{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T21:53:14Z","timestamp":1786571594663,"version":"build-2736575974"},"reference-count":109,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,6,18]],"date-time":"2024-06-18T00:00:00Z","timestamp":1718668800000},"content-version":"vor","delay-in-days":75,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DEB-1542597"],"award-info":[{"award-number":["DEB-1542597"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI-2010755"],"award-info":[{"award-number":["DBI-2010755"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000952","name":"Paul G. Allen Family Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000952","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100017023","name":"Paul G. Allen Frontiers Group","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100017023","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,4,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>As the sister group to all other animals, ctenophores (comb jellies) are important for understanding the emergence and diversification of numerous animal traits. Efforts to explore the evolutionary processes that promoted diversification within Ctenophora are hindered by undersampling genomic diversity within this clade. To address this gap, we present the sequence, assembly and initial annotation of the genome of Beroe ovata. Beroe possess unique morphology, behavior, ecology and development. Unlike their generalist carnivorous kin, beroid ctenophores feed exclusively on other ctenophores. Accordingly, our analyses revealed a loss of chitinase, an enzyme critical for the digestion of most non-ctenophore prey, but superfluous for ctenophorivores. Broadly, our genomic analysis revealed that extensive gene loss and changes in gene regulation have shaped the unique biology of B. ovata. Despite the gene losses in B. ovata, our phylogenetic analyses on photosensitive opsins and several early developmental regulatory genes show that these genes are conserved in B. ovata. This additional sampling contributes to a more complete reconstruction of the ctenophore ancestor and points to the need for extensive comparisons within this ancient and diverse clade of animals. To promote further exploration of these data, we present BovaDB (http:\/\/ryanlab.whitney.ufl.edu\/bovadb\/), a portal for the B. ovata genome.<\/jats:p>","DOI":"10.1093\/nargab\/lqae072","type":"journal-article","created":{"date-parts":[[2024,6,18]],"date-time":"2024-06-18T10:38:37Z","timestamp":1718707117000},"source":"Crossref","is-referenced-by-count":13,"title":["Morphological and dietary changes encoded in the genome of <i>Beroe ovata<\/i>, a ctenophore-eating ctenophore"],"prefix":"10.1093","volume":"6","author":[{"given":"Alexandra\u00a0M","family":"Vargas","sequence":"first","affiliation":[{"name":"Whitney Laboratory for Marine Bioscience, University of Florida ,\u00a0 St. Augustine , FL\u00a0 32080 , USA"},{"name":"Department of Biological Sciences, University of North Carolina at Charlotte , Charlotte , NC\u00a0 28223 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melissa\u00a0B","family":"DeBiasse","sequence":"additional","affiliation":[{"name":"Whitney Laboratory for Marine Bioscience, University of Florida ,\u00a0 St. Augustine , FL\u00a0 32080 , USA"},{"name":"Department of Biology, Radford University , Radford , VA\u00a0 24142 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lana\u00a0L","family":"Dykes","sequence":"additional","affiliation":[{"name":"Whitney Laboratory for Marine Bioscience, University of Florida ,\u00a0 St. Augustine , FL\u00a0 32080 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5993-9106","authenticated-orcid":false,"given":"Allison","family":"Edgar","sequence":"additional","affiliation":[{"name":"Whitney Laboratory for Marine Bioscience, University of Florida ,\u00a0 St. Augustine , FL\u00a0 32080 , USA"},{"name":"Federated Department of Biological Sciences, New Jersey Institute of Technology , Newark , NJ\u00a007102,\u00a0 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"T\u00a0Danielle","family":"Hayes","sequence":"additional","affiliation":[{"name":"Whitney Laboratory for Marine Bioscience, University of Florida ,\u00a0 St. Augustine , FL\u00a0 32080 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel\u00a0J","family":"Groso","sequence":"additional","affiliation":[{"name":"Whitney Laboratory for Marine Bioscience, University of Florida ,\u00a0 St. Augustine , FL\u00a0 32080 , USA"},{"name":"Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center , Seattle , WA\u00a0 98109 , USA"},{"name":"Human Biology Division, Fred Hutchinson Cancer Center , Seattle , WA\u00a0 98109 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leslie\u00a0S","family":"Babonis","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolutionary Biology, Cornell University , Ithaca , NY\u00a0 14853 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark\u00a0Q","family":"Martindale","sequence":"additional","affiliation":[{"name":"Whitney Laboratory for Marine Bioscience, University of Florida ,\u00a0 St. Augustine , FL\u00a0 32080 , USA"},{"name":"Department of Biology, University of Florida ,\u00a0 Gainesville , FL\u00a0 32611 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5478-0522","authenticated-orcid":false,"given":"Joseph\u00a0F","family":"Ryan","sequence":"additional","affiliation":[{"name":"Whitney Laboratory for Marine Bioscience, University of Florida ,\u00a0 St. Augustine , FL\u00a0 32080 , USA"},{"name":"Department of Biology, University of Florida ,\u00a0 Gainesville , FL\u00a0 32611 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,6,18]]},"reference":[{"key":"2024061808223718500_B1","doi-asserted-by":"crossref","first-page":"pdb.emo106","DOI":"10.1101\/pdb.emo106","article-title":"Comb jellies (Ctenophora): a model for basal metazoan evolution and development","volume":"2008","author":"Pang","year":"2008","journal-title":"Cold Spring Harb. Protoc."},{"key":"2024061808223718500_B2","volume-title":"Die ctenophoren des Golfes von Neapel und der angrenzenden Meeres-abschnitte","author":"Chun","year":"1880"},{"key":"2024061808223718500_B3","first-page":"648","article-title":"Vergleichend-embryologische Studien. IV. Ueber die gastrulation und mesodermbildung der Ctenophoren","volume":"42","author":"Metschnikoff","year":"1885","journal-title":"Z. Wiss. Zool."},{"key":"2024061808223718500_B4","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1006\/dbio.1999.9427","article-title":"Intracellular fate mapping in a basal metazoan, the ctenophore Mnemiopsis leidyi, reveals the origins of mesoderm and the existence of indeterminate cell lineages","volume":"214","author":"Martindale","year":"1999","journal-title":"Dev. Biol."},{"key":"2024061808223718500_B5","doi-asserted-by":"crossref","first-page":"650","DOI":"10.1002\/jez.b.21244","article-title":"Insights into the early evolution of SOX genes from expression analyses in a ctenophore","volume":"310B","author":"Jager","year":"2008","journal-title":"J. Exp. Zool. B Mol. Dev. Evol."},{"key":"2024061808223718500_B6","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1007\/s00427-008-0222-3","article-title":"Developmental expression of homeobox genes in the ctenophore Mnemiopsis leidyi","volume":"218","author":"Pang","year":"2008","journal-title":"Dev. Genes Evol."},{"key":"2024061808223718500_B7","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/j.ydbio.2010.10.019","article-title":"Somatic stem cells express Piwi and Vasa genes in an adult ctenophore: ancient association of \u201cgermline genes\u201d with stemness","volume":"350","author":"Ali\u00e9","year":"2011","journal-title":"Dev. Biol."},{"key":"2024061808223718500_B8","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1002\/jez.b.21386","article-title":"New insights on ctenophore neural anatomy: immunofluorescence study in Pleurobrachia pileus (M\u00fcller, 1776)","volume":"316","author":"Jager","year":"2011","journal-title":"J. Exp. Zool. B Mol. Dev. Evol."},{"key":"2024061808223718500_B9","doi-asserted-by":"crossref","first-page":"e84363","DOI":"10.1371\/journal.pone.0084363","article-title":"Evidence for involvement of Wnt signalling in body polarities, cell proliferation, and the neuro-sensory system in an adult ctenophore","volume":"8","author":"Jager","year":"2013","journal-title":"PLoS One"},{"key":"2024061808223718500_B10","doi-asserted-by":"crossref","first-page":"1466","DOI":"10.1002\/jmor.21398","article-title":"Development of the nervous system in the early hatching larvae of the ctenophore Mnemiopsis leidyi","volume":"282","author":"Norekian","year":"2021","journal-title":"J. Morphol."},{"key":"2024061808223718500_B11","article-title":"Phylum Ctenophora: list of all valid species names","author":"Mills","year":"2017"},{"key":"2024061808223718500_B12","doi-asserted-by":"crossref","first-page":"1242592","DOI":"10.1126\/science.1242592","article-title":"The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution","volume":"342","author":"Ryan","year":"2013","journal-title":"Science"},{"key":"2024061808223718500_B13","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1038\/nature13400","article-title":"The ctenophore genome and the evolutionary origins of neural systems","volume":"510","author":"Moroz","year":"2014","journal-title":"Nature"},{"key":"2024061808223718500_B14","doi-asserted-by":"crossref","first-page":"jkab302","DOI":"10.1093\/g3journal\/jkab302","article-title":"A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis","volume":"11","author":"Schultz","year":"2021","journal-title":"G3 (Bethesda)"},{"key":"2024061808223718500_B15","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1038\/s41586-023-05936-6","article-title":"Ancient gene linkages support ctenophores as sister to other animals","volume":"618","author":"Schultz","year":"2023","journal-title":"Nature"},{"key":"2024061808223718500_B16","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1186\/1471-2164-15-316","article-title":"A customized web portal for the genome of the ctenophore Mnemiopsis leidyi","volume":"15","author":"Moreland","year":"2014","journal-title":"BMC Genomics"},{"key":"2024061808223718500_B17","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1093\/database\/baaa029","article-title":"The Mnemiopsis Genome Project Portal: integrating new gene expression resources and improving data visualization","volume":"2020","author":"Moreland","year":"2020","journal-title":"Database"},{"key":"2024061808223718500_B18","doi-asserted-by":"crossref","first-page":"e2300397","DOI":"10.1002\/pmic.202300397","article-title":"An AI-generated proteome-scale dataset of predicted protein structures for the ctenophore Mnemiopsis leidyi","author":"Moreland","year":"2024","journal-title":"Proteomics"},{"key":"2024061808223718500_B19","doi-asserted-by":"crossref","first-page":"421","DOI":"10.2307\/1537369","article-title":"Regeneration in Mnemiopsis leidyi, Agassiz","volume":"71","author":"Coonfield","year":"1936","journal-title":"Biol. Bull."},{"key":"2024061808223718500_B20","doi-asserted-by":"crossref","first-page":"556","DOI":"10.1016\/0012-1606(86)90026-6","article-title":"The ontogeny and maintenance of adult symmetry properties in the ctenophore, Mnemiopsis mccradyi","volume":"118","author":"Martindale","year":"1986","journal-title":"Dev. Biol."},{"key":"2024061808223718500_B21","doi-asserted-by":"crossref","first-page":"867","DOI":"10.3390\/genes12060867","article-title":"Whole-body regeneration in the lobate ctenophore Mnemiopsis leidyi","volume":"12","author":"Edgar","year":"2021","journal-title":"Genes"},{"key":"2024061808223718500_B22","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1016\/0146-6291(78)90590-8","article-title":"On the natural history and distribution of oceanic ctenophores","volume":"25","author":"Harbison","year":"1978","journal-title":"Deep Sea Res."},{"key":"2024061808223718500_B23","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1006\/jmsc.1994.1036","article-title":"Patterns of abundance for Mnemiopsis in US coastal waters: a comparative overview","volume":"51","author":"Kremer","year":"1994","journal-title":"ICES J. Mar. Sci."},{"key":"2024061808223718500_B24","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1007\/s10750-012-1037-9","article-title":"Transitions of Mnemiopsis leidyi (Ctenophora: Lobata) from a native to an exotic species: a review","volume":"690","author":"Costello","year":"2012","journal-title":"Hydrobiologia"},{"key":"2024061808223718500_B25","doi-asserted-by":"crossref","first-page":"zootaxa.4194.1.1","DOI":"10.11646\/zootaxa.4194.1.1","article-title":"Census of Cnidaria (Medusozoa) and Ctenophora from South American marine waters","volume":"4194","author":"Oliveira","year":"2016","journal-title":"Zootaxa"},{"key":"2024061808223718500_B26","doi-asserted-by":"crossref","first-page":"104791","DOI":"10.1016\/j.marenvres.2019.104791","article-title":"Patterns of invasive ctenophore Mnemiopsis leidyi distribution and variability in different recipient environments of the Eurasian seas: a review","volume":"152","author":"Shiganova","year":"2019","journal-title":"Mar. Environ. Res."},{"key":"2024061808223718500_B27","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1007\/BF00402849","article-title":"The feeding behavior of Beroe ovata","volume":"24","author":"Swanberg","year":"1974","journal-title":"Mar. Biol."},{"key":"2024061808223718500_B28","doi-asserted-by":"crossref","first-page":"463","DOI":"10.2307\/1542367","article-title":"Reversible epithelial adhesion closes the mouth of Beroe, a carnivorous marine jelly","volume":"181","author":"Tamm","year":"1991","journal-title":"Biol. Bull."},{"key":"2024061808223718500_B29","first-page":"57","article-title":"Evolutions et interactions tissulaires au cours de la r\u00e9g\u00e9n\u00e9ration des l\u00e8vres de Beroe ovata (Chamisso et Eysenhardt) Ct\u00e9naire Nudict\u00e9nide","volume":"11","author":"Franc","year":"1970","journal-title":"Cah. Biol. Mar."},{"key":"2024061808223718500_B30","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1242\/jcs.89.1.67","article-title":"Development of macrociliary cells in Beroe. I. Actin bundles and centriole migration","volume":"89","author":"Tamm","year":"1988","journal-title":"J. Cell Sci."},{"key":"2024061808223718500_B31","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1006\/mpev.2001.1036","article-title":"A molecular phylogenetic framework for the phylum Ctenophora using 18S rRNA genes","volume":"21","author":"Podar","year":"2001","journal-title":"Mol. Phylogenet. Evol."},{"key":"2024061808223718500_B32","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1016\/j.zool.2014.06.004","article-title":"Exploring the potential of small RNA subunit and ITS sequences for resolving phylogenetic relationships within the phylum Ctenophora","volume":"118","author":"Simion","year":"2015","journal-title":"Zoology"},{"key":"2024061808223718500_B33","doi-asserted-by":"crossref","first-page":"1737","DOI":"10.1038\/s41559-017-0331-3","article-title":"Ctenophore relationships and their placement as the sister group to all other animals","volume":"1","author":"Whelan","year":"2017","journal-title":"Nat. Ecol. 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