{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,27]],"date-time":"2026-04-27T17:36:54Z","timestamp":1777311414764,"version":"3.51.4"},"reference-count":114,"publisher":"The Royal Society","issue":"2061","license":[{"start":{"date-parts":[[2025,12,17]],"date-time":"2025-12-17T00:00:00Z","timestamp":1765929600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/royalsociety.org\/-\/media\/journals\/author\/Licence-to-Publish-20062019-final.pdf"},{"start":{"date-parts":[[2025,12,17]],"date-time":"2025-12-17T00:00:00Z","timestamp":1765929600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/royalsociety.org\/journals\/ethics-policies\/data-sharing-mining\/"}],"funder":[{"DOI":"10.13039\/100010434","name":"'la Caixa' Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010434","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010909","name":"Excellent Young Scientists Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100010909","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,12,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Cephalopods play a central ecological role across all oceans and depths. However, under the current climate crisis, their physiology and behaviour are impacted, and we are beginning to comprehend the effects of environmental stressors at a molecular level. Here, we study the Hawaiian bobtail squid (Euprymna scolopes), known for its specific binary symbiosis with the bioluminescent bacterium Vibrio fischeri acquired post-hatching. We aim to understand the response (i.e. developmental and molecular) of E. scolopes after embryogenetic exposure to different conditions: (i) standard conditions (control), (ii) increased CO2 (\u2206pH 0.4 units), (iii) warming (+3\u00b0C), or (iv) a combination of the two treatments. We observed a decrease in hatching success across all treatments relative to the control, and elevated temperature shortened the developmental time. Using transcriptomics, we identified modulation in metabolic pathways and energy production, at the expense of development under increased CO2. In addition to finding differentially expressed genes related to RNA editing, we also identified several splicing events linked to phenotypic plasticity in response to increased CO2 and temperature. The data also suggest that the initiation of the symbiosis may be negatively affected by these environmental drivers of change in the biosphere, although the animal may counter these via coping mechanisms.<\/jats:p>","DOI":"10.1098\/rspb.2025.1636","type":"journal-article","created":{"date-parts":[[2025,12,26]],"date-time":"2025-12-26T18:46:06Z","timestamp":1766774766000},"source":"Crossref","is-referenced-by-count":1,"title":["Developmental and transcriptomic responses of Hawaiian bobtail squid early stages to ocean warming and acidification"],"prefix":"10.1098","volume":"292","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0880-9360","authenticated-orcid":false,"given":"Eve","family":"Otjacques","sequence":"first","affiliation":[{"name":"Faculdade de Ci\u00eancias da Universidade de Lisboa, Laborat\u00f3rio Mar\u00edtimo da Guia 1 , ,","place":["Av. Nossa Senhora do Cabo, 939, 2750-374 Cascais, Portugal"],"department":["MARE\u2014Marine and Environmental Sciences Centre & ARNET\u2014Aquatic Research Network"]},{"name":"Carnegie Science 2 , , ,","place":["Church Laboratory, California Institute of Technology, 1200 E. California Blvd. Pasadena, CA, USA, 91125"],"department":["Division of Biosphere Sciences and Engineering"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1729-7256","authenticated-orcid":false,"given":"Jos\u00e9 Ricardo","family":"Paula","sequence":"additional","affiliation":[{"name":"Faculdade de Ci\u00eancias da Universidade de Lisboa, Laborat\u00f3rio Mar\u00edtimo da Guia 1 , ,","place":["Av. Nossa Senhora do Cabo, 939, 2750-374 Cascais, Portugal"],"department":["MARE\u2014Marine and Environmental Sciences Centre & ARNET\u2014Aquatic Research Network"]},{"name":"Faculdade de Ci\u00eancias da Universidade de Lisboa 3 , ,","place":["Campo Grande,1749-016 Lisboa, Portugal"],"department":["Departamento de Biologia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4112-4830","authenticated-orcid":false,"given":"Edward G.","family":"Ruby","sequence":"additional","affiliation":[{"name":"Carnegie Science 2 , , ,","place":["Church Laboratory, California Institute of Technology, 1200 E. California Blvd. Pasadena, CA, USA, 91125"],"department":["Division of Biosphere Sciences and Engineering"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9621-6660","authenticated-orcid":false,"given":"Jos\u00e9 C.","family":"Xavier","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, University of Coimbra 4 , ,","place":["3000-456 Coimbra, Portugal"],"department":["Centre for Functional Ecology (CFE)"]},{"name":"Natural Environment Research Council (NERC), High Cross, Madingley Road 5 , , ,","place":["Cambridge, Cambridgeshire, UK, CB3 0ET"],"department":["British Antarctic Survey (BAS)"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6046-6238","authenticated-orcid":false,"given":"Margaret J.","family":"McFall-Ngai","sequence":"additional","affiliation":[{"name":"Carnegie Science 2 , , ,","place":["Church Laboratory, California Institute of Technology, 1200 E. California Blvd. Pasadena, CA, USA, 91125"],"department":["Division of Biosphere Sciences and Engineering"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rui","family":"Rosa","sequence":"additional","affiliation":[{"name":"Faculdade de Ci\u00eancias da Universidade de Lisboa, Laborat\u00f3rio Mar\u00edtimo da Guia 1 , ,","place":["Av. Nossa Senhora do Cabo, 939, 2750-374 Cascais, Portugal"],"department":["MARE\u2014Marine and Environmental Sciences Centre & ARNET\u2014Aquatic Research Network"]},{"name":"Faculdade de Ci\u00eancias da Universidade de Lisboa 3 , ,","place":["Campo Grande,1749-016 Lisboa, Portugal"],"department":["Departamento de Biologia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3620-2731","authenticated-orcid":false,"given":"Celia","family":"Schunter","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, The University of Hong Kong 6 , ,","place":["Pok Fu Lam, Hong Kong SAR"],"department":["Swire Institute of Marine Science"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"175","published-online":{"date-parts":[[2025,12,17]]},"reference":[{"key":"2026010403560949000_R1","doi-asserted-by":"crossref","first-page":"162","DOI":"10.5670\/oceanog.2018.205","article-title":"Categorizing and naming marine heatwaves","volume":"31","author":"Hobday","year":"2018","journal-title":"Oceanography"},{"key":"2026010403560949000_R2","first-page":"447","volume-title":"IPCC special report on the ocean and cryosphere in a changing climate","author":"Bindoff","year":"2019"},{"key":"2026010403560949000_R3","first-page":"1211","volume-title":"Climate change 2021: The Physical Science Basis. Working Group I Contribution to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change","author":"Fox-Kemper","year":"2021"},{"key":"2026010403560949000_R4","doi-asserted-by":"crossref","unstructured":"IPCC\n          . Climate change 2023: Synthesis Report. Contribution of Working Groups I, II and III to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change. (eds Core Writing Team,LeeH, RomeroJ), pp. 35\u2013115. Geneva, Switzerland: Intergovernmental Panel on Climate Change (IPCC). Seehttps:\/\/doi.org\/10.59327\/IPCC\/AR6-9789291691647.","DOI":"10.59327\/IPCC\/AR6-9789291691647"},{"key":"2026010403560949000_R5","first-page":"1","article-title":"Effect of increased atmospheric CO2 on shallow water marine benthos","volume":"110","author":"Shirayama","year":"2005","journal-title":"J. Geophys. Res."},{"key":"2026010403560949000_R6","doi-asserted-by":"crossref","first-page":"1737","DOI":"10.1126\/science.1152509","article-title":"Coral reefs under rapid climate change and ocean acidification","volume":"318","author":"Hoegh-Guldberg","year":"2007","journal-title":"Science"},{"key":"2026010403560949000_R7","doi-asserted-by":"crossref","first-page":"149","DOI":"10.3354\/cr00760","article-title":"Vulnerability of Antarctic shelf biodiversity to predicted regional warming","volume":"37","author":"Barnes","year":"2008","journal-title":"Clim. Res."},{"key":"2026010403560949000_R8","doi-asserted-by":"crossref","first-page":"995","DOI":"10.1038\/nclimate1982","article-title":"Sensitivities of extant animal taxa to ocean acidification","volume":"3","author":"Wittmann","year":"2013","journal-title":"Nat. Clim. Chang."},{"key":"2026010403560949000_R9","doi-asserted-by":"crossref","DOI":"10.1038\/srep41443","article-title":"Seagrass ecophysiological performance under ocean warming and acidification","volume":"7","author":"Repolho","year":"2017","journal-title":"Sci. Rep."},{"key":"2026010403560949000_R10","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1002\/ecm.1297","article-title":"Living in a high CO2 world: a global meta-analysis shows multiple trait-mediated fish responses to ocean acidification","volume":"88","author":"Cattano","year":"2018","journal-title":"Ecol. Monogr."},{"key":"2026010403560949000_R11","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-019-49086-0","article-title":"Neurobiological and behavioural responses of cleaning mutualisms to ocean warming and acidification","volume":"9","author":"Paula","year":"2019","journal-title":"Sci. Rep."},{"key":"2026010403560949000_R12","doi-asserted-by":"crossref","DOI":"10.3390\/biology9070147","article-title":"Cuttlefish buoyancy in response to food availability and ocean acidification","volume":"9","author":"Otjacques","year":"2020","journal-title":"Biology"},{"key":"2026010403560949000_R13","doi-asserted-by":"crossref","first-page":"215","DOI":"10.3390\/oceans1040016","article-title":"Effect of acute seawater temperature increase on the survival of a fish ectoparasite","volume":"1","author":"Shodipo","year":"2020","journal-title":"Oceans"},{"key":"2026010403560949000_R14","doi-asserted-by":"crossref","first-page":"1240","DOI":"10.1093\/icb\/icad102","article-title":"Climate-change impacts on cephalopods: a meta-analysis","volume":"63","author":"Borges","year":"2023","journal-title":"Integr. Comp. Biol."},{"key":"2026010403560949000_R15","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/B978-0-12-817945-1.00005-8","volume-title":"Predicting future oceans: sustainability of ocean and human systems amidst global environmental change","author":"Fr\u00f6licher","year":"2019"},{"key":"2026010403560949000_R16","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1146\/annurev-marine-032720-095144","article-title":"Marine heatwaves","volume":"13","author":"Oliver","year":"2021","journal-title":"Annu. Rev. Mar. Sci."},{"key":"2026010403560949000_R17","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1098\/rstb.1996.0096","article-title":"The role of cephalopods in the world\u2019s oceans: general conclusions and the future","volume":"351","author":"Clarke","year":"1996","journal-title":"Phil. Trans. R. Soc. Lond. B"},{"key":"2026010403560949000_R18","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1007\/s11160-019-09554-2","article-title":"The ecological role of cephalopods and their representation in ecosystem models","volume":"29","author":"de la Chesnais","year":"2019","journal-title":"Rev. Fish Biol. Fish."},{"key":"2026010403560949000_R19","doi-asserted-by":"crossref","first-page":"2692","DOI":"10.1111\/1365-2656.13333","article-title":"Functional traits explain trophic allometries of cephalopods","volume":"89","author":"Murphy","year":"2020","journal-title":"J. Anim. Ecol."},{"key":"2026010403560949000_R20","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1080\/23308249.2015.1026226","article-title":"World squid fisheries","volume":"23","author":"Arkhipkin","year":"2015","journal-title":"Rev. Fish. Sci. Aquac."},{"key":"2026010403560949000_R21","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1017\/S0025315414000782","article-title":"Future challenges in cephalopod research","volume":"95","author":"Xavier","year":"2015","journal-title":"J. Mar. Biol. Assoc. U. K."},{"key":"2026010403560949000_R22","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1080\/23308249.2019.1680603","article-title":"World octopus fisheries","volume":"29","author":"Sauer","year":"2021","journal-title":"Rev. Fish. Sci. Aquac."},{"key":"2026010403560949000_R23","doi-asserted-by":"crossref","first-page":"20776","DOI":"10.1073\/pnas.0806886105","article-title":"Synergistic effects of climate-related variables suggest future physiological impairment in a top oceanic predator","volume":"105","author":"Rosa","year":"2008","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2026010403560949000_R24","doi-asserted-by":"crossref","first-page":"2585","DOI":"10.1111\/gcb.14098","article-title":"Predatory strategies and behaviours in cephalopods are altered by elevated CO2","volume":"24","author":"Spady","year":"2018","journal-title":"Glob. Chang. Biol."},{"key":"2026010403560949000_R25","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0038282","article-title":"Ocean warming enhances malformations, premature hatching, metabolic suppression and oxidative stress in the early life stages of a keystone squid","volume":"7","author":"Rosa","year":"2012","journal-title":"PLoS One"},{"key":"2026010403560949000_R26","doi-asserted-by":"crossref","first-page":"20131695","DOI":"10.1098\/rspb.2013.1695","article-title":"Lower hypoxia thresholds of cuttlefish early life stages living in a warm acidified ocean","volume":"280","author":"Rosa","year":"2013","journal-title":"Proc. R. Soc. B"},{"key":"2026010403560949000_R27","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1242\/jeb.096081","article-title":"Differential impacts of ocean acidification and warming on winter and summer progeny of a coastal squid (Loligo vulgaris)","volume":"217","author":"Rosa","year":"2014","journal-title":"J. Exp. Biol."},{"key":"2026010403560949000_R28","doi-asserted-by":"crossref","first-page":"104812","DOI":"10.1016\/j.marenvres.2019.104812","article-title":"Elevated seawater pCO2 affects reproduction and embryonic development in the pygmy squid, Idiosepius pygmaeus","volume":"153","author":"Spady","year":"2020","journal-title":"Mar. Environ. Res."},{"key":"2026010403560949000_R29","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0063714","article-title":"Adverse effects of ocean acidification on early development of squid (Doryteuthis pealeii)","volume":"8","author":"Kaplan","year":"2013","journal-title":"PLoS One"},{"key":"2026010403560949000_R30","doi-asserted-by":"crossref","DOI":"10.3390\/biology11101394","article-title":"Camouflage and exploratory avoidance of newborn cuttlefish under warming and acidification","volume":"11","author":"Court","year":"2022","journal-title":"Biology"},{"key":"2026010403560949000_R31","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1023\/A:1019624425971","article-title":"Phenotypic plasticity: linking molecular mechanisms with evolutionary outcomes","volume":"16","author":"Schlichting","year":"2002","journal-title":"Evol. Ecol."},{"key":"2026010403560949000_R32","doi-asserted-by":"crossref","DOI":"10.3389\/fgene.2020.538226","article-title":"Genetic constraints, transcriptome plasticity, and the evolutionary response to climate change","volume":"11","author":"Logan","year":"2020","journal-title":"Front. Genet."},{"key":"2026010403560949000_R33","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/s12983-020-0350-9","article-title":"Ocean acidification promotes broad transcriptomic responses in marine metazoans: a literature survey","volume":"17","author":"Strader","year":"2020","journal-title":"Front. Zool."},{"key":"2026010403560949000_R34","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1152\/physiol.00029.2012","article-title":"A role for A-to-I RNA editing in temperature adaptation","volume":"27","author":"Garrett","year":"2012","journal-title":"Physiology"},{"key":"2026010403560949000_R35","doi-asserted-by":"crossref","first-page":"651","DOI":"10.3390\/biology2020651","article-title":"Predicting the response of molluscs to the impact of ocean acidification","volume":"2","author":"Parker","year":"2013","journal-title":"Biology"},{"key":"2026010403560949000_R36","doi-asserted-by":"crossref","first-page":"2544","DOI":"10.1016\/j.cell.2023.05.004","article-title":"Temperature-dependent RNA editing in octopus extensively recodes the neural proteome","volume":"186","author":"Birk","year":"2023","journal-title":"Cell"},{"key":"2026010403560949000_R37","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1186\/s12864-024-10542-5","article-title":"Transcriptomic responses in the nervous system and correlated behavioural changes of a cephalopod exposed to ocean acidification","volume":"25","author":"Thomas","year":"2024","journal-title":"BMC Genom"},{"key":"2026010403560949000_R38","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1038\/s41579-021-00567-y","article-title":"A lasting symbiosis: how the Hawaiian bobtail squid finds and keeps its bioluminescent bacterial partner","volume":"19","author":"Nyholm","year":"2021","journal-title":"Nat. Rev. Microbiol."},{"key":"2026010403560949000_R39","doi-asserted-by":"crossref","first-page":"632","DOI":"10.1038\/nrmicro957","article-title":"The winnowing: establishing the squid-vibrio symbiosis","volume":"2","author":"Nyholm","year":"2004","journal-title":"Nat. Rev. Microbiol."},{"key":"2026010403560949000_R40","doi-asserted-by":"crossref","first-page":"1885","DOI":"10.1111\/evo.13819","article-title":"Adaptation to temperature stress by Vibrio fischeri facilitates this microbe\u2019s symbiosis with the Hawaiian bobtail squid (Euprymna scolopes","volume":"73","author":"Cohen","year":"2019","journal-title":"Evolution"},{"key":"2026010403560949000_R41","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1099\/mic.0.000884","article-title":"Adaptation to pH stress by Vibrio fischeri can affect its symbiosis with the Hawaiian bobtail squid (Euprymna scolopes)","volume":"166","author":"Cohen","year":"2020","journal-title":"Microbiology"},{"key":"2026010403560949000_R42","unstructured":"Lewis\n              E\n            , WallaceDWR. 1998Program Developed for CO2 System Calculations. Oak Ridge, TN: Carbon dioxide information analysis center, Oak Ridge National Laboratory, US Department of Energy."},{"key":"2026010403560949000_R43","unstructured":"Therneau\n              T\n            \n          . 2024A package for survival analysis in R. R package. 2024:3.6-4. Seehttps:\/\/CRAN.R-project.org\/package=survival."},{"key":"2026010403560949000_R44","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1007\/978-1-4757-3294-8_3","volume-title":"Modeling Survival Data: Extending the Cox Model","author":"Therneau","year":"2000"},{"key":"2026010403560949000_R45","doi-asserted-by":"crossref","unstructured":"Kassambara\n              A\n            , KosinskiM, survminerBP. 2016Drawing survival curves using \u2018ggplot2\u2019. R package. 2016:0.4.9. Seehttps:\/\/CRAN.R-project.org\/package=survminer.","DOI":"10.32614\/CRAN.package.survminer"},{"key":"2026010403560949000_R46","unstructured":"Andrews\n              S\n            \n          . 2010FastQC: a quality control tool for high throughput sequence data. Seehttps:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/."},{"key":"2026010403560949000_R47","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2026010403560949000_R48","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with Kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol."},{"key":"2026010403560949000_R49","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.2988","article-title":"Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies","volume":"5","author":"Cabau","year":"2017","journal-title":"PeerJ"},{"key":"2026010403560949000_R50","doi-asserted-by":"crossref","first-page":"D590","DOI":"10.1093\/nar\/gks1219","article-title":"The SILVA ribosomal RNA gene database project: improved data processing and web-based tools","volume":"41","author":"Quast","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2026010403560949000_R51","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"2026010403560949000_R52","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1038\/s41597-023-02903-8","article-title":"Gene modelling and annotation for the Hawaiian bobtail squid, Euprymna scolopes","volume":"11","author":"Rogers","year":"2024","journal-title":"Sci. Data"},{"key":"2026010403560949000_R53","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2026010403560949000_R54","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","article-title":"featureCounts: an efficient general purpose program for assigning sequence reads to genomic features","volume":"30","author":"Liao","year":"2014","journal-title":"Bioinformatics"},{"key":"2026010403560949000_R55","doi-asserted-by":"crossref","first-page":"5825","DOI":"10.1093\/molbev\/msab293","article-title":"eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale","volume":"38","author":"Cantalapiedra","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"2026010403560949000_R56","doi-asserted-by":"crossref","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":"2026010403560949000_R57","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-9-559","article-title":"WGCNA: an R package for weighted correlation network analysis","volume":"9","author":"Langfelder","year":"2008","journal-title":"BMC Bioinform."},{"key":"2026010403560949000_R58","unstructured":"Carlson\n              M\n            , Pag\u00e8sH. 2024AnnotationForge: tools for building SQLite-based annotation data packages. R package. 2024:1.42.2. Seehttps:\/\/bioconductor.org\/packages\/AnnotationForge."},{"key":"2026010403560949000_R59","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: an R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"OMICS J. Integr. Biol."},{"key":"2026010403560949000_R60","doi-asserted-by":"crossref","first-page":"1083","DOI":"10.1038\/s41596-023-00944-2","article-title":"rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data","volume":"19","author":"Wang","year":"2024","journal-title":"Nat. Protoc."},{"key":"2026010403560949000_R61","doi-asserted-by":"crossref","first-page":"R1100","DOI":"10.1152\/ajpregu.00653.2010","article-title":"Elevated seawater PCO\u2082 differentially affects branchial acid-base transporters over the course of development in the cephalopod Sepia officinalis","volume":"300","author":"Hu","year":"2011","journal-title":"Am. J. Physiol. Regul. Integr. Comp. Physiol."},{"key":"2026010403560949000_R62","doi-asserted-by":"crossref","DOI":"10.1111\/gcb.70243","article-title":"Climate-driven warming disrupts the symbiosis of bobtail squid Euprymna scolopes and the luminous bacterium Vibrio fischeri","volume":"31","author":"Otjacques","year":"2025","journal-title":"Glob. Chang. Biol."},{"key":"2026010403560949000_R63","doi-asserted-by":"crossref","DOI":"10.3389\/fphys.2020.00501","article-title":"Antagonistic interactions and clutch-dependent sensitivity induce variable responses to ocean acidification and warming in squid (Doryteuthis pealeii) embryos and paralarvae","volume":"11","author":"Zakroff","year":"2020","journal-title":"Front. Physiol."},{"key":"2026010403560949000_R64","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1007\/s00360-013-0783-y","article-title":"Developmental and physiological challenges of octopus (Octopus vulgaris) early life stages under ocean warming","volume":"184","author":"Repolho","year":"2014","journal-title":"J. Comp. Physiol. B"},{"key":"2026010403560949000_R65","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00227-019-3510-8","article-title":"Dose-dependence and small-scale variability in responses to ocean acidification during squid, Doryteuthis pealeii, development","volume":"166","author":"Zakroff","year":"2019","journal-title":"Mar. Biol."},{"key":"2026010403560949000_R66","doi-asserted-by":"crossref","first-page":"1199","DOI":"10.2108\/zsj.18.1199","article-title":"Vacuolar-type H+ -ATPase and Na+, K+-ATPase expression in gills of Atlantic Salmon (Salmo salar) during Isolated and combined exposure to hyperoxia and hypercapnia in fresh water","volume":"18","author":"Seidelin","year":"2001","journal-title":"Zool. Sci."},{"key":"2026010403560949000_R67","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1002\/jez.a.10251","article-title":"Compensation for hypercapnia by a euryhaline elasmobranch: effect of salinity and roles of gills and kidneys in fresh water","volume":"297A","author":"Choe","year":"2003","journal-title":"J. Exp. Zool. Comp. Exp. Biol."},{"key":"2026010403560949000_R68","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1007\/s00360-009-0412-y","article-title":"Acid\u2013base regulatory ability of the cephalopod (Sepia officinalis) in response to environmental hypercapnia","volume":"180","author":"Gutowska","year":"2010","journal-title":"J. Comp. Physiol. B"},{"key":"2026010403560949000_R69","doi-asserted-by":"crossref","first-page":"R1700","DOI":"10.1152\/ajpregu.00107.2011","article-title":"New insights into ion regulation of cephalopod molluscs: a role of epidermal ionocytes in acid-base regulation during embryogenesis","volume":"301","author":"Hu","year":"2011","journal-title":"Am. J. Physiol. Regul. Integr. Comp. Physiol."},{"key":"2026010403560949000_R70","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1038\/nrm2272","article-title":"Vacuolar ATPases: rotary proton pumps in physiology and pathophysiology","volume":"8","author":"Forgac","year":"2007","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"2026010403560949000_R71","doi-asserted-by":"crossref","first-page":"1762","DOI":"10.1242\/jeb.028803","article-title":"Regulation of the V-ATPase in kidney epithelial cells: dual role in acid\u2013base homeostasis and vesicle trafficking","volume":"212","author":"Brown","year":"2009","journal-title":"J. Exp. Biol."},{"key":"2026010403560949000_R72","first-page":"55","article-title":"Branchial NH4+-dependent acid\u2013base transport mechanisms and energy metabolism of squid (Sepioteuthis lessoniana) affected by seawater acidification","volume":"11","author":"Hu","year":"2014","journal-title":"Front. Zool"},{"key":"2026010403560949000_R73","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1080\/10236249409378913","article-title":"Coordination of metabolism, acid-base regulation and haemocyanin function in cephalopods","volume":"25","author":"P\u00f6rtner","year":"1995","journal-title":"Mar. Freshw. Behav. Physiol."},{"key":"2026010403560949000_R74","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1152\/advan.00046.2004","article-title":"Ion homeostasis, channels, and transporters: an update on cellular mechanisms","volume":"28","author":"Dubyak","year":"2004","journal-title":"Adv. Physiol. Educ."},{"key":"2026010403560949000_R75","doi-asserted-by":"crossref","first-page":"1248","DOI":"10.1111\/mec.13111","article-title":"Differential proteomic responses of selectively bred and wild-type Sydney rock oyster populations exposed to elevated CO2","volume":"24","author":"Thompson","year":"2015","journal-title":"Mol. Ecol."},{"key":"2026010403560949000_R76","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2164-15-951","article-title":"Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas","volume":"15","author":"Timmins-Schiffman","year":"2014","journal-title":"BMC Genom."},{"key":"2026010403560949000_R77","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/j.jprot.2014.08.010","article-title":"Proteomic and metabolomic responses of Pacific oyster Crassostrea gigas to elevated pCO2 exposure","volume":"112","author":"Wei","year":"2015","journal-title":"J. Proteomics"},{"key":"2026010403560949000_R78","doi-asserted-by":"crossref","first-page":"1503","DOI":"10.1002\/2211-5463.12695","article-title":"Effects of acidification on the proteome during early development of Babylonia areolata","volume":"9","author":"Di","year":"2019","journal-title":"FEBS Open Bio."},{"key":"2026010403560949000_R79","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2164-15-789","article-title":"Gene expression profiling in gills of the great spider crab Hyas araneus in response to ocean acidification and warming","volume":"15","author":"Harms","year":"2014","journal-title":"BMC Genom."},{"key":"2026010403560949000_R80","doi-asserted-by":"crossref","DOI":"10.3389\/fphys.2021.761117","article-title":"An explanation based on energy-related changes for blue mussel Mytilus edulis coping with seawater acidification","volume":"12","author":"Guo","year":"2021","journal-title":"Front. Physiol."},{"key":"2026010403560949000_R81","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1016\/j.dci.2016.10.004","article-title":"Molecular characterization and function of the Prohibitin2 gene in Litopenaeus vannamei responses to Vibrio alginolyticus","volume":"67","author":"Gu","year":"2017","journal-title":"Dev. Comp. Immunol."},{"key":"2026010403560949000_R82","doi-asserted-by":"crossref","DOI":"10.1016\/j.fsi.2024.109770","article-title":"Molecular characterization, expression profiling, and functional analysis of prohibitin 1 in red seabream, Pagrus major","volume":"152","author":"Choi","year":"2024","journal-title":"Fish Shellfish Immunol."},{"key":"2026010403560949000_R83","doi-asserted-by":"crossref","first-page":"1483","DOI":"10.1126\/science.1094291","article-title":"Convergence of Wnt, \u00df-Catenin, and cadherin pathways","volume":"303","author":"Nelson","year":"2004","journal-title":"Science"},{"key":"2026010403560949000_R84","doi-asserted-by":"crossref","first-page":"3286","DOI":"10.1101\/gad.11.24.3286","article-title":"Wnt signaling: a common theme in animal development","volume":"11","author":"Cadigan","year":"1997","journal-title":"Genes Dev."},{"key":"2026010403560949000_R85","doi-asserted-by":"crossref","first-page":"448","DOI":"10.1038\/nature01611","article-title":"Wnt proteins are lipid-modified and can act as stem cell growth factors","volume":"423","author":"Willert","year":"2003","journal-title":"Nature"},{"key":"2026010403560949000_R86","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1083\/jcb.124.5.729","article-title":"Wnt-1 modulates cell-cell adhesion in mammalian cells by stabilizing beta-catenin binding to the cell adhesion protein cadherin","volume":"124","author":"Hinck","year":"1994","journal-title":"J. Cell Biol."},{"key":"2026010403560949000_R87","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1083\/jcb.200307111","article-title":"A core function for p120-catenin in cadherin turnover","volume":"163","author":"Davis","year":"2003","journal-title":"J. Cell Biol."},{"key":"2026010403560949000_R88","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1002\/lno.10617","article-title":"Molecular and geochemical perspectives on the influence of CO2 on calcification in coral cell cultures","volume":"63","author":"Drake","year":"2018","journal-title":"Limnol. Oceanogr."},{"key":"2026010403560949000_R89","doi-asserted-by":"crossref","DOI":"10.1016\/j.scitotenv.2020.140177","article-title":"Transcriptional changes of Pacific oyster Crassostrea gigas reveal essential role of calcium signal pathway in response to CO2-driven acidification","volume":"741","author":"Wang","year":"2020","journal-title":"Sci. Total Environ."},{"key":"2026010403560949000_R90","doi-asserted-by":"crossref","DOI":"10.3389\/fmars.2021.782583","article-title":"Ocean acidification triggers cell signaling, suppress immune and calcification in the Pacific Oyster Larvae","volume":"8","author":"Dineshram","year":"2021","journal-title":"Front. Mar. Sci."},{"key":"2026010403560949000_R91","doi-asserted-by":"crossref","DOI":"10.1016\/j.marpolbul.2021.112282","article-title":"Ocean acidification but not hypoxia alters the gonad performance in the thick shell mussel Mytilus coruscus","volume":"167","author":"Wang","year":"2021","journal-title":"Mar. Pollut. Bull."},{"key":"2026010403560949000_R92","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nature08197","article-title":"Recent progress in the biology and physiology of sirtuins","volume":"460","author":"Finkel","year":"2009","journal-title":"Nature"},{"key":"2026010403560949000_R93","doi-asserted-by":"crossref","first-page":"110528","DOI":"10.1016\/j.cbpa.2019.110528","article-title":"Sirtuins as regulators of the cellular stress response and metabolism in marine ectotherms","volume":"236","author":"Vasquez","year":"2019","journal-title":"Comp. Biochem. Physiol., Part A Mol. Integr. Physiol."},{"key":"2026010403560949000_R94","doi-asserted-by":"crossref","DOI":"10.3390\/ijms232113307","article-title":"SIRT4 expression ameliorates the detrimental effect of heat stress via AMPK\/mTOR signaling pathway in BMECs","volume":"23","author":"Ding","year":"2022","journal-title":"Int. J. Mol. Sci."},{"key":"2026010403560949000_R95","first-page":"4515","article-title":"Sirtuins regulate proteomic responses near thermal tolerance limits in the blue mussels Mytilus galloprovincialis and Mytilus trossulus","volume":"220","author":"Vasquez","year":"2017","journal-title":"J. Exp. Biol."},{"key":"2026010403560949000_R96","doi-asserted-by":"crossref","first-page":"110902","DOI":"10.1016\/j.cbpb.2023.110902","article-title":"Uncovering the roles of sirtuin activity and food availability during the onset of the heat shock response in the California mussel (Mytilus californianus): implications for antioxidative stress responses","volume":"269","author":"May","year":"2024","journal-title":"Comp. Biochem. Physiol. B Biochem. Mol. Biol."},{"key":"2026010403560949000_R97","doi-asserted-by":"crossref","DOI":"10.1016\/j.scitotenv.2022.156962","article-title":"Temperature increases induce metabolic adjustments in the early developmental stages of bigfin reef squid (Sepioteuthis lessoniana)","volume":"844","author":"Kuan","year":"2022","journal-title":"Sci. Total Environ."},{"key":"2026010403560949000_R98","doi-asserted-by":"crossref","DOI":"10.1002\/ece3.8738","article-title":"The alternative splicing landscape of a coral reef fish during a marine heatwave","volume":"12","author":"Chan","year":"2022","journal-title":"Ecol. Evol."},{"key":"2026010403560949000_R99","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/j.canlet.2017.03.013","article-title":"Splicing factors of SR and hnRNP families as regulators of apoptosis in cancer","volume":"396","author":"K\u0119dzierska","year":"2017","journal-title":"Cancer Lett."},{"key":"2026010403560949000_R100","article-title":"Alternative splicing and related RNA binding proteins in human health and disease","volume":"9","author":"Tao","year":"2024","journal-title":"Signal Transduct. Target. Ther."},{"key":"2026010403560949000_R101","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1007\/s10126-023-10281-w","article-title":"Alternative splicing reveals acute stress response of Litopenaeus vannamei at high alkalinity","volume":"26","author":"Shi","year":"2024","journal-title":"Mar. Biotechnol."},{"key":"2026010403560949000_R102","doi-asserted-by":"crossref","first-page":"3775","DOI":"10.1093\/molbev\/msab154","article-title":"Adaptive proteome diversification by nonsynonymous A-to-I RNA editing in coleoid cephalopods","volume":"38","author":"Shoshan","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"2026010403560949000_R103","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1146\/annurev-biochem-060208-105251","article-title":"Functions and regulation of RNA editing by ADAR deaminases","volume":"79","author":"Nishikura","year":"2010","journal-title":"Annu. Rev. Biochem."},{"key":"2026010403560949000_R104","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1016\/j.cell.2017.03.025","article-title":"Trade-off between transcriptome plasticity and genome evolution in cephalopods","volume":"169","author":"Liscovitch-Brauer","year":"2017","journal-title":"Cell"},{"key":"2026010403560949000_R105","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/S0171-2985(97)80025-3","article-title":"Regulation of NF-\u03baB activation by MAP kinase cascades","volume":"198","author":"Schulze-Osthoff","year":"1997","journal-title":"Immunobiology"},{"key":"2026010403560949000_R106","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1038\/18465","article-title":"The kinase TAK1 can activate the NIK-I\u03baB as well as the MAP kinase cascade in the IL-1 signalling pathway","volume":"398","author":"Ninomiya-Tsuji","year":"1999","journal-title":"Nature"},{"key":"2026010403560949000_R107","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/S0952-7915(99)00050-3","article-title":"NF-\u03baB and the innate immune response","volume":"12","author":"Hatada","year":"2000","journal-title":"Curr. Opin. Immunol."},{"key":"2026010403560949000_R108","doi-asserted-by":"crossref","first-page":"6934","DOI":"10.1128\/AEM.71.11.6934-6946.2005","article-title":"Identifying components of the NF-\u03baB pathway in the beneficial Euprymna scolopes-Vibrio fischeri light organ symbiosis","volume":"71","author":"Goodson","year":"2005","journal-title":"Appl. Environ. Microbiol."},{"key":"2026010403560949000_R109","doi-asserted-by":"crossref","first-page":"102120","DOI":"10.1016\/j.aqrep.2024.102120","article-title":"The investigation on stress mechanisms of Sepia esculenta larvae in the context of global warming and ocean acidification","volume":"36","author":"Wang","year":"2024","journal-title":"Aquac. Rep."},{"key":"2026010403560949000_R110","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1016\/S0272-7714(02)00363-3","article-title":"Large diurnal temperature fluctuations in the nearshore water column","volume":"57","author":"Kaplan","year":"2003","journal-title":"Estuar. Coast. Shelf Sci."},{"key":"2026010403560949000_R111","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.csr.2016.01.004","article-title":"Temperature variability caused by internal tides in the coral reef ecosystem of Hanauma bay, Hawai\u2018i","volume":"116","author":"Smith","year":"2016","journal-title":"Cont. Shelf Res."},{"key":"2026010403560949000_R112","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1128\/JB.180.1.59-64.1998","article-title":"A new niche for Vibrio logei, the predominant light organ symbiont of squids in the genus Sepiola","volume":"180","author":"Fidopiastis","year":"1998","journal-title":"J. Bacteriol."},{"key":"2026010403560949000_R113","article-title":"Developmental and transcriptomic responses of Hawaiian bobtail squid early stages to ocean warming and acidification. figshare. Dataset.","author":"Otjacques","year":"2025"},{"key":"2026010403560949000_R114","article-title":"Supplementary material from: Developmental and transcriptomic responses of Hawaiian bobtail squid early stages to ocean warming and acidification. Figshare.","author":"Otjacques","year":"2025"}],"container-title":["Proceedings of the Royal Society B Biological Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/royalsocietypublishing.org\/rspb\/article-pdf\/doi\/10.1098\/rspb.2025.1636\/4439634\/rspb.2025.1636.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/royalsocietypublishing.org\/rspb\/article-pdf\/doi\/10.1098\/rspb.2025.1636\/4439634\/rspb.2025.1636.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,4]],"date-time":"2026-01-04T08:56:29Z","timestamp":1767516989000},"score":1,"resource":{"primary":{"URL":"https:\/\/royalsocietypublishing.org\/rspb\/article\/292\/2061\/20251636\/364703\/Developmental-and-transcriptomic-responses-of"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,17]]},"references-count":114,"journal-issue":{"issue":"2061","published-print":{"date-parts":[[2025,12,17]]}},"URL":"https:\/\/doi.org\/10.1098\/rspb.2025.1636","relation":{},"ISSN":["1471-2954"],"issn-type":[{"value":"1471-2954","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,17]]},"article-number":"20251636"}}