{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,9]],"date-time":"2026-11-09T19:12:47Z","timestamp":1794251567581,"version":"4.9.0"},"reference-count":65,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,11,23]],"date-time":"2025-11-23T00:00:00Z","timestamp":1763856000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2025,12,22]],"date-time":"2025-12-22T00:00:00Z","timestamp":1766361600000},"content-version":"vor","delay-in-days":29,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["42276111"],"award-info":[{"award-number":["42276111"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Commun Biol"],"DOI":"10.1038\/s42003-025-09202-5","type":"journal-article","created":{"date-parts":[[2025,11,23]],"date-time":"2025-11-23T09:35:27Z","timestamp":1763890527000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Metabolic reprogramming and mitochondrial dysfunction underlie \u03b2 gonia arrest and niche cell dysfunction in sterile triploid oysters"],"prefix":"10.1038","volume":"8","author":[{"given":"Huihui","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xi","family":"Lin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunxue","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3937-9324","authenticated-orcid":false,"given":"Qi","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,11,23]]},"reference":[{"key":"9202_CR1","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1016\/j.cell.2008.02.003","volume":"132","author":"RM Cinalli","year":"2008","unstructured":"Cinalli, R. M., Rangan, P. & Lehmann, R. Germ cells are forever. Cell 132, 559\u2013562 (2008).","journal-title":"Cell"},{"key":"9202_CR2","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1016\/j.pbi.2017.11.002","volume":"41","author":"K Nakajima","year":"2018","unstructured":"Nakajima, K. Be my baby: patterning toward plant germ cells. Curr. Opin. Plant Biol. 41, 110\u2013115 (2018).","journal-title":"Curr. Opin. Plant Biol."},{"key":"9202_CR3","doi-asserted-by":"publisher","first-page":"836","DOI":"10.1038\/nrg1711","volume":"6","author":"L Comai","year":"2005","unstructured":"Comai, L. The advantages and disadvantages of being polyploid. Nat. Rev. Genet. 6, 836\u2013846 (2005).","journal-title":"Nat. Rev. Genet."},{"key":"9202_CR4","unstructured":"Galtsoff, P. S. The American Oyster, Crassostrea Virginica Gmelin (U.S. Government Printing Office, 1964)."},{"key":"9202_CR5","doi-asserted-by":"publisher","first-page":"309","DOI":"10.2307\/1542288","volume":"187","author":"X Guo","year":"1994","unstructured":"Guo, X. & Allen, S. K. Reproductive potential and genetics of triploid Pacific oysters, Crassostrea gigas (Thunberg). Biol. Bull. 187, 309\u2013318 (1994).","journal-title":"Biol. Bull."},{"key":"9202_CR6","doi-asserted-by":"publisher","first-page":"162","DOI":"10.1016\/j.jembe.2010.08.030","volume":"395","author":"A Jouaux","year":"2010","unstructured":"Jouaux, A., Heude-Berthelin, C., Sourdaine, P., Mathieu, M. & Kellner, K. Gametogenic stages in triploid oysters Crassostrea gigas: irregular locking of gonial proliferation and subsequent reproductive effort. J. Exp. Mar. Biol. Ecol. 395, 162\u2013170 (2010).","journal-title":"J. Exp. Mar. Biol. Ecol."},{"key":"9202_CR7","doi-asserted-by":"crossref","unstructured":"Wanninger, A. & Wollesen, T. Mollusca. In Evolutionary Developmental Biology of Invertebrates 2: Lophotrochozoa (Spiralia) (ed. Wanninger, A.) 103\u2013153 (Springer, 2015).","DOI":"10.1007\/978-3-7091-1871-9_7"},{"key":"9202_CR8","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1007\/s00418-017-1560-x","volume":"148","author":"L Milani","year":"2017","unstructured":"Milani, L. et al. VASA expression suggests shared germ line dynamics in bivalve molluscs. Histochem. Cell Biol. 148, 157\u2013171 (2017).","journal-title":"Histochem. Cell Biol."},{"key":"9202_CR9","doi-asserted-by":"publisher","first-page":"109499","DOI":"10.1016\/j.isci.2024.109499","volume":"27","author":"H Wang","year":"2024","unstructured":"Wang, H., Yu, H. & Li, Q. Integrative analysis of single-nucleus RNA-seq and bulk RNA-seq reveals germline cells development dynamics and niches in the Pacific oyster gonad. iScience 27, 109499 (2024).","journal-title":"iScience"},{"key":"9202_CR10","doi-asserted-by":"publisher","first-page":"111639","DOI":"10.1016\/j.cbpa.2024.111639","volume":"294","author":"H Wang","year":"2024","unstructured":"Wang, H., Yu, H. & Li, Q. Exploration of cell\u2013cell interactions and the notch signaling pathway in the gonadal niche of Crassostrea gigas. Comp. Biochem. Phys. A 294, 111639 (2024).","journal-title":"Comp. Biochem. Phys. A"},{"key":"9202_CR11","doi-asserted-by":"publisher","first-page":"737814","DOI":"10.1016\/j.aquaculture.2021.737814","volume":"549","author":"Q Yang","year":"2022","unstructured":"Yang, Q., Yu, H. & Li, Q. Refinement of a classification system for gonad development in the triploid oyster Crassostrea gigas. Aquaculture 549, 737814 (2022).","journal-title":"Aquaculture"},{"key":"9202_CR12","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1007\/s10126-024-10283-2","volume":"26","author":"Q Yang","year":"2024","unstructured":"Yang, Q., Yu, H. & Li, Q. Comparative transcriptome analysis reveals the role of ribosome reduction in impeding oogenesis in female triploid Crassostrea Gigas. Mar. Biotechnol. 26, 125\u2013135 (2024).","journal-title":"Mar. Biotechnol."},{"key":"9202_CR13","doi-asserted-by":"publisher","first-page":"e112094","DOI":"10.1371\/journal.pone.0112094","volume":"9","author":"NM Dheilly","year":"2014","unstructured":"Dheilly, N. M., Jouaux, A., Boudry, P., Favrel, P. & Lelong, C. Transcriptomic profiling of gametogenesis in triploid Pacific Oysters Crassostrea gigas: towards an understanding of partial sterility associated with triploidy. PLoS ONE 9, e112094 (2014).","journal-title":"PLoS ONE"},{"key":"9202_CR14","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijbiomac.2024.136062","volume":"280","author":"T Yu","year":"2024","unstructured":"Yu, T. et al. Single-cell RNA sequencing revealed the roles of macromolecule epidermal growth factor receptor (EGFR) in the hybrid sterility of hermaphroditic Argopecten scallops. Int. J. Biol. Macromol. 280, 136062 (2024).","journal-title":"Int. J. Biol. Macromol."},{"key":"9202_CR15","doi-asserted-by":"publisher","first-page":"1777","DOI":"10.1016\/j.cell.2022.04.003","volume":"185","author":"A Chen","year":"2022","unstructured":"Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays. Cell 185, 1777\u20131792.e21 (2022).","journal-title":"Cell"},{"key":"9202_CR16","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1016\/j.aquaculture.2013.01.009","volume":"388-391","author":"A Jouaux","year":"2013","unstructured":"Jouaux, A. et al. Impact of energy storage strategies on gametogenesis and reproductive effort in diploid and triploid Pacific oysters Crassostrea gigas\u2014involvement of insulin signaling. Aquaculture 388-391, 173\u2013181 (2013).","journal-title":"Aquaculture"},{"key":"9202_CR17","doi-asserted-by":"publisher","first-page":"107414","DOI":"10.1016\/j.bioelechem.2019.107414","volume":"132","author":"J Okuda-Shimazaki","year":"2020","unstructured":"Okuda-Shimazaki, J., Yoshida, H. & Sode, K. FAD dependent glucose dehydrogenases\u2014discovery and engineering of representative glucose sensing enzymes. Bioelectrochemistry 132, 107414 (2020).","journal-title":"Bioelectrochemistry"},{"key":"9202_CR18","doi-asserted-by":"publisher","first-page":"1909","DOI":"10.1093\/emboj\/16.8.1909","volume":"16","author":"AJ Waskiewicz","year":"1997","unstructured":"Waskiewicz, A. J., Flynn, A., Proud, C. G. & Cooper, J. A. Mitogen-activated protein kinases activate the serine\/threonine kinases Mnk1 and Mnk2. EMBO J. 16, 1909\u20131920 (1997).","journal-title":"EMBO J."},{"key":"9202_CR19","doi-asserted-by":"publisher","first-page":"4279","DOI":"10.1007\/s11033-014-3299-y","volume":"41","author":"SS Azam","year":"2014","unstructured":"Azam, S. S., Abro, A., Raza, S. & Saroosh, A. Structure and dynamics studies of sterol 24-C-methyltransferase with mechanism based inactivators for the disruption of ergosterol biosynthesis. Mol. Biol. Rep. 41, 4279\u20134293 (2014).","journal-title":"Mol. Biol. Rep."},{"key":"9202_CR20","doi-asserted-by":"publisher","first-page":"101257","DOI":"10.1016\/j.molmet.2021.101257","volume":"53","author":"S Yu","year":"2021","unstructured":"Yu, S., Meng, S., Xiang, M. & Ma, H. Phosphoenolpyruvate carboxykinase in cell metabolism: roles and mechanisms beyond gluconeogenesis. Mol. Metab. 53, 101257 (2021).","journal-title":"Mol. Metab."},{"key":"9202_CR21","doi-asserted-by":"publisher","first-page":"136769","DOI":"10.1016\/j.ijbiomac.2024.136769","volume":"282","author":"Q Yang","year":"2024","unstructured":"Yang, Q., Yu, H., Du, S. & Li, Q. Overexpression of CDC42 causes accumulation of DNA damage leading to failure of oogenesis in triploid Pacific oyster Crassostrea gigas. Int. J. Biol. Macromol. 282, 136769 (2024).","journal-title":"Int. J. Biol. Macromol."},{"key":"9202_CR22","doi-asserted-by":"publisher","DOI":"10.1016\/j.neo.2024.101075","volume":"58","author":"LH Giang","year":"2024","unstructured":"Giang, L. H. et al. RRM2 inhibition alters cell cycle through ATM\/Rb\/E2F1 pathway in atypical teratoid rhabdoid tumor. Neoplasia 58, 101075 (2024).","journal-title":"Neoplasia"},{"key":"9202_CR23","doi-asserted-by":"publisher","first-page":"867","DOI":"10.1210\/jcem-36-5-867","volume":"36","author":"U Goebelsmann","year":"1973","unstructured":"Goebelsmann, U. et al. Male pseudohermaphroditism due to testicular 17\u03b2-hydroxysteroid dehydrogenase deficiency1. J. Clin. Endocr. Metab. 36, 867\u2013879 (1973).","journal-title":"J. Clin. Endocr. Metab."},{"key":"9202_CR24","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1007\/s101269900017","volume":"2","author":"C Berthelin","year":"2000","unstructured":"Berthelin, C., Kellner, K. & Mathieu, M. Histological characterization and glucose incorporation into glycogen of the Pacific oyster Crassostrea gigas storage cells. Mar. Biotechnol. 2, 136\u2013145 (2000).","journal-title":"Mar. Biotechnol."},{"key":"9202_CR25","doi-asserted-by":"publisher","first-page":"422","DOI":"10.1016\/j.ceb.2010.05.004","volume":"22","author":"FR Maxfield","year":"2010","unstructured":"Maxfield, F. R. & van Meer, G. Cholesterol, the central lipid of mammalian cells. Curr. Opin. Cell Biol. 22, 422\u2013429 (2010).","journal-title":"Curr. Opin. Cell Biol."},{"key":"9202_CR26","doi-asserted-by":"publisher","first-page":"2565","DOI":"10.1016\/j.celrep.2017.08.056","volume":"20","author":"BM Evers","year":"2017","unstructured":"Evers, B. M. et al. Lipidomic and transcriptomic basis of lysosomal dysfunction in progranulin deficiency. Cell Rep. 20, 2565\u20132574 (2017).","journal-title":"Cell Rep."},{"key":"9202_CR27","doi-asserted-by":"publisher","DOI":"10.1016\/j.aquaculture.2022.738983","volume":"563","author":"G Zheng","year":"2023","unstructured":"Zheng, G. et al. Induction of high triploid rate blunt snout bream (Megalobrama amblycephala) by hydrostatic pressure and analysis of gonadal sterility mechanism. Aquaculture 563, 738983 (2023).","journal-title":"Aquaculture"},{"key":"9202_CR28","doi-asserted-by":"publisher","first-page":"264","DOI":"10.1111\/raq.12092","volume":"8","author":"TJ Benfey","year":"2016","unstructured":"Benfey, T. J. Effectiveness of triploidy as a management tool for reproductive containment of farmed fish: Atlantic salmon (Salmo salar) as a case study. Rev. Aquac. 8, 264\u2013282 (2016).","journal-title":"Rev. Aquac."},{"key":"9202_CR29","doi-asserted-by":"publisher","first-page":"256","DOI":"10.1038\/s41438-021-00687-9","volume":"8","author":"S Tian","year":"2021","unstructured":"Tian, S. et al. A 2.09\u2009Mb fragment translocation on chromosome 6 causes abnormalities during meiosis and leads to less seed watermelon. Hortic. Res. 8, 256 (2021).","journal-title":"Hortic. Res."},{"key":"9202_CR30","doi-asserted-by":"publisher","first-page":"483","DOI":"10.1534\/genetics.166.1.483","volume":"166","author":"PJ van Dijk","year":"2004","unstructured":"van Dijk, P. J. & Bakx-Schotman, J. M. T. Formation of unreduced megaspores (diplospory) in apomictic dandelions (Taraxacum officinale, s.l.) is controlled by a sex-specific dominant locus. Genetics 166, 483\u2013492 (2004).","journal-title":"Genetics"},{"key":"9202_CR31","doi-asserted-by":"publisher","first-page":"738477","DOI":"10.1016\/j.aquaculture.2022.738477","volume":"560","author":"Q Yang","year":"2022","unstructured":"Yang, Q., Yu, H. & Li, Q. Disruption of cell division prevents gametogenesis in triploid Pacific oysters (Crassostrea gigas). Aquaculture 560, 738477 (2022).","journal-title":"Aquaculture"},{"key":"9202_CR32","doi-asserted-by":"publisher","first-page":"e1642","DOI":"10.1002\/wrna.1642","volume":"12","author":"N Mukherjee","year":"2021","unstructured":"Mukherjee, N. & Mukherjee, C. Germ cell ribonucleoprotein granules in different clades of life: from insects to mammals. Wiley Interdiscip. Rev.: RNA 12, e1642 (2021).","journal-title":"Wiley Interdiscip. Rev.: RNA"},{"key":"9202_CR33","doi-asserted-by":"publisher","first-page":"803","DOI":"10.1038\/s41576-024-00744-8","volume":"25","author":"MC Pamula","year":"2024","unstructured":"Pamula, M. C. & Lehmann, R. How germ granules promote germ cell fate. Nat. Rev. Genet. 25, 803\u2013821 (2024).","journal-title":"Nat. Rev. Genet."},{"key":"9202_CR34","doi-asserted-by":"publisher","first-page":"1017","DOI":"10.1007\/s10126-024-10351-7","volume":"26","author":"Y Zhou","year":"2024","unstructured":"Zhou, Y. et al. Characterization of piRNAs in diploid and triploid Pacific oyster gonads: exploring their potential roles in triploid sterility. Mar. Biotechnol. 26, 1017\u20131029 (2024).","journal-title":"Mar. Biotechnol."},{"key":"9202_CR35","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1016\/j.cub.2007.02.027","volume":"17","author":"Y Chen","year":"2007","unstructured":"Chen, Y., Pane, A. & Sch\u00fcpbach, T. Cutoff and aubergine mutations result in retrotransposon upregulation and checkpoint activation in Drosophila. Curr. Biol. 17, 637\u2013642 (2007).","journal-title":"Curr. Biol."},{"key":"9202_CR36","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-21635-0","volume":"12","author":"M Spichal","year":"2021","unstructured":"Spichal, M. et al. Germ granule dysfunction is a hallmark and mirror of Piwi mutant sterility. Nat. Commun. 12, 1420 (2021).","journal-title":"Nat. Commun."},{"key":"9202_CR37","doi-asserted-by":"publisher","first-page":"891","DOI":"10.1016\/j.cell.2006.11.016","volume":"127","author":"G Seydoux","year":"2006","unstructured":"Seydoux, G. & Braun, R. E. Pathway to totipotency: lessons from germ cells. Cell 127, 891\u2013904 (2006).","journal-title":"Cell"},{"key":"9202_CR38","doi-asserted-by":"publisher","first-page":"2106","DOI":"10.1172\/JCI90281","volume":"127","author":"Y-H Shin","year":"2017","unstructured":"Shin, Y.-H. et al. Transcription factors SOHLH1 and SOHLH2 coordinate oocyte differentiation without affecting meiosis I. J. Clin. Investig. 127, 2106\u20132117 (2017).","journal-title":"J. Clin. Investig."},{"key":"9202_CR39","doi-asserted-by":"publisher","first-page":"1579","DOI":"10.1242\/dev.00365","volume":"130","author":"RT Cox","year":"2003","unstructured":"Cox, R. T. & Spradling, A. C. A Balbiani body and the fusome mediate mitochondrial inheritance during Drosophila oogenesis. Development 130, 1579\u20131590 (2003).","journal-title":"Development"},{"key":"9202_CR40","doi-asserted-by":"crossref","unstructured":"Boulais, M. et al. Involvement of mitochondrial activity and OXPHOS in ATP synthesis during the motility phase of spermatozoa in the Pacific oyster, Crassostrea gigas. Biol. Reprod. 93, 118 (2015).","DOI":"10.1095\/biolreprod.115.128538"},{"key":"9202_CR41","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1016\/j.aquaculture.2017.05.035","volume":"479","author":"M Boulais","year":"2017","unstructured":"Boulais, M. et al. ATP content and viability of spermatozoa drive variability of fertilization success in the Pacific oyster (Crassostrea gigas). Aquaculture 479, 114\u2013119 (2017).","journal-title":"Aquaculture"},{"key":"9202_CR42","doi-asserted-by":"publisher","first-page":"1639","DOI":"10.1038\/s41556-024-01513-9","volume":"26","author":"DP Narendra","year":"2024","unstructured":"Narendra, D. P. & Youle, R. J. The role of PINK1-Parkin in mitochondrial quality control. Nat. Cell Biol. 26, 1639\u20131651 (2024).","journal-title":"Nat. Cell Biol."},{"key":"9202_CR43","doi-asserted-by":"publisher","first-page":"2504","DOI":"10.1080\/15548627.2016.1239679","volume":"12","author":"SM Man","year":"2016","unstructured":"Man, S. M. & Kanneganti, T.-D. Regulation of lysosomal dynamics and autophagy by CTSB\/cathepsin B. Autophagy 12, 2504\u20132505 (2016).","journal-title":"Autophagy"},{"key":"9202_CR44","doi-asserted-by":"publisher","first-page":"170","DOI":"10.2174\/1570159X18666200522202319","volume":"19","author":"DM Belousov","year":"2021","unstructured":"Belousov, D. M., Mikhaylenko, E. V., Somasundaram, S. G., Kirkland, C. E. & Aliev, G. The dawn of mitophagy: what do we know by now?. Curr. Neuropharmacol. 19, 170 (2021).","journal-title":"Curr. Neuropharmacol."},{"key":"9202_CR45","doi-asserted-by":"publisher","first-page":"e183","DOI":"10.1016\/j.fertnstert.2023.08.536","volume":"120","author":"AR Eguren","year":"2023","unstructured":"Eguren, A. R. et al. Mitophagy-regulating gene parkin is required for female fertility. Fertil. Steril. 120, e183 (2023).","journal-title":"Fertil. Steril."},{"key":"9202_CR46","doi-asserted-by":"publisher","first-page":"8423","DOI":"10.1096\/fj.201802361R","volume":"33","author":"PA Parekh","year":"2019","unstructured":"Parekh, P. A. et al. Undifferentiated spermatogonia regulate Cyp26b1 expression through NOTCH signaling and drive germ cell differentiation. FASEB J. 33, 8423\u20138435 (2019).","journal-title":"FASEB J."},{"key":"9202_CR47","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1016\/j.ydbio.2012.12.015","volume":"375","author":"I Manosalva","year":"2013","unstructured":"Manosalva, I., Gonz\u00e1lez, A. & Kageyama, R. Hes1 in the somatic cells of the murine ovary is necessary for oocyte survival and maturation. Dev. Biol. 375, 140\u2013151 (2013).","journal-title":"Dev. Biol."},{"key":"9202_CR48","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.10832","volume":"4","author":"HS Seidel","year":"2015","unstructured":"Seidel, H. S. & Kimble, J. Cell-cycle quiescence maintains Caenorhabditis elegans germline stem cells independent of GLP-1\/Notch. eLife 4, e10832 (2015).","journal-title":"eLife"},{"key":"9202_CR49","doi-asserted-by":"publisher","first-page":"11695","DOI":"10.1016\/S0021-9258(20)71265-2","volume":"259","author":"S Eriksson","year":"1984","unstructured":"Eriksson, S., Gr\u00e4slund, A., Skog, S., Thelander, L. & Tribukait, B. Cell cycle-dependent regulation of mammalian ribonucleotide reductase. The S phase-correlated increase in subunit M2 is regulated by de novo protein synthesis. J. Biol. Chem. 259, 11695\u201311700 (1984).","journal-title":"J. Biol. Chem."},{"key":"9202_CR50","doi-asserted-by":"publisher","first-page":"378","DOI":"10.3390\/biology11030378","volume":"11","author":"H Wang","year":"2022","unstructured":"Wang, H., Yu, H., Li, Q. & Liu, S. Transcription analysis for core networks of lncRNAs-mRNAs: implication for potential role in sterility of Crassostrea gigas. Biology 11, 378 (2022).","journal-title":"Biology"},{"key":"9202_CR51","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1016\/j.aquaculture.2008.06.026","volume":"282","author":"J Normand","year":"2008","unstructured":"Normand, J., Le Pennec, M. & Boudry, P. Comparative histological study of gametogenesis in diploid and triploid Pacific oysters (Crassostrea gigas) reared in an estuarine farming site in France during the 2003 heatwave. Aquaculture 282, 124\u2013129 (2008).","journal-title":"Aquaculture"},{"key":"9202_CR52","doi-asserted-by":"publisher","DOI":"10.1186\/1477-7827-9-45","volume":"9","author":"Y Matsuda","year":"2011","unstructured":"Matsuda, Y., Ito, Y., Hashimoto, H., Yokoi, H. & Suzuki, T. Detection of vitellogenin incorporation into zebrafish oocytes by FITC fluorescence. Reprod. Biol. Endocrinol. 9, 45 (2011).","journal-title":"Reprod. Biol. Endocrinol."},{"key":"9202_CR53","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1016\/0012-1606(82)90309-8","volume":"89","author":"MD Brennan","year":"1982","unstructured":"Brennan, M. D., Weiner, A. J., Goralski, T. J. & Mahowald, A. P. The follicle cells are a major site of vitellogenin synthesis in Drosophila melanogaster. Dev. Biol. 89, 225\u2013236 (1982).","journal-title":"Dev. Biol."},{"key":"9202_CR54","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1093\/humupd\/6.3.279","volume":"6","author":"R Canipari","year":"2000","unstructured":"Canipari, R. Oocyte-granulosa cell interactions. Hum. Reprod. Update 6, 279\u2013289 (2000).","journal-title":"Hum. Reprod. Update"},{"key":"9202_CR55","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1007\/s10126-018-9798-4","volume":"20","author":"C Yue","year":"2018","unstructured":"Yue, C., Li, Q. & Yu, H. Gonad transcriptome analysis of the Pacific oyster Crassostrea gigas identifies potential genes regulating the sex determination and differentiation process. Mar. Biotechnol. 20, 206\u2013219 (2018).","journal-title":"Mar. Biotechnol."},{"key":"9202_CR56","doi-asserted-by":"publisher","unstructured":"Wang, H. H. et al. Custom analysis scripts for triploid oyster single-nucleus RNA-seq and spatial transcriptomics. Zenodo https:\/\/doi.org\/10.5281\/zenodo.17367717 (2025).","DOI":"10.5281\/zenodo.17367717"},{"key":"9202_CR57","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-020-1950-6","volume":"21","author":"S Yang","year":"2020","unstructured":"Yang, S. et al. Decontamination of ambient RNA in single-cell RNA-seq with DecontX. Genome Biol. 21, 1\u201315 (2020).","journal-title":"Genome Biol."},{"key":"9202_CR58","doi-asserted-by":"publisher","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","volume":"16","author":"I Korsunsky","year":"2019","unstructured":"Korsunsky, I. et al. Fast, sensitive and accurate integration of single-cell data with harmony. Nat. Methods 16, 1289\u20131296 (2019).","journal-title":"Nat. Methods"},{"key":"9202_CR59","doi-asserted-by":"publisher","first-page":"D870","DOI":"10.1093\/nar\/gkac947","volume":"51","author":"C Hu","year":"2023","unstructured":"Hu, C. et al. CellMarker 2.0: an updated database of manually curated cell markers in human\/mouse and web tools based on scRNA-seq data. Nucleic Acids Res. 51, D870\u2013D876 (2023).","journal-title":"Nucleic Acids Res."},{"key":"9202_CR60","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1038\/nbt.4314","volume":"37","author":"E Becht","year":"2019","unstructured":"Becht, E. et al. Dimensionality reduction for visualizing single-cell data using UMAP. Nat. Biotechnol. 37, 38\u201344 (2019).","journal-title":"Nat. Biotechnol."},{"key":"9202_CR61","doi-asserted-by":"publisher","first-page":"716","DOI":"10.1016\/j.cell.2018.05.061","volume":"174","author":"Dijk","year":"2018","unstructured":"Dijk et al. Recovering gene interactions from single-cell data using data diffusion. Cell 174, 716\u2013729.e27 (2018).","journal-title":"Cell"},{"key":"9202_CR62","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1038\/s41587-021-01139-4","volume":"40","author":"V Kleshchevnikov","year":"2022","unstructured":"Kleshchevnikov, V. et al. Cell2location maps fine-grained cell types in spatial transcriptomics. Nat. Biotechnol. 40, 661\u2013671 (2022).","journal-title":"Nat. Biotechnol."},{"key":"9202_CR63","doi-asserted-by":"publisher","first-page":"979","DOI":"10.1038\/nmeth.4402","volume":"14","author":"X Qiu","year":"2017","unstructured":"Qiu, X. et al. Reversed graph embedding resolves complex single-cell trajectories. Nat. Methods 14, 979\u2013982 (2017).","journal-title":"Nat. Methods"},{"key":"9202_CR64","doi-asserted-by":"publisher","first-page":"1408","DOI":"10.1038\/s41587-020-0591-3","volume":"38","author":"V Bergen","year":"2020","unstructured":"Bergen, V., Lange, M., Peidli, S., Wolf, F. A. & Theis, F. J. Generalizing RNA velocity to transient cell states through dynamical modeling. Nat. Biotechnol. 38, 1408\u20131414 (2020).","journal-title":"Nat. Biotechnol."},{"key":"9202_CR65","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-21246-9","volume":"12","author":"S Jin","year":"2021","unstructured":"Jin, S. et al. Inference and analysis of cell\u2013cell communication using CellChat. Nat. Commun. 12, 1088 (2021).","journal-title":"Nat. Commun."}],"container-title":["Communications Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-09202-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-09202-5","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-09202-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,22]],"date-time":"2025-12-22T13:02:16Z","timestamp":1766408536000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-09202-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,23]]},"references-count":65,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["9202"],"URL":"https:\/\/doi.org\/10.1038\/s42003-025-09202-5","relation":{},"ISSN":["2399-3642"],"issn-type":[{"value":"2399-3642","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,23]]},"assertion":[{"value":"5 May 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 November 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 November 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"1802"}}