{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,10]],"date-time":"2026-10-10T15:00:12Z","timestamp":1791644412256,"version":"4.3.4"},"reference-count":58,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,9,18]],"date-time":"2025-09-18T00:00:00Z","timestamp":1758153600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000009","name":"Foundation for the National Institutes of Health","doi-asserted-by":"publisher","award":["1R35GM140897"],"award-info":[{"award-number":["1R35GM140897"]}],"id":[{"id":"10.13039\/100000009","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1R35GM140897"],"award-info":[{"award-number":["1R35GM140897"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006418","name":"Brown University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006418","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["IOS-1923445"],"award-info":[{"award-number":["IOS-1923445"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Developmental Biology"],"published-print":{"date-parts":[[2026,1]]},"DOI":"10.1016\/j.ydbio.2025.09.013","type":"journal-article","created":{"date-parts":[[2025,9,18]],"date-time":"2025-09-18T06:50:48Z","timestamp":1758178248000},"page":"130-141","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":3,"special_numbering":"C","title":["A transcriptomic atlas of adult tissues of the sea urchin Lytechinus variegatus identifies early transitions in gonadogenesis"],"prefix":"10.1016","volume":"529","author":[{"given":"Cosmo","family":"Pieplow","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Madison","family":"Silvia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Allex N.","family":"Gourlay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew L.","family":"Rhyne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathalie","family":"Oulhen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gary M.","family":"Wessel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.ydbio.2025.09.013_bib1","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/bs.mcb.2018.11.006","article-title":"Procuring animals and culturing of eggs and embryos","volume":"150","author":"Adams","year":"2019","journal-title":"Methods Cell Biol."},{"key":"10.1016\/j.ydbio.2025.09.013_bib2","doi-asserted-by":"crossref","DOI":"10.1093\/dnares\/dsaa007","article-title":"Transcriptomic analysis of sea star development through metamorphosis to the highly derived pentameral body plan with a focus on neural transcription factors","volume":"27","author":"Byrne","year":"2020","journal-title":"DNA Res."},{"key":"10.1016\/j.ydbio.2025.09.013_bib3","doi-asserted-by":"crossref","DOI":"10.1242\/dev.165753","article-title":"Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust","volume":"145","author":"Choi","year":"2018","journal-title":"Development"},{"key":"10.1016\/j.ydbio.2025.09.013_bib4","article-title":"Recombinant SpTransformer proteins bind to specific sites on sea urchin phagocytes and modulate SpTransformer gene expression and immune responsiveness","volume":"15","author":"Crow","year":"2024","journal-title":"Front. Immunol."},{"key":"10.1016\/j.ydbio.2025.09.013_bib5","doi-asserted-by":"crossref","first-page":"1080","DOI":"10.1093\/gbe\/evaa101","article-title":"Chromosomal-level genome assembly of the Sea Urchin Lytechinus variegatus substantially improves functional genomic analyses","volume":"12","author":"Davidson","year":"2020","journal-title":"Genome Biol. Evol"},{"key":"10.1016\/j.ydbio.2025.09.013_bib6","doi-asserted-by":"crossref","DOI":"10.1242\/dev.167288","article-title":"Conserved regulatory state expression controlled by divergent developmental gene regulatory networks in echinoids","volume":"145","author":"Erkenbrack","year":"2018","journal-title":"Development"},{"key":"10.1016\/j.ydbio.2025.09.013_bib7","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1002\/mrd.21091","article-title":"The molecular machinery of germ line specification","volume":"77","author":"Ewen-Campen","year":"2010","journal-title":"Mol. Reprod. Dev."},{"key":"10.1016\/j.ydbio.2025.09.013_bib8","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-017-17854-5","article-title":"SOX30 is required for male fertility in mice","volume":"7","author":"Feng","year":"2017","journal-title":"Sci. Rep."},{"key":"10.1016\/j.ydbio.2025.09.013_bib9","series-title":"Methods Cell Biology","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/S0091-679X(04)74003-0","article-title":"Echinoderm eggs and embryos: procurement and culture","author":"Foltz","year":"2004"},{"key":"10.1016\/j.ydbio.2025.09.013_bib10","series-title":"Methods in Cell Biology: Echinoderms","author":"Foltz","year":"2019"},{"key":"10.1016\/j.ydbio.2025.09.013_bib11","doi-asserted-by":"crossref","first-page":"931","DOI":"10.1002\/mrd.23181","article-title":"Single cell RNA-seq in the sea urchin embryo show marked cell-type specificity in the Delta\/Notch pathway","volume":"86","author":"Foster","year":"2019","journal-title":"Mol. Reprod. Dev."},{"key":"10.1016\/j.ydbio.2025.09.013_bib12","doi-asserted-by":"crossref","first-page":"6091","DOI":"10.1073\/pnas.0801201105","article-title":"Transfer of a large gene regulatory apparatus to a new developmental address in echinoid evolution","volume":"105","author":"Gao","year":"2008","journal-title":"Proc. Natl. Acad. Sci."},{"key":"10.1016\/j.ydbio.2025.09.013_bib13","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1016\/bs.mcb.2018.11.004","article-title":"Culturing echinoderm larvae through metamorphosis","volume":"150","author":"Hodin","year":"2019","journal-title":"Methods Cell Biol."},{"key":"10.1016\/j.ydbio.2025.09.013_bib14","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1016\/j.ydbio.2019.12.002","article-title":"The developmental transcriptome for Lytechinus variegatus exhibits temporally punctuated gene expression changes","volume":"460","author":"Hogan","year":"2020","journal-title":"Dev. Biol."},{"key":"10.1016\/j.ydbio.2025.09.013_bib15","first-page":"381","article-title":"The mechanics of sea urchin development","volume":"26","author":"Horstadius","year":"1950","journal-title":"Ann. Biol."},{"key":"10.1016\/j.ydbio.2025.09.013_bib16","series-title":"The Invertebrates: Echinodermata","author":"Hyman","year":"1955"},{"key":"10.1016\/j.ydbio.2025.09.013_bib17","series-title":"The Invertebrtes: Echinodermata","author":"Hyman","year":"1955"},{"key":"10.1016\/j.ydbio.2025.09.013_bib18","doi-asserted-by":"crossref","DOI":"10.1242\/dev.202991","article-title":"Stable germline transgenesis using the Minos Tc1\/mariner element in the sea urchin Lytechinus pictus","volume":"151","author":"Jackson","year":"2024","journal-title":"Development"},{"key":"10.1016\/j.ydbio.2025.09.013_bib19","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1016\/j.ydbio.2006.07.035","article-title":"Germ line determinants are not localized early in sea urchin development, but do accumulate in the small micromere lineage","volume":"300","author":"Juliano","year":"2006","journal-title":"Dev. Biol."},{"key":"10.1016\/j.ydbio.2025.09.013_bib20","series-title":"The Biology of the Cell Surface P","author":"Just","year":"1939"},{"key":"10.1016\/j.ydbio.2025.09.013_bib21","doi-asserted-by":"crossref","first-page":"4143","DOI":"10.1007\/s00204-020-02915-y","article-title":"Shedding new light on early sex determination in zebrafish","volume":"94","author":"King","year":"2020","journal-title":"Arch. Toxicol."},{"key":"10.1016\/j.ydbio.2025.09.013_bib22","doi-asserted-by":"crossref","first-page":"875","DOI":"10.1083\/jcb.149.4.875","article-title":"Zebrafish vasa RNA but not its protein is a component of the germ plasm and segregates asymmetrically before germline specification","volume":"149","author":"Knaut","year":"2000","journal-title":"JCB (J. Cell Biol.)"},{"key":"10.1016\/j.ydbio.2025.09.013_bib23","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/S0925-4773(97)00178-0","article-title":"Sea urchin ovoperoxidase: oocyte-specific member of a heme-dependent peroxidase superfamily that functions in the block to polyspermy","volume":"70","author":"LaFleur","year":"1998","journal-title":"Mech. Dev."},{"key":"10.1016\/j.ydbio.2025.09.013_bib24","series-title":"Conflict between Somatic and Gonadal Growth in Sea Urchins: a Review, the Workshop on the Coordination of Green Sea Urchin Research in Atlantic Canada","author":"Lawrence","year":"2000"},{"key":"10.1016\/j.ydbio.2025.09.013_bib25","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1038\/s42003-020-1091-1","article-title":"Genomic insights of body plan transitions from bilateral to pentameral symmetry in Echinoderms","volume":"3","author":"Li","year":"2020","journal-title":"Commun. Biol."},{"key":"10.1016\/j.ydbio.2025.09.013_bib26","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1016\/j.ydbio.2015.11.018","article-title":"Genome editing in sea urchin embryos by using a CRISPR\/Cas9 system","volume":"409","author":"Lin","year":"2016","journal-title":"Dev. Biol."},{"key":"10.1016\/j.ydbio.2025.09.013_bib27","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"10.1016\/j.ydbio.2025.09.013_bib28","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1530\/JOE-19-0277","article-title":"FOXL2 antagonises the male developmental pathway in embryonic chicken gonads","volume":"243","author":"Major","year":"2019","journal-title":"J. Endocrinol."},{"key":"10.1016\/j.ydbio.2025.09.013_bib29","doi-asserted-by":"crossref","DOI":"10.1242\/dev.198614","article-title":"Developmental single-cell transcriptomics in the Lytechinus variegatus sea urchin embryo","volume":"148","author":"Massri","year":"2021","journal-title":"Development"},{"key":"10.1016\/j.ydbio.2025.09.013_bib30","doi-asserted-by":"crossref","first-page":"2639","DOI":"10.1242\/dev.048967","article-title":"Evolutionary crossroads in developmental biology: sea urchins","volume":"138","author":"McClay","year":"2011","journal-title":"Development"},{"key":"10.1016\/j.ydbio.2025.09.013_bib31","first-page":"23","article-title":"The biology of Lytechinus variegatus","volume":"13","author":"Moore","year":"1963","journal-title":"Bull. Mar. Sci."},{"key":"10.1016\/j.ydbio.2025.09.013_bib32","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/bs.mcb.2018.11.010","article-title":"The painted sea urchin, Lytechinus pictus, as a genetically-enabled developmental model","volume":"150","author":"Nesbit","year":"2019","journal-title":"Methods Cell Biol."},{"key":"10.1016\/j.ydbio.2025.09.013_bib33","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1038\/287795a0","article-title":"Mutations affecting segment number and polarity in Drosophila","volume":"287","author":"Nusslein-Volhard","year":"1980","journal-title":"Nature"},{"key":"10.1016\/j.ydbio.2025.09.013_bib34","doi-asserted-by":"crossref","DOI":"10.1002\/mrd.23721","article-title":"Conservation and contrast in cell states of echinoderm ovaries","volume":"91","author":"Oulhen","year":"2024","journal-title":"Mol. Reprod. Dev."},{"key":"10.1016\/j.ydbio.2025.09.013_bib35","doi-asserted-by":"crossref","first-page":"1201","DOI":"10.1242\/dev.144170","article-title":"Transient translational quiescence in primordial germ cells","volume":"144","author":"Oulhen","year":"2017","journal-title":"Development"},{"key":"10.1016\/j.ydbio.2025.09.013_bib36","doi-asserted-by":"crossref","first-page":"1046","DOI":"10.1002\/mrd.22757","article-title":"Albinism as a visual, in vivo guide for CRISPR\/Cas9 functionality in the sea urchin embryo","volume":"83","author":"Oulhen","year":"2016","journal-title":"Mol. Reprod. Dev."},{"key":"10.1016\/j.ydbio.2025.09.013_bib37","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.70416","article-title":"Single-cell RNA sequencing of the Strongylocentrotus purpuratus larva reveals the blueprint of major cell types and nervous system of a non-chordate deuterostome","volume":"10","author":"Paganos","year":"2021","journal-title":"eLife"},{"key":"10.1016\/j.ydbio.2025.09.013_bib38","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1007\/978-1-0716-0974-3_12","article-title":"Methodology for whole mount and fluorescent RNA in situ hybridization in echinoderms: single, double, and beyond","volume":"2219","author":"Perillo","year":"2021","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.ydbio.2025.09.013_bib39","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1016\/j.ydbio.2024.10.003","article-title":"Sex specific gene expression is present prior to metamorphosis in the sea urchin","volume":"517","author":"Pieplow","year":"2025","journal-title":"Dev. Biol."},{"key":"10.1016\/j.ydbio.2025.09.013_bib40","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2024.114021","article-title":"Genomic signatures of exceptional longevity and negligible aging in the long-lived red sea urchin","volume":"43","author":"Polinski","year":"2024","journal-title":"Cell Rep."},{"key":"10.1016\/j.ydbio.2025.09.013_bib41","doi-asserted-by":"crossref","DOI":"10.1146\/annurev-earth-031621-113343","article-title":"Origin and early evolution of echinoderms","volume":"52","author":"Rahman","year":"2024","journal-title":"Annu. Rev. Earth Planet Sci."},{"key":"10.1016\/j.ydbio.2025.09.013_bib42","doi-asserted-by":"crossref","first-page":"941","DOI":"10.1126\/science.1133609","article-title":"The genome of the sea urchin Strongylocentrotus purpuratus","volume":"314","author":"Sea Urchin Genome Sequencing","year":"2006","journal-title":"Science"},{"key":"10.1016\/j.ydbio.2025.09.013_bib43","doi-asserted-by":"crossref","first-page":"4645","DOI":"10.1242\/dev.127.21.4645","article-title":"FIGalpha, a germ cell-specific transcription factor required for ovarian follicle formation","volume":"127","author":"Soyal","year":"2000","journal-title":"Development"},{"key":"10.1016\/j.ydbio.2025.09.013_bib44","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/j.ydbio.2024.05.012","article-title":"Localization and origins of juvenile skeletogenic cells in the sea urchin Lytechinuspictus","volume":"514","author":"Tate","year":"2024","journal-title":"Dev. Biol."},{"key":"10.1016\/j.ydbio.2025.09.013_bib45","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1111\/anu.12403","article-title":"Effects of dietary carbohydrate on weight gain and gonad production in small sea urchins, Lytechinus variegatus","volume":"23","author":"Taylor","year":"2017","journal-title":"Aquac. Nutr."},{"key":"10.1016\/j.ydbio.2025.09.013_bib46","doi-asserted-by":"crossref","first-page":"1366","DOI":"10.1038\/s41467-019-09059-3","article-title":"A stem group echinoderm from the basal Cambrian of China and the origins of Ambulacraria","volume":"10","author":"Topper","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.ydbio.2025.09.013_bib47","series-title":"Developments in Aquaculture and Fisheries Science","first-page":"155","article-title":"Chapter 10 - nutrition","author":"Watts","year":"2013"},{"key":"10.1016\/j.ydbio.2025.09.013_bib48","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1006\/dbio.1995.1033","article-title":"A protein of the sea urchin cortical granules is targeted to the fertilization envelope and contains an LDL-receptor-like motif","volume":"167","author":"Wessel","year":"1995","journal-title":"Dev. Biol."},{"key":"10.1016\/j.ydbio.2025.09.013_bib49","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1002\/mrd.22223","article-title":"The biology of the germ line in echinoderms","volume":"81","author":"Wessel","year":"2014","journal-title":"Mol. Reprod. Dev."},{"key":"10.1016\/j.ydbio.2025.09.013_bib50","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1016\/S0074-7696(01)09012-X","article-title":"The biology of cortical granules","volume":"209","author":"Wessel","year":"2001","journal-title":"Int. Rev. Cytol."},{"key":"10.1016\/j.ydbio.2025.09.013_bib51","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1073\/pnas.2109636118","article-title":"Bindin is essential for fertilization in the sea urchin","volume":"118","author":"Wessel","year":"2021","journal-title":"Proc. Natl. Acad. Sci. U. S. A"},{"key":"10.1016\/j.ydbio.2025.09.013_bib52","doi-asserted-by":"crossref","first-page":"942","DOI":"10.1002\/mrd.21090","article-title":"Cell surface changes in the egg at fertilization","volume":"76","author":"Wessel","year":"2009","journal-title":"Mol. Reprod. Dev."},{"key":"10.1016\/j.ydbio.2025.09.013_bib53","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-024-79312-3","article-title":"A molecular basis for spine color morphs in the sea urchin Lytechinus variegatus","volume":"14","author":"Wise","year":"2024","journal-title":"Sci. Rep."},{"key":"10.1016\/j.ydbio.2025.09.013_bib54","series-title":"Phenotypic and Genetic Diversity in the Sea Urchin Lytechinus variegatus (Order No. 3453400)","author":"Wise","year":"2011"},{"key":"10.1016\/j.ydbio.2025.09.013_bib55","doi-asserted-by":"crossref","DOI":"10.1016\/j.cub.2025.05.065","article-title":"A new Cambrian stem-group echinoderm reveals the evolution of the anteroposterior axis","author":"Woodgate","year":"2025","journal-title":"Curr. Biol. : CB"},{"key":"10.1016\/j.ydbio.2025.09.013_bib56","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1016\/S0091-679X(04)74004-2","article-title":"Culture of echinoderm larvae through metamorphosis","volume":"74","author":"Wray","year":"2004","journal-title":"Methods Cell Biol."},{"key":"10.1016\/j.ydbio.2025.09.013_bib57","doi-asserted-by":"crossref","first-page":"964","DOI":"10.1093\/gbe\/evu070","article-title":"Transcriptomic analysis of the highly derived radial body plan of a Sea Urchin","volume":"6","author":"Wygoda","year":"2014","journal-title":"Genome Biol. Evol."},{"key":"10.1016\/j.ydbio.2025.09.013_bib58","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1111\/dgd.12768","article-title":"Temnopleurus reevesii as a new sea urchin model in genetics","volume":"64","author":"Yaguchi","year":"2022","journal-title":"Dev. Growth Differ."}],"container-title":["Developmental Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0012160625002714?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0012160625002714?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,6,7]],"date-time":"2026-06-07T08:19:33Z","timestamp":1780820373000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0012160625002714"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1]]},"references-count":58,"alternative-id":["S0012160625002714"],"URL":"https:\/\/doi.org\/10.1016\/j.ydbio.2025.09.013","relation":{},"ISSN":["0012-1606"],"issn-type":[{"value":"0012-1606","type":"print"}],"subject":[],"published":{"date-parts":[[2026,1]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"A transcriptomic atlas of adult tissues of the sea urchin Lytechinus variegatus identifies early transitions in gonadogenesis","name":"articletitle","label":"Article Title"},{"value":"Developmental Biology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.ydbio.2025.09.013","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}]}}