{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T10:50:33Z","timestamp":1762253433623,"version":"3.41.2"},"reference-count":42,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2020,7,4]],"date-time":"2020-07-04T00:00:00Z","timestamp":1593820800000},"content-version":"vor","delay-in-days":185,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100011437","name":"State Key Laboratory of Marine Environmental Science","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100011437","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology","award":["No.2018SDKJ0406\u20133"],"award-info":[{"award-number":["No.2018SDKJ0406\u20133"]}]},{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"publisher","award":["NSFC 31661143029 and 41776116"],"award-info":[{"award-number":["NSFC 31661143029 and 41776116"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Symbiodiniaceae dinoflagellates are essential endosymbionts of reef building corals and some other invertebrates. Information of their genome structure and function is critical for understanding coral symbiosis and bleaching. With the rapid development of sequencing technology, genome draft assemblies of several Symbiodiniaceae species and diverse marine algal genomes have become publicly available but spread in multiple separate locations. Here, we present a Symbiodiniaceae and Algal Genomic Resource Database (SAGER), a user-friendly online repository for integrating existing genomic data of Symbiodiniaceae species and diverse marine algal gene sets from MMETSP and PhyloDB databases. Relevant algal data are included to facilitate comparative analyses. The database is freely accessible at http:\/\/sampgr.org.cn. It provides comprehensive tools for studying gene function, expression and comparative genomics, including search tools to identify gene information from Symbiodiniaceae species, and BLAST tool to find orthologs from marine algae and protists. Moreover, SAGER integrates transcriptome datasets derived from diverse culture conditions of corresponding Symbiodiniaceae species. SAGER was developed with the capacity to incorporate future Symbiodiniaceae and algal genome and transcriptome data, and will serve as an open-access and sustained platform providing genomic and molecular tools that can be conveniently used to study Symbiodiniaceae and other marine algae.<\/jats:p>\n               <jats:p>Database URL: http:\/\/sampgr.org.cn<\/jats:p>","DOI":"10.1093\/database\/baaa051","type":"journal-article","created":{"date-parts":[[2020,6,8]],"date-time":"2020-06-08T11:09:11Z","timestamp":1591614551000},"source":"Crossref","is-referenced-by-count":25,"title":["SAGER: a database of Symbiodiniaceae and Algal Genomic Resource"],"prefix":"10.1093","volume":"2020","author":[{"given":"Liying","family":"Yu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China"}]},{"given":"Tangcheng","family":"Li","sequence":"first","affiliation":[{"name":"State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China"}]},{"given":"Ling","family":"Li","sequence":"first","affiliation":[{"name":"State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China"}]},{"given":"Xin","family":"Lin","sequence":"first","affiliation":[{"name":"State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China"}]},{"given":"Hongfei","family":"Li","sequence":"first","affiliation":[{"name":"State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China"}]},{"given":"Chichi","family":"Liu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China"}]},{"given":"Chentao","family":"Guo","sequence":"first","affiliation":[{"name":"State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China"}]},{"given":"Senjie","family":"Lin","sequence":"first","affiliation":[{"name":"State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China"},{"name":"Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,7,4]]},"reference":[{"key":"2020070409343083300_ref1","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1146\/annurev.ecolsys.34.011802.132417","article-title":"Flexibility and specificity in coral\u2013algal symbiosis, diversity, ecology and biogeography of Symbiodinium","volume":"34","author":"Baker","year":"2003","journal-title":"Annu. Rev. Ecol. Evol. Syst."},{"key":"2020070409343083300_ref2","doi-asserted-by":"crossref","first-page":"e94297","DOI":"10.1371\/journal.pone.0094297","article-title":"Deep-sequencing method for quantifying background abundances of Symbiodinium types: exploring the rare Symbiodinium biosphere in reef-building corals","volume":"9","author":"Quigley","year":"2014","journal-title":"PLoS One"},{"key":"2020070409343083300_ref3","doi-asserted-by":"crossref","first-page":"147","DOI":"10.3354\/meps284147","article-title":"Closely related Symbiodinium spp. differ in relative dominance in coral reef host communities across environmental, latitudinal and biogeographic gradients","volume":"284","author":"LaJeunesse","year":"2004","journal-title":"Mar. Ecol. Prog. Ser."},{"key":"2020070409343083300_ref4","doi-asserted-by":"crossref","first-page":"765","DOI":"10.1038\/35081151","article-title":"Reef corals bleach to survive change","volume":"411","author":"Baker","year":"2001","journal-title":"Nature"},{"key":"2020070409343083300_ref5","doi-asserted-by":"crossref","first-page":"3823","DOI":"10.1111\/gcb.12658","article-title":"The cumulative impact of annual coral bleaching can turn some coral species winners into losers","volume":"20","author":"Grottoli","year":"2014","journal-title":"Glob. Chang. Biol."},{"key":"2020070409343083300_ref6","first-page":"839","article-title":"Climate change, coral bleaching and the future of the world's coral reefs","volume":"50","author":"Hoegh-Guldberg","year":"1999","journal-title":"Mar. Freshw. Res."},{"key":"2020070409343083300_ref7","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1007\/978-94-007-0114-4_22","volume-title":"Coral Reefs: An Ecosystem in Transition","author":"Hoegh-Guldberg","year":"2011"},{"key":"2020070409343083300_ref8","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1007\/s10113-010-0189-2","article-title":"Coral reef ecosystems and anthropogenic climate change","volume":"11","author":"Hoegh-Guldberg","year":"2011","journal-title":"Reg. Environ. Change"},{"key":"2020070409343083300_ref9","doi-asserted-by":"crossref","first-page":"15021","DOI":"10.1038\/s41598-017-15029-w","article-title":"Signatures of adaptation and symbiosis in genomes and transcriptomes of Symbiodinium","volume":"7","author":"Gonzalez-Pech","year":"2017","journal-title":"Sci. Rep."},{"key":"2020070409343083300_ref10","doi-asserted-by":"crossref","first-page":"336","DOI":"10.3389\/fmicb.2014.00336","article-title":"A genomic approach to coral-dinoflagellate symbiosis: studies of Acropora digitifera and Symbiodinium minutum","volume":"5","author":"Shinzato","year":"2014","journal-title":"Front. Microbiol."},{"key":"2020070409343083300_ref11","doi-asserted-by":"crossref","first-page":"2201","DOI":"10.1093\/molbev\/msw119","article-title":"Sex, scavengers, and chaperones: transcriptome secrets of divergent Symbiodinium thermal tolerances","volume":"33","author":"Levin","year":"2016","journal-title":"Mol. Biol. Evol."},{"key":"2020070409343083300_ref12","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1086\/BBLv223n1p44","article-title":"Study of cnidarian-algal symbiosis in the \"omics\" age","volume":"223","author":"Meyer","year":"2012","journal-title":"Biol. Bull."},{"key":"2020070409343083300_ref13","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1111\/tpj.12789","article-title":"Symbiodinium transcriptome and global responses of cells to immediate changes in light intensity when grown under autotrophic or mixotrophic conditions","volume":"82","author":"Xiang","year":"2015","journal-title":"Plant J."},{"key":"2020070409343083300_ref14","doi-asserted-by":"crossref","first-page":"691","DOI":"10.1126\/science.aad0408","article-title":"The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis","volume":"350","author":"Lin","year":"2015","journal-title":"Science"},{"key":"2020070409343083300_ref15","doi-asserted-by":"crossref","first-page":"1399","DOI":"10.1016\/j.cub.2013.05.062","article-title":"Draft assembly of the Symbiodinium minutum nuclear genome reveals dinoflagellate gene structure","volume":"23","author":"Shoguchi","year":"2013","journal-title":"Curr. Biol."},{"key":"2020070409343083300_ref16","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1038\/s42003-018-0098-3","article-title":"Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis","volume":"1","author":"Liu","year":"2018","journal-title":"Commun. Biol."},{"key":"2020070409343083300_ref17","doi-asserted-by":"crossref","first-page":"102","DOI":"10.3390\/microorganisms8010102","article-title":"Genome Improvement and Core Gene Set Refinement of Fugacium kawagutii","volume":"8","author":"Li","year":"2020","journal-title":"Microorganisms"},{"key":"2020070409343083300_ref18","doi-asserted-by":"crossref","first-page":"39734","DOI":"10.1038\/srep39734","article-title":"Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle","volume":"6","author":"Aranda","year":"2016","journal-title":"Sci. Rep."},{"key":"2020070409343083300_ref19","doi-asserted-by":"crossref","first-page":"458","DOI":"10.1186\/s12864-018-4857-9","article-title":"Two divergent Symbiodinium genomes reveal conservation of a gene cluster for sunscreen biosynthesis and recently lost genes","volume":"19","author":"Shoguchi","year":"2018","journal-title":"BMC Genomics"},{"key":"2020070409343083300_ref20","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2020070409343083300_ref21","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"2020070409343083300_ref22","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1186\/s13059-016-0924-1","article-title":"JBrowse: a dynamic web platform for genome visualization and nalysis","volume":"17","author":"Buels","year":"2016","journal-title":"Genome Biol."},{"key":"2020070409343083300_ref23","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giy158","article-title":"Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes","volume":"8","author":"Johnson","year":"2019","journal-title":"GigaScience"},{"key":"2020070409343083300_ref24","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.1001889","article-title":"The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing","volume":"12","author":"Keeling","year":"2014","journal-title":"PLoS Biol."},{"key":"2020070409343083300_ref25","doi-asserted-by":"crossref","first-page":"2922","DOI":"10.1093\/molbev\/msz185","article-title":"Sequenceserver: A modern graphical user interface for custom BLAST databases","volume":"36","author":"Priyam","year":"2019","journal-title":"Mol. Biol. Evol."},{"key":"2020070409343083300_ref26","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1093\/gbe\/evw019","article-title":"Gene expression variation resolves species and individual strains among coral-associated dinoflagellates within the genus Symbiodinium","volume":"8","author":"Parkinson","year":"2016","journal-title":"Genome. Biol. Evol."},{"key":"2020070409343083300_ref27","first-page":"7","author":"Lin","year":"2019","journal-title":"Transcriptomic responses to thermal stress and varied phosphorus conditions in Fugacium kawagutii. Microorganisms"},{"key":"2020070409343083300_ref28","doi-asserted-by":"crossref","first-page":"135767","DOI":"10.1016\/j.scitotenv.2019.135767","article-title":"RNA-seq profiling of Fugacium kawagutii reveals strong responses in metabolic processes and symbiosis potential to deficiencies of iron and other trace metals","volume":"705","author":"Li","year":"2020","journal-title":"Sci. Total Environ."},{"key":"2020070409343083300_ref29","doi-asserted-by":"crossref","first-page":"704","DOI":"10.1186\/1471-2164-14-704","article-title":"Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals","volume":"14","author":"Baumgarten","year":"2013","journal-title":"BMC Genomics"},{"key":"2020070409343083300_ref30","doi-asserted-by":"crossref","first-page":"4506","DOI":"10.1111\/1462-2920.13899","article-title":"Transcriptomic and physiological analyses of the dinoflagellate Karenia mikimotoi reveal non-alkaline phosphatase-based molecular machinery of ATP utilisation","volume":"19","author":"Luo","year":"2017","journal-title":"Environ. Microbiol."},{"key":"2020070409343083300_ref31","doi-asserted-by":"crossref","first-page":"3674","DOI":"10.1093\/bioinformatics\/bti610","article-title":"Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research","volume":"21","author":"Conesa","year":"2005","journal-title":"Bioinformatics"},{"key":"2020070409343083300_ref32","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":"2020070409343083300_ref33","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":"2020070409343083300_ref34","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1186\/1471-2105-12-323","article-title":"RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome","volume":"12","author":"Li","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2020070409343083300_ref35","doi-asserted-by":"crossref","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","article-title":"CD-HIT: accelerated for clustering the next-generation sequencing data","volume":"28","author":"Fu","year":"2012","journal-title":"Bioinformatics"},{"key":"2020070409343083300_ref36","doi-asserted-by":"crossref","first-page":"2817","DOI":"10.1038\/s41396-019-0472-2","article-title":"Dieltranscriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection","volume":"13","author":"Kolody","year":"2019","journal-title":"ISME J."},{"key":"2020070409343083300_ref37","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1111\/jpy.12947","article-title":"Evidence that inconsistent gene prediction can mislead analysis of dinoflagellate genomes","volume":"56","author":"Chen","year":"2020","journal-title":"J. Phycol."},{"key":"2020070409343083300_ref38","doi-asserted-by":"crossref","first-page":"2090","DOI":"10.1038\/s41564-019-0532-4","article-title":"A genomic view of the reef-building coral Porites lutea and its microbial symbionts","volume":"4","author":"Robbins","year":"2019","journal-title":"Nature Microbiol."},{"key":"2020070409343083300_ref39","doi-asserted-by":"crossref","first-page":"16802","DOI":"10.1038\/s41598-018-34575-5","article-title":"Transcriptomic changes with increasing algal symbiont reveal the detailed process underlying establishment of coral-algal symbiosis","volume":"8","author":"Yuyama","year":"2018","journal-title":"Sci. Rep."},{"key":"2020070409343083300_ref40","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1002\/ece3.5910","article-title":"Symbiotic lifestyle triggers drastic changes in the gene expression of the algal endosymbiont Breviolum minutum (Symbiodiniaceae)","volume":"10","author":"Maor-Landaw","year":"2019","journal-title":"Ecol. Evol."},{"key":"2020070409343083300_ref41","doi-asserted-by":"crossref","first-page":"134323","DOI":"10.1016\/j.scitotenv.2019.134323","article-title":"Comparative metatranscriptomic profiling and microRNA sequencing to reveal active metabolic pathways associated with a dinoflagellate bloom","volume":"699","author":"Yu","year":"2020","journal-title":"Sci. Total Environ."},{"key":"2020070409343083300_ref42","doi-asserted-by":"crossref","first-page":"590","DOI":"10.3389\/fmicb.2019.00590","article-title":"Metatranscriptomic signatures associated with phytoplankton regime shift from diatom dominance to a dinoflagellate bloom","volume":"10","author":"Zhang","year":"2019","journal-title":"Front. 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