The genome of the jellyfish Aurelia and the evolution of animal complexity

Gold, David A.; Katsuki, Takeo; Li, Yang; Yan, Xifeng; Regulski, Michael; Ibberson, David; Holstein, Thomas W.; Steele, Robert E.; Jacobs, David K.; Greenspan, Ralph J.

doi:10.1038/s41559-018-0719-8

Cited by 85 publications

(105 citation statements)

References 88 publications

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“…3), and for analysis of gene expression dynamics at various stages of the life cycle and in different tissues (Figs. [3][4][5]. To generate expression tables, quality-filtered reads from all RNA-Seq libraries available for a given species were mapped back to the reference transcripts with Bowtie 2, and transcript abundance was estimated with RSEM version 1.2.5 (ref.…”

Section: Methodsmentioning

confidence: 99%

Medusozoan genomes inform the evolution of the jellyfish body plan

et al. 2019

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Cnidarians are astonishingly diverse in body form and lifestyle, including the presence of a jellyfish stage in medusozoans and its absence in anthozoans. Here, we sequence the genomes of Aurelia aurita (a scyphozoan) and Morbakka virulenta (a cubozoan) to understand the molecular mechanisms responsible for the origin of the jellyfish body plan. We show that the magnitude of genetic differences between the two jellyfish types is equivalent, on average, to the level of genetic differences between humans and sea urchins in the bilaterian lineage. About one-third of Aurelia genes with jellyfish-specific expression have no matches in the genomes of the coral and sea anemone, indicating that the polyp-to-jellyfish transition requires a combination of conserved and novel, medusozoa-specific genes. While no genomic region is specifically associated with the ability to produce a jellyfish stage, the arrangement of genes involved in the development of a nematocyte—a phylum-specific cell type—is highly structured and conserved in cnidarian genomes; thus, it represents a phylotypic gene cluster.

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Section: Methodsmentioning

confidence: 99%

Medusozoan genomes inform the evolution of the jellyfish body plan

et al. 2019

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“…It was, therefore, unclear whether neuropeptides were present in all cnidarians and, if so, what the structures of these neuropeptides were. This question, however, can now be solved, because the genomes from many cnidarians have been sequenced and numerous cnidarian transcriptomes are also available [37][38][39][40][41][42][43][44][45][46][47][48][49][50][51]. Last year, we developed a bioinformatics tool that could analyze cnidarian genomes and transcriptomes for the presence of neuropeptide preprohormones genes [37].…”

Section: Introductionmentioning

confidence: 99%

A comparative genomics study of neuropeptide genes in the cnidarian subclasses Hexacorallia and Ceriantharia

Koch

Grimmelikhuijzen

2020

BMC Genomics

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Background Nervous systems originated before the split of Proto- and Deuterostomia, more than 600 million years ago. Four animal phyla (Cnidaria, Placozoa, Ctenophora, Porifera) diverged before this split and studying these phyla could give us important information on the evolution of the nervous system. Here, we have annotated the neuropeptide preprohormone genes of twenty species belonging to the subclass Hexacorallia or Ceriantharia (Anthozoa: Cnidaria), using thirty-seven publicly accessible genome or transcriptome databases. Studying hexacorals is important, because they are versatile laboratory models for development (e.g., Nematostella vectensis) and symbiosis (e.g., Exaiptasia diaphana) and also are prominent reef-builders. Results We found that each hexacoral or ceriantharian species contains five to ten neuropeptide preprohormone genes. Many of these preprohormones contain multiple copies of immature neuropeptides, which can be up to 50 copies of identical or similar neuropeptide sequences. We also discovered preprohormones that only contained one neuropeptide sequence positioned directly after the signal sequence. Examples of them are neuropeptides that terminate with the sequence RWamide (the Antho-RWamides). Most neuropeptide sequences are N-terminally protected by pyroglutamyl (pQ) or one or more prolyl residues, while they are C-terminally protected by an amide group. Previously, we isolated and sequenced small neuropeptides from hexacorals that were N-terminally protected by an unusual L-3-phenyllactyl group. In our current analysis, we found that these N-phenyllactyl-peptides are derived from N-phenylalanyl-peptides located directly after the signal sequence of the preprohormone. The N-phenyllactyl- peptides appear to be confined to the hexacorallian order Actiniaria and do not occur in other cnidarians. On the other hand, (1) the neuropeptide Antho-RFamide (pQGRFamide); (2) peptides with the C-terminal sequence GLWamide; and (3) tetrapeptides with the X1PRX2amide consensus sequence (most frequently GPRGamide) are ubiquitous in Hexacorallia. Conclusions We found GRFamide, GLWamide, and X1PRX2amide peptides in all tested Hexacorallia. Previously, we discovered these three neuropeptide classes also in Cubozoa, Scyphozoa, and Staurozoa, indicating that these neuropeptides originated in the common cnidarian ancestor and are evolutionarily ancient. In addition to these ubiquitous neuropeptides, other neuropeptides appear to be confined to specific cnidarian orders or subclasses.

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“…With this, we identified 2,568 (A. ervi, Additional File 4) and 968 317 (L. fabarum, Additional File 5) putative orphans (Supplementary Table 9). The 318 evolutionary origin of these orphan genes is not known (Gold et al 2018; Van Oss & Carvunis 2019), but their retention or evolution could be important to understanding 320 specific functions or traits in these taxa. The higher number of orphan genes in A. ervi 321 partially explains the absolute difference in the number of annotated genes between 322 both taxa.…”

Section: Gc Content 219mentioning

confidence: 99%