have remarkable morphological and biochemical innovations that allow them to actively hunt in the water column and were some of the first animals to become free-swimming. The class Scyphozoa, or true jellyfish, are characterized by a predominant medusa life-stage consisting of a bell and venomous tentacles used for hunting and defense, as well as using pulsed jet propulsion for mobility. Here, we present the genome of the giant Nomura’s jellyfish ( Nemopilema nomurai ) to understand the genetic basis of these key innovations. Results We sequenced the genome and transcriptomes of the bell and tentacles of the giant Nomura’s jellyfish as well as transcriptomes across tissues and developmental stages of the Sanderia malayensis jellyfish. Analyses of the Nemopilema and other cnidarian genomes revealed adaptations associated with swimming, marked by codon bias in muscle contraction and expansion of neurotransmitter genes, along with expanded Myosin type II family and venom domains, possibly contributing to jellyfish mobility and active predation. We also identified gene family expansions of Wnt and posterior Hox genes and discovered the important role of retinoic acid signaling in this ancient lineage of metazoans, which together may be related to the unique jellyfish body plan (medusa formation). Conclusions Taken together, the Nemopilema jellyfish genome and transcriptomes genetically confirm their unique morphological and physiological traits, which may have contributed to the success of jellyfish as early multi-cellular predators. Electronic supplementary material The online version of this article (10.1186/s12915-019-0643-7) contains supplementary material, which is available to authorized users.

Phylogenetic and Selection Analysis of an Expanded Family of Putatively Pore-Forming Jellyfish Toxins (Cnidaria: Medusozoa)

“…All analyses were conducted using 147 transcriptome assemblies, of which 143 are publicly available. The exceptions are Sanderia malayensis , which was assembled using Trinity v2.8.5 ( Grabherr, Haas, Yassour et al 2011 ; Haas et al 2013 ) from publicly available sequence-read archives (SRAs; Kim et al 2019 ) ( supplementary table S2 , Supplementary Material online), and four cerianthid transcriptomes from Klompen et al (2020) , which were built using Trinity v2.2 from publicly available SRAs. In addition, our analysis included the preliminary H. symbiolongicarpus genome assembl y available at NHGRI ( https://research.nhgri.nih.gov/hydractinia/, last accessed April 12, 2019 ).…”

Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing

“…In recent years, the genomes of several cnidarian species have been published with varying levels of assembly contiguity. These include the anthozoans Nematostella vectensis, Aiptasia strain CC7 and Acropora digitifera [21][22][23] , hydrozoans Hydra magnipapillata and Clytia hemisphaerica 24,25 , myxozoans Kudoa iwatai and Myxobolus cerebralis 26 , cubozoan Morbakka virulenta and the scyphozoans Aurelia and Nemopilema nomurai [27][28][29] . These data have given important insights into gene family evolution (for example 30,31 ), but our understanding of animal genome evolution is still somewhat constrained by restricted taxonomic sampling and the limited contiguity of several genomes.…”

The complete mitochondrial genome of a Dokdo shrimp, Lebbeus groenlandicus

“…The total DNA of L. groenlandicus was extracted and processed according to the previously described method (Kim et al. 2019 ). The voucher specimen is deposited at the Library of Marine Samples, KIOST, Geoje 53201, Republic of Korea (No.…”