Chloroplast genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana: comparison with other plastid genomes of the red lineage
The chloroplast genomes of the pennate diatom Phaeodactylum tricornutum and the centric diatom Thalassiosira pseudonana have been completely sequenced and are compared with those of other secondary plastids of the red lineage: the centric diatom Odontella sinensis, the haptophyte Emiliania huxleyi,...
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| Veröffentlicht in: | Molecular genetics and genomics : MGG 2007-04, Vol.277 (4), p.427-439 |
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| creator | Oudot-Le Secq, Marie-Pierre Grimwood, Jane Shapiro, Harris Armbrust, E Virginia Bowler, Chris Green, Beverley R |
| description | The chloroplast genomes of the pennate diatom Phaeodactylum tricornutum and the centric diatom Thalassiosira pseudonana have been completely sequenced and are compared with those of other secondary plastids of the red lineage: the centric diatom Odontella sinensis, the haptophyte Emiliania huxleyi, and the cryptophyte Guillardia theta. All five chromist genomes are compact, with small intergenic regions and no introns. The three diatom genomes are similar in gene content with 127-130 protein-coding genes, and genes for 27 tRNAs, three ribosomal RNAs and two small RNAs (tmRNA and signal recognition particle RNA). All three genomes have open-reading frames corresponding to ORFs148, 355 and 380 of O. sinensis, which have been assigned the names ycf88, ycf89 and ycf90. Gene order is not strictly conserved, but there are a number of conserved gene clusters showing remnants of red algal origin. The acpP, tsf and psb28 genes appear to be on the way from the plastid to the host nucleus, indicating that endosymbiotic gene transfer is a continuing process. |
| doi_str_mv | 10.1007/s00438-006-0199-4 |
| format | Article |
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All five chromist genomes are compact, with small intergenic regions and no introns. The three diatom genomes are similar in gene content with 127-130 protein-coding genes, and genes for 27 tRNAs, three ribosomal RNAs and two small RNAs (tmRNA and signal recognition particle RNA). All three genomes have open-reading frames corresponding to ORFs148, 355 and 380 of O. sinensis, which have been assigned the names ycf88, ycf89 and ycf90. Gene order is not strictly conserved, but there are a number of conserved gene clusters showing remnants of red algal origin. The acpP, tsf and psb28 genes appear to be on the way from the plastid to the host nucleus, indicating that endosymbiotic gene transfer is a continuing process.</description><identifier>ISSN: 1617-4615</identifier><identifier>EISSN: 1617-4623</identifier><identifier>DOI: 10.1007/s00438-006-0199-4</identifier><identifier>PMID: 17252281</identifier><language>eng</language><publisher>Germany: Springer Nature B.V</publisher><subject>Bacteria ; Chloroplasts - genetics ; Coccolithus huxleyi ; Diatoms - genetics ; DNA, Intergenic - genetics ; Emiliania huxleyi ; Evolution, Molecular ; Genome ; Guillardia theta ; Odontella sinensis ; Open Reading Frames - genetics ; Phaeodactylum tricornutum ; Plankton ; Proteins ; Thalassiosira pseudonana</subject><ispartof>Molecular genetics and genomics : MGG, 2007-04, Vol.277 (4), p.427-439</ispartof><rights>Springer-Verlag 2007</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c384t-d279a8217aad994463c6898978d9faf1e4a246ac313900754dfe55ba2324bcc63</citedby><cites>FETCH-LOGICAL-c384t-d279a8217aad994463c6898978d9faf1e4a246ac313900754dfe55ba2324bcc63</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,780,784,885,27923,27924</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17252281$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/biblio/1153492$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Oudot-Le Secq, Marie-Pierre</creatorcontrib><creatorcontrib>Grimwood, Jane</creatorcontrib><creatorcontrib>Shapiro, Harris</creatorcontrib><creatorcontrib>Armbrust, E Virginia</creatorcontrib><creatorcontrib>Bowler, Chris</creatorcontrib><creatorcontrib>Green, Beverley R</creatorcontrib><creatorcontrib>Joint Genome Institute (JGI)</creatorcontrib><title>Chloroplast genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana: comparison with other plastid genomes of the red lineage</title><title>Molecular genetics and genomics : MGG</title><addtitle>Mol Genet Genomics</addtitle><description>The chloroplast genomes of the pennate diatom Phaeodactylum tricornutum and the centric diatom Thalassiosira pseudonana have been completely sequenced and are compared with those of other secondary plastids of the red lineage: the centric diatom Odontella sinensis, the haptophyte Emiliania huxleyi, and the cryptophyte Guillardia theta. 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The acpP, tsf and psb28 genes appear to be on the way from the plastid to the host nucleus, indicating that endosymbiotic gene transfer is a continuing process.</description><subject>Bacteria</subject><subject>Chloroplasts - genetics</subject><subject>Coccolithus huxleyi</subject><subject>Diatoms - genetics</subject><subject>DNA, Intergenic - genetics</subject><subject>Emiliania huxleyi</subject><subject>Evolution, Molecular</subject><subject>Genome</subject><subject>Guillardia theta</subject><subject>Odontella sinensis</subject><subject>Open Reading Frames - genetics</subject><subject>Phaeodactylum tricornutum</subject><subject>Plankton</subject><subject>Proteins</subject><subject>Thalassiosira pseudonana</subject><issn>1617-4615</issn><issn>1617-4623</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2007</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqFkc1u1TAQhSNERUvhAdggi0V3of6Lf9ihKwpIlWBR1tZc22lcJXawHaE-By-My71qJTasZhbfOWfs03VvCH5PMJaXBWPOVI-x6DHRuufPujMiiOy5oOz5406G0-5lKXcYEymofNGdEkkHShU5637vpjnltM5QKrr1MS2-oDSiOnnkAtS0FPR9Ap8c2Ho_bwuqOdiU41bbDtGhmwmauIRUQga0Fr-5FCHCB2TTskIOJUX0K9QJpWaa0d-o4P4Ny96hOUQPt_5VdzLCXPzr4zzvflx9utl96a-_ff66-3jdW6Z47R2VGhQlEsBpzblgViittFROjzASz4FyAZYRpttvDdyNfhj2QBnle2sFO-_eHXxTO8gUG6q3k00xelsNIQPjmjbo4gCtOf3cfKlmCcX6eYbo01aMxLS5q-G_IMWCUKWHp9hH8C5tObaXGoUFw1xh3SBygGxOpWQ_mjWHBfK9Idg8lG8O5ZtWvnko3_CmeXs03vaLd0-KY9vsDwGprBs</recordid><startdate>20070401</startdate><enddate>20070401</enddate><creator>Oudot-Le Secq, Marie-Pierre</creator><creator>Grimwood, Jane</creator><creator>Shapiro, Harris</creator><creator>Armbrust, E Virginia</creator><creator>Bowler, Chris</creator><creator>Green, Beverley R</creator><general>Springer Nature B.V</general><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>3V.</scope><scope>7SS</scope><scope>7TK</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><scope>OTOTI</scope></search><sort><creationdate>20070401</creationdate><title>Chloroplast genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana: comparison with other plastid genomes of the red lineage</title><author>Oudot-Le Secq, Marie-Pierre ; Grimwood, Jane ; Shapiro, Harris ; Armbrust, E Virginia ; Bowler, Chris ; Green, Beverley R</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c384t-d279a8217aad994463c6898978d9faf1e4a246ac313900754dfe55ba2324bcc63</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2007</creationdate><topic>Bacteria</topic><topic>Chloroplasts - genetics</topic><topic>Coccolithus huxleyi</topic><topic>Diatoms - genetics</topic><topic>DNA, Intergenic - genetics</topic><topic>Emiliania huxleyi</topic><topic>Evolution, Molecular</topic><topic>Genome</topic><topic>Guillardia theta</topic><topic>Odontella sinensis</topic><topic>Open Reading Frames - genetics</topic><topic>Phaeodactylum tricornutum</topic><topic>Plankton</topic><topic>Proteins</topic><topic>Thalassiosira pseudonana</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Oudot-Le Secq, Marie-Pierre</creatorcontrib><creatorcontrib>Grimwood, Jane</creatorcontrib><creatorcontrib>Shapiro, Harris</creatorcontrib><creatorcontrib>Armbrust, E Virginia</creatorcontrib><creatorcontrib>Bowler, Chris</creatorcontrib><creatorcontrib>Green, Beverley R</creatorcontrib><creatorcontrib>Joint Genome Institute (JGI)</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - 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All five chromist genomes are compact, with small intergenic regions and no introns. The three diatom genomes are similar in gene content with 127-130 protein-coding genes, and genes for 27 tRNAs, three ribosomal RNAs and two small RNAs (tmRNA and signal recognition particle RNA). All three genomes have open-reading frames corresponding to ORFs148, 355 and 380 of O. sinensis, which have been assigned the names ycf88, ycf89 and ycf90. Gene order is not strictly conserved, but there are a number of conserved gene clusters showing remnants of red algal origin. The acpP, tsf and psb28 genes appear to be on the way from the plastid to the host nucleus, indicating that endosymbiotic gene transfer is a continuing process.</abstract><cop>Germany</cop><pub>Springer Nature B.V</pub><pmid>17252281</pmid><doi>10.1007/s00438-006-0199-4</doi><tpages>13</tpages></addata></record> |
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| ispartof | Molecular genetics and genomics : MGG, 2007-04, Vol.277 (4), p.427-439 |
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| subjects | Bacteria Chloroplasts - genetics Coccolithus huxleyi Diatoms - genetics DNA, Intergenic - genetics Emiliania huxleyi Evolution, Molecular Genome Guillardia theta Odontella sinensis Open Reading Frames - genetics Phaeodactylum tricornutum Plankton Proteins Thalassiosira pseudonana |
| title | Chloroplast genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana: comparison with other plastid genomes of the red lineage |
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