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

Gold, David A. and Katsuki, Takeo and Li, Yang and Yan, Xifeng and Regulski, Michael and Ibberson, David and Holstein, Thomas and Steele, Robert E. and Jacobs, David K. and Greenspan, Ralph J. (2019) The genome of the jellyfish Aurelia and the evolution of animal complexity. Nature Ecology & Evolution, 3 (1). pp. 96-104. ISSN 2397-334X.

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We present the genome of the moon jellyfish Aurelia, a genome from a cnidarian with a medusa life stage. Our analyses suggest that gene gain and loss in Aurelia is comparable to what has been found in its morphologically simpler relatives—the anthozoan corals and sea anemones. RNA sequencing analysis does not support the hypothesis that taxonomically restricted (orphan) genes play an oversized role in the development of the medusa stage. Instead, genes broadly conserved across animals and eukaryotes play comparable roles throughout the life cycle. All life stages of Aurelia are significantly enriched in the expression of genes that are hypothesized to interact in protein networks found in bilaterian animals. Collectively, our results suggest that increased life cycle complexity in Aurelia does not correlate with an increased number of genes. This leads to two possible evolutionary scenarios: either medusozoans evolved their complex medusa life stage (with concomitant shifts into new ecological niches) primarily by re-working genetic pathways already present in the last common ancestor of cnidarians, or the earliest cnidarians had a medusa life stage, which was subsequently lost in the anthozoans. While we favour the earlier hypothesis, the latter is consistent with growing evidence that many of the earliest animals were more physically complex than previously hypothesized.

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Gold, David A.0000-0003-0135-4022
Katsuki, Takeo0000-0003-2366-2990
Holstein, Thomas0000-0003-0480-4674
Greenspan, Ralph J.0000-0002-6787-2845
Additional Information:© 2018 The Author(s). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit Received 03 May 2017; Accepted 12 October 2018; Published 03 December 2018. We thank K. Kosik and N. Nakanishi for their insights during the development of this project; R. Warren for his advice on genome assembly strategy; V. Levesque and the Birch Aquarium at Scripps for providing Aurelia strains; and S. Johnson, D. Le, D. Lam, and A. Hsu for technical assistance. D.A.G. gratefully acknowledges funding from a National Institutes of Health Training Grant in Genomic Analysis and Interpretation (T32HG002536) and a Cordes Postdoctoral Fellowship from the Division of Biology and Biological Engineering at Caltech. This work was also supported by grants from the W.M. Keck Foundation (R.J.G.), the Gordon and Betty Moore Foundation (R.J.G.), the DFG (T.H.), a fellowship from the Uehara Memorial Foundation (T.K.) and the NASA Astrobiology Institute–Foundations of Complex Life: Evolution, Preservation and Detection on Earth and Beyond (D.K.J.). Data availability: The genome assembly, as well as raw reads underlying the genomic and transcriptomic sequencing, are deposited in NCBI under BioProject PRJNA490213. A genome browser is also hosted at The Supplementary Data contain relevant input, intermediate and output data from all bioinformatics analyses performed in this paper. Annotations of the Aurelia gene models are provided in the Supplementary Data. Author Contributions: R.J.G. and T.K. sequenced and assembled the genome with input from R.E.S. M.R. contributed 100-bp paired-end reads, and D.I. and T.H. provided mate-pair reads with 4-kbp inserts. X.Y. and Y.L. worked on the initial error correction of PacBio reads. D.K.J. and D.A.G. oversaw transcriptome sequencing and assembly. D.A.G. performed downstream analyses of genome annotation with input from T.K., R.J.G., R.E.S. and D.K.J. D.A.G. designed the figures and drafted the manuscript. All authors reviewed and approved the final paper. The authors declare no competing interests.
Funding AgencyGrant Number
NIH Predoctoral FellowshipT32HG002536
W. M. Keck FoundationUNSPECIFIED
Gordon and Betty Moore FoundationUNSPECIFIED
Uehara Memorial FoundationUNSPECIFIED
Record Number:CaltechAUTHORS:20181210-125542487
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:91643
Deposited By: Tony Diaz
Deposited On:10 Dec 2018 21:42
Last Modified:21 Dec 2018 17:05

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