A New Dinoflagellate Genome Illuminates a Conserved Gene Cluster Involved in Sunscreen Biosynthesis
Abstract Photosynthetic dinoflagellates of the Family Symbiodiniaceae live symbiotically with many organisms that inhabit coral reefs and are currently classified into fifteen groups, including seven genera. Draft genomes from four genera, Symbiodinium, Breviolum, Fugacium, and Cladocopium, which ha...
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creator | Shoguchi, Eiichi Beedessee, Girish Hisata, Kanako Tada, Ipputa Narisoko, Haruhi Satoh, Noriyuki Kawachi, Masanobu Shinzato, Chuya |
description | Abstract
Photosynthetic dinoflagellates of the Family Symbiodiniaceae live symbiotically with many organisms that inhabit coral reefs and are currently classified into fifteen groups, including seven genera. Draft genomes from four genera, Symbiodinium, Breviolum, Fugacium, and Cladocopium, which have been isolated from corals, have been reported. However, no genome is available from the genus Durusdinium, which occupies an intermediate phylogenetic position in the Family Symbiodiniaceae and is well known for thermal tolerance (resistance to bleaching). We sequenced, assembled, and annotated the genome of Durusdinium trenchii, isolated from the coral, Favia speciosa, in Okinawa, Japan. Assembled short reads amounted to 670 Mb with ∼47% GC content. This GC content was intermediate among taxa belonging to the Symbiodiniaceae. Approximately 30,000 protein-coding genes were predicted in the D. trenchii genome, fewer than in other genomes from the Symbiodiniaceae. However, annotations revealed that the D. trenchii genome encodes a cluster of genes for synthesis of mycosporine-like amino acids, which absorb UV radiation. Interestingly, a neighboring gene in the cluster encodes a glucose–methanol–choline oxidoreductase with a flavin adenine dinucleotide domain that is also found in Symbiodinium tridacnidorum. This conservation seems to partially clarify an ancestral genomic structure in the Symbiodiniaceae and its loss in late-branching lineages, including Breviolum and Cladocopium, after splitting from the Durusdinium lineage. Our analysis suggests that approximately half of the taxa in the Symbiodiniaceae may maintain the ability to synthesize mycosporine-like amino acids. Thus, this work provides a significant genomic resource for understanding the genomic diversity of Symbiodiniaceae in corals. |
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Photosynthetic dinoflagellates of the Family Symbiodiniaceae live symbiotically with many organisms that inhabit coral reefs and are currently classified into fifteen groups, including seven genera. Draft genomes from four genera, Symbiodinium, Breviolum, Fugacium, and Cladocopium, which have been isolated from corals, have been reported. However, no genome is available from the genus Durusdinium, which occupies an intermediate phylogenetic position in the Family Symbiodiniaceae and is well known for thermal tolerance (resistance to bleaching). We sequenced, assembled, and annotated the genome of Durusdinium trenchii, isolated from the coral, Favia speciosa, in Okinawa, Japan. Assembled short reads amounted to 670 Mb with ∼47% GC content. This GC content was intermediate among taxa belonging to the Symbiodiniaceae. Approximately 30,000 protein-coding genes were predicted in the D. trenchii genome, fewer than in other genomes from the Symbiodiniaceae. However, annotations revealed that the D. trenchii genome encodes a cluster of genes for synthesis of mycosporine-like amino acids, which absorb UV radiation. Interestingly, a neighboring gene in the cluster encodes a glucose–methanol–choline oxidoreductase with a flavin adenine dinucleotide domain that is also found in Symbiodinium tridacnidorum. This conservation seems to partially clarify an ancestral genomic structure in the Symbiodiniaceae and its loss in late-branching lineages, including Breviolum and Cladocopium, after splitting from the Durusdinium lineage. Our analysis suggests that approximately half of the taxa in the Symbiodiniaceae may maintain the ability to synthesize mycosporine-like amino acids. Thus, this work provides a significant genomic resource for understanding the genomic diversity of Symbiodiniaceae in corals.</description><identifier>ISSN: 1759-6653</identifier><identifier>EISSN: 1759-6653</identifier><identifier>DOI: 10.1093/gbe/evaa235</identifier><identifier>PMID: 33146374</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Amino Acids - biosynthesis ; Biosynthetic Pathways - genetics ; Dinoflagellida - genetics ; Genes ; Genome ; Genome Report ; Ultraviolet Rays</subject><ispartof>Genome biology and evolution, 2021-02, Vol.13 (2)</ispartof><rights>The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. 2020</rights><rights>The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.</rights><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c522t-a9a3ea5053b2c9810f5aa84f54125d36c908a7aa447857356c2ddacf060eac253</citedby><cites>FETCH-LOGICAL-c522t-a9a3ea5053b2c9810f5aa84f54125d36c908a7aa447857356c2ddacf060eac253</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7875005/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7875005/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,1598,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33146374$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Shoguchi, Eiichi</creatorcontrib><creatorcontrib>Beedessee, Girish</creatorcontrib><creatorcontrib>Hisata, Kanako</creatorcontrib><creatorcontrib>Tada, Ipputa</creatorcontrib><creatorcontrib>Narisoko, Haruhi</creatorcontrib><creatorcontrib>Satoh, Noriyuki</creatorcontrib><creatorcontrib>Kawachi, Masanobu</creatorcontrib><creatorcontrib>Shinzato, Chuya</creatorcontrib><title>A New Dinoflagellate Genome Illuminates a Conserved Gene Cluster Involved in Sunscreen Biosynthesis</title><title>Genome biology and evolution</title><addtitle>Genome Biol Evol</addtitle><description>Abstract
Photosynthetic dinoflagellates of the Family Symbiodiniaceae live symbiotically with many organisms that inhabit coral reefs and are currently classified into fifteen groups, including seven genera. Draft genomes from four genera, Symbiodinium, Breviolum, Fugacium, and Cladocopium, which have been isolated from corals, have been reported. However, no genome is available from the genus Durusdinium, which occupies an intermediate phylogenetic position in the Family Symbiodiniaceae and is well known for thermal tolerance (resistance to bleaching). We sequenced, assembled, and annotated the genome of Durusdinium trenchii, isolated from the coral, Favia speciosa, in Okinawa, Japan. Assembled short reads amounted to 670 Mb with ∼47% GC content. This GC content was intermediate among taxa belonging to the Symbiodiniaceae. Approximately 30,000 protein-coding genes were predicted in the D. trenchii genome, fewer than in other genomes from the Symbiodiniaceae. However, annotations revealed that the D. trenchii genome encodes a cluster of genes for synthesis of mycosporine-like amino acids, which absorb UV radiation. Interestingly, a neighboring gene in the cluster encodes a glucose–methanol–choline oxidoreductase with a flavin adenine dinucleotide domain that is also found in Symbiodinium tridacnidorum. This conservation seems to partially clarify an ancestral genomic structure in the Symbiodiniaceae and its loss in late-branching lineages, including Breviolum and Cladocopium, after splitting from the Durusdinium lineage. Our analysis suggests that approximately half of the taxa in the Symbiodiniaceae may maintain the ability to synthesize mycosporine-like amino acids. Thus, this work provides a significant genomic resource for understanding the genomic diversity of Symbiodiniaceae in corals.</description><subject>Amino Acids - biosynthesis</subject><subject>Biosynthetic Pathways - genetics</subject><subject>Dinoflagellida - genetics</subject><subject>Genes</subject><subject>Genome</subject><subject>Genome Report</subject><subject>Ultraviolet Rays</subject><issn>1759-6653</issn><issn>1759-6653</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNp9kUFPGzEQha2qqAToqffKp6pSFfCu1_bupRKkNERCcADO1sQ7G1x57dTeTcW_Z1dJo3DhNE8zn96M5hHyJWPnGav4xWqJF7gByLn4QCaZEtVUSsE_HuhjcpLSH8akLCT_RI45zwahigkxl_QO_9Ff1ofGwQqdgw7pHH1okS6c61vrh06iQGfBJ4wbrMcx0pnrU4eRLvwmuLFrPX3ofTIR0dMrG9KL754x2XRGjhpwCT_v6il5-n39OLuZ3t7PF7PL26kRed5NoQKOIJjgy9xUZcYaAVAWjSiyXNRcmoqVoACKQpVCcSFNXtdgGiYZgskFPyU_t77rftlibdB3EZxeR9tCfNEBrH478fZZr8JGq1IJxkaD7zuDGP72mDrd2mTGn3gMfdJ5IZRUKiv4gP7YoiaGlCI2-zUZ02MseohF72IZ6K-Hl-3Z_zkMwLctEPr1u06vdoiYoA</recordid><startdate>20210203</startdate><enddate>20210203</enddate><creator>Shoguchi, Eiichi</creator><creator>Beedessee, Girish</creator><creator>Hisata, Kanako</creator><creator>Tada, Ipputa</creator><creator>Narisoko, Haruhi</creator><creator>Satoh, Noriyuki</creator><creator>Kawachi, Masanobu</creator><creator>Shinzato, Chuya</creator><general>Oxford University Press</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20210203</creationdate><title>A New Dinoflagellate Genome Illuminates a Conserved Gene Cluster Involved in Sunscreen Biosynthesis</title><author>Shoguchi, Eiichi ; Beedessee, Girish ; Hisata, Kanako ; Tada, Ipputa ; Narisoko, Haruhi ; Satoh, Noriyuki ; Kawachi, Masanobu ; Shinzato, Chuya</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c522t-a9a3ea5053b2c9810f5aa84f54125d36c908a7aa447857356c2ddacf060eac253</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Amino Acids - biosynthesis</topic><topic>Biosynthetic Pathways - genetics</topic><topic>Dinoflagellida - genetics</topic><topic>Genes</topic><topic>Genome</topic><topic>Genome Report</topic><topic>Ultraviolet Rays</topic><toplevel>online_resources</toplevel><creatorcontrib>Shoguchi, Eiichi</creatorcontrib><creatorcontrib>Beedessee, Girish</creatorcontrib><creatorcontrib>Hisata, Kanako</creatorcontrib><creatorcontrib>Tada, Ipputa</creatorcontrib><creatorcontrib>Narisoko, Haruhi</creatorcontrib><creatorcontrib>Satoh, Noriyuki</creatorcontrib><creatorcontrib>Kawachi, Masanobu</creatorcontrib><creatorcontrib>Shinzato, Chuya</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Genome biology and evolution</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Shoguchi, Eiichi</au><au>Beedessee, Girish</au><au>Hisata, Kanako</au><au>Tada, Ipputa</au><au>Narisoko, Haruhi</au><au>Satoh, Noriyuki</au><au>Kawachi, Masanobu</au><au>Shinzato, Chuya</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A New Dinoflagellate Genome Illuminates a Conserved Gene Cluster Involved in Sunscreen Biosynthesis</atitle><jtitle>Genome biology and evolution</jtitle><addtitle>Genome Biol Evol</addtitle><date>2021-02-03</date><risdate>2021</risdate><volume>13</volume><issue>2</issue><issn>1759-6653</issn><eissn>1759-6653</eissn><abstract>Abstract
Photosynthetic dinoflagellates of the Family Symbiodiniaceae live symbiotically with many organisms that inhabit coral reefs and are currently classified into fifteen groups, including seven genera. Draft genomes from four genera, Symbiodinium, Breviolum, Fugacium, and Cladocopium, which have been isolated from corals, have been reported. However, no genome is available from the genus Durusdinium, which occupies an intermediate phylogenetic position in the Family Symbiodiniaceae and is well known for thermal tolerance (resistance to bleaching). We sequenced, assembled, and annotated the genome of Durusdinium trenchii, isolated from the coral, Favia speciosa, in Okinawa, Japan. Assembled short reads amounted to 670 Mb with ∼47% GC content. This GC content was intermediate among taxa belonging to the Symbiodiniaceae. Approximately 30,000 protein-coding genes were predicted in the D. trenchii genome, fewer than in other genomes from the Symbiodiniaceae. However, annotations revealed that the D. trenchii genome encodes a cluster of genes for synthesis of mycosporine-like amino acids, which absorb UV radiation. Interestingly, a neighboring gene in the cluster encodes a glucose–methanol–choline oxidoreductase with a flavin adenine dinucleotide domain that is also found in Symbiodinium tridacnidorum. This conservation seems to partially clarify an ancestral genomic structure in the Symbiodiniaceae and its loss in late-branching lineages, including Breviolum and Cladocopium, after splitting from the Durusdinium lineage. Our analysis suggests that approximately half of the taxa in the Symbiodiniaceae may maintain the ability to synthesize mycosporine-like amino acids. Thus, this work provides a significant genomic resource for understanding the genomic diversity of Symbiodiniaceae in corals.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>33146374</pmid><doi>10.1093/gbe/evaa235</doi><oa>free_for_read</oa></addata></record> |
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subjects | Amino Acids - biosynthesis Biosynthetic Pathways - genetics Dinoflagellida - genetics Genes Genome Genome Report Ultraviolet Rays |
title | A New Dinoflagellate Genome Illuminates a Conserved Gene Cluster Involved in Sunscreen Biosynthesis |
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