Complete Chloroplast Genome Sequence of Phagomixotrophic Green Alga Cymbomonas tetramitiformis
Identifieur interne : 000096 ( Pmc/Corpus ); précédent : 000095; suivant : 000097Complete Chloroplast Genome Sequence of Phagomixotrophic Green Alga Cymbomonas tetramitiformis
Auteurs : Anchittha Satjarak ; Amber E. Paasch ; Linda E. Graham ; Eunsoo KimSource :
- Genome Announcements [ 2169-8287 ] ; 2016.
Abstract
We report here the complete chloroplast genome sequence of
Url:
DOI: 10.1128/genomeA.00551-16
PubMed: 27313295
PubMed Central: 4911474
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Complete Chloroplast Genome Sequence of Phagomixotrophic Green Alga <italic>Cymbomonas tetramitiformis</italic></title><author><name sortKey="Satjarak, Anchittha" sort="Satjarak, Anchittha" uniqKey="Satjarak A" first="Anchittha" last="Satjarak">Anchittha Satjarak</name><affiliation><nlm:aff id="aff1"><addr-line>Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA</addr-line></nlm:aff></affiliation></author><author><name sortKey="Paasch, Amber E" sort="Paasch, Amber E" uniqKey="Paasch A" first="Amber E." last="Paasch">Amber E. Paasch</name><affiliation><nlm:aff id="aff2"><addr-line>Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA</addr-line></nlm:aff></affiliation></author><author><name sortKey="Graham, Linda E" sort="Graham, Linda E" uniqKey="Graham L" first="Linda E." last="Graham">Linda E. Graham</name><affiliation><nlm:aff id="aff1"><addr-line>Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA</addr-line></nlm:aff></affiliation></author><author><name sortKey="Kim, Eunsoo" sort="Kim, Eunsoo" uniqKey="Kim E" first="Eunsoo" last="Kim">Eunsoo Kim</name><affiliation><nlm:aff id="aff2"><addr-line>Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA</addr-line></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27313295</idno><idno type="pmc">4911474</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4911474</idno><idno type="RBID">PMC:4911474</idno><idno type="doi">10.1128/genomeA.00551-16</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000096</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Complete Chloroplast Genome Sequence of Phagomixotrophic Green Alga <italic>Cymbomonas tetramitiformis</italic></title><author><name sortKey="Satjarak, Anchittha" sort="Satjarak, Anchittha" uniqKey="Satjarak A" first="Anchittha" last="Satjarak">Anchittha Satjarak</name><affiliation><nlm:aff id="aff1"><addr-line>Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA</addr-line></nlm:aff></affiliation></author><author><name sortKey="Paasch, Amber E" sort="Paasch, Amber E" uniqKey="Paasch A" first="Amber E." last="Paasch">Amber E. Paasch</name><affiliation><nlm:aff id="aff2"><addr-line>Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA</addr-line></nlm:aff></affiliation></author><author><name sortKey="Graham, Linda E" sort="Graham, Linda E" uniqKey="Graham L" first="Linda E." last="Graham">Linda E. Graham</name><affiliation><nlm:aff id="aff1"><addr-line>Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA</addr-line></nlm:aff></affiliation></author><author><name sortKey="Kim, Eunsoo" sort="Kim, Eunsoo" uniqKey="Kim E" first="Eunsoo" last="Kim">Eunsoo Kim</name><affiliation><nlm:aff id="aff2"><addr-line>Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA</addr-line></nlm:aff></affiliation></author></analytic><series><title level="j">Genome Announcements</title><idno type="eISSN">2169-8287</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>We report here the complete chloroplast genome sequence of <italic>Cymbomonas tetramitiformis</italic> strain PLY262, which is a prasinophycean green alga that retains a phagomixotrophic mode of nutrition. The genome is 84,524 bp in length, with a G+C content of 37%, and contains 3 rRNAs, 26 tRNAs, and 76 protein-coding genes.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Graham, Le" uniqKey="Graham L">LE Graham</name></author><author><name sortKey="Graham, Jm" uniqKey="Graham J">JM Graham</name></author><author><name sortKey="Wilcox, Lw" uniqKey="Wilcox L">LW Wilcox</name></author><author><name sortKey="Cook, Me" uniqKey="Cook M">ME Cook</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lewis, La" uniqKey="Lewis L">LA Lewis</name></author><author><name sortKey="Mccourt, Rm" uniqKey="Mccourt R">RM McCourt</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Maruyama, S" uniqKey="Maruyama S">S Maruyama</name></author><author><name sortKey="Kim, E" uniqKey="Kim E">E Kim</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bolger, Am" 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Genome Announc</journal-id><journal-id journal-id-type="iso-abbrev">Genome Announc</journal-id><journal-id journal-id-type="hwp">ga</journal-id><journal-id journal-id-type="pmc">ga</journal-id><journal-id journal-id-type="publisher-id">GA</journal-id><journal-title-group><journal-title>Genome Announcements</journal-title></journal-title-group><issn pub-type="epub">2169-8287</issn><publisher><publisher-name>American Society for Microbiology</publisher-name><publisher-loc>1752 N St., N.W., Washington, DC</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">27313295</article-id><article-id pub-id-type="pmc">4911474</article-id><article-id pub-id-type="publisher-id">genomeA00551-16</article-id><article-id pub-id-type="doi">10.1128/genomeA.00551-16</article-id><article-categories><subj-group subj-group-type="heading"><subject>Eukaryotes</subject></subj-group></article-categories><title-group><article-title>Complete Chloroplast Genome Sequence of Phagomixotrophic Green Alga <italic>Cymbomonas tetramitiformis</italic></article-title><alt-title alt-title-type="running-head">Genome Announcement</alt-title><alt-title alt-title-type="short-authors">Satjarak et al.</alt-title></title-group><contrib-group><contrib contrib-type="author" corresp="yes"><name><surname>Satjarak</surname><given-names>Anchittha</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Paasch</surname><given-names>Amber E.</given-names></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref></contrib><contrib contrib-type="author"><name><surname>Graham</surname><given-names>Linda E.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Kim</surname><given-names>Eunsoo</given-names></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref></contrib><aff id="aff1"><label>a</label><addr-line>Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA</addr-line></aff><aff id="aff2"><label>b</label><addr-line>Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA</addr-line></aff></contrib-group><author-notes><corresp id="cor1">Address correspondence to Anchittha Satjarak, <email>satjarak@wisc.edu</email>.</corresp></author-notes><pub-date pub-type="epub"><day>16</day><month>6</month><year>2016</year></pub-date><pub-date pub-type="collection"><season>May-Jun</season><year>2016</year></pub-date><volume>4</volume><issue>3</issue><elocation-id>e00551-16</elocation-id><history><date date-type="received"><day>29</day><month>4</month><year>2016</year></date><date date-type="accepted"><day>10</day><month>5</month><year>2016</year></date></history><permissions><copyright-statement>Copyright © 2016 Satjarak et al.</copyright-statement><copyright-year>2016</copyright-year><copyright-holder>Satjarak et al.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International license</ext-link>.</license-p></license></permissions><self-uri content-type="pdf" xlink:href="jga003164020001.pdf"></self-uri><abstract><p>We report here the complete chloroplast genome sequence of <italic>Cymbomonas tetramitiformis</italic> strain PLY262, which is a prasinophycean green alga that retains a phagomixotrophic mode of nutrition. The genome is 84,524 bp in length, with a G+C content of 37%, and contains 3 rRNAs, 26 tRNAs, and 76 protein-coding genes.</p></abstract><funding-group><award-group id="award1"><funding-source>Richard Gilder Graduate School</funding-source><principal-award-recipient>Amber E Paasch</principal-award-recipient></award-group><award-group id="award2"><funding-source>an NSF CAREER grant</funding-source><award-id>1453639</award-id><principal-award-recipient>Eunsoo Kim</principal-award-recipient></award-group></funding-group><counts><fig-count count="0"></fig-count><table-count count="0"></table-count><equation-count count="0"></equation-count><ref-count count="15"></ref-count><page-count count="2"></page-count><word-count count="1156"></word-count></counts><custom-meta-group><custom-meta><meta-name>cover-date</meta-name><meta-value>May/June 2016</meta-value></custom-meta></custom-meta-group></article-meta></front><body><sec id="h0.0"><title>GENOME ANNOUNCEMENT</title><p><italic>Cymbomonas tetramitiformis</italic> is a marine prasinophycean green alga that bears a single chloroplast and lacks a cell wall (<xref rid="B1" ref-type="bibr">1</xref>). Within the prasinophytes, a paraphyletic assemblage of green algae that typically display features that are considered plesiomorphic for the <italic>Chloroplastida</italic> (green algae plus land plants), <italic>C. tetramitiformis</italic> falls into the order <italic>Pyramimonadales</italic> (prasinophyte clade I), which also includes <italic>Halosphaera</italic>, <italic>Pyramimonas</italic>, and <italic>Pterosperma</italic> (<xref rid="B2" ref-type="bibr">2</xref>). Unlike most other green algae, <italic>C. tetramitiformis</italic> retains the capacity to feed on bacteria while harvesting energy via photosynthesis (<xref rid="B3" ref-type="bibr">3</xref>).</p><p><italic>C. tetramitiformis</italic> PLY262, acquired from the Plymouth Culture Collection of Marine Microalgae, was grown in f/2-Si at 18°C with a 12-h light/dark cycle. The total algal DNA was extracted using a Qiagen QIAamp minikit, according to the tissue-DNA protocol, and sent to the New York Genome Center (New York, NY) for whole-genome shotgun library preparation and sequencing on the Illumina MiSeq platform. A total of 19,183,050 paired sequences, each up to 300 bp in length, were generated. The raw reads were trimmed by Trimmomatic version 0.33 (<xref rid="B4" ref-type="bibr">4</xref>) in order to have a minimum quality score of 28 on the Phred 64 scale. The chloroplast genome was constructed by MIRA version 4.0.2 and MITObim version 1.8 (<xref rid="B5" ref-type="bibr">5</xref>) using the partial sequence of the <italic>C. tetramitiformis</italic> rbcL gene (GenBank accession no. L34687.1 [<xref rid="B6" ref-type="bibr">6</xref>]) as bait. The fold coverage of every position of the genome was calculated by mapping the trimmed reads to the newly assembled chloroplast genome using BWA nonmodel species alignment version 0.7.4 (<xref rid="B7" ref-type="bibr">7</xref>) and Bedtools genome coverage BAM version 2.19.1 (<xref rid="B8" ref-type="bibr">8</xref>) implemented in iPlant Collaborative (<xref rid="B9" ref-type="bibr">9</xref>). Open reading frames with length of at least 90 bp were predicted by conducting a BLAST search against the NCBI nonredundant protein database. tRNAs and rRNAs were predicted using tRNAscan-SE version 1.21 (<xref rid="B10" ref-type="bibr">10</xref>) and RNAmmer version 1.2 (<xref rid="B11" ref-type="bibr">11</xref>), respectively.</p><p>The complete chloroplast genome sequence was assembled into a circular-mapping molecule of 84,524 bp in length (1,200-fold coverage), with a G+C content of 37%. The genome was annotated with a total of 105 genes, including 76 protein-coding genes, 26 tRNAs, and 3 rRNAs. The region that contains three rRNAs and two tRNAs appears twice in the genome in the inverted orientation, the structure that is also found in the chloroplast DNA (cpDNA) of other prasinophyte and streptophyte algae (<xref rid="B12" ref-type="bibr">12</xref>). No introns were detected. A notable feature of <italic>C. tetramitiformis</italic>, unlike the closely related <italic>Pyramimonas parkeae</italic> (<xref rid="B13" ref-type="bibr">13</xref>), is the absence of all three genes (<italic>chlL</italic>, <italic>chlB</italic>, and <italic>chlN</italic>) encoding subunits of light-independent protochlorophyllide oxidoreductase (LIPOR) either in the chloroplast or nuclear genome (GenBank accession no. LGRX00000000). In fact, the loss of this gene set has been reported from cpDNA of a diverse range of photosynthetic eukaryotes, including the prasinophytes <italic>Micromonas pusilla</italic> and <italic>Ostreococcus tauri</italic>, as well as members of chlorarachniophytes, euglenids, rhodophytes, cryptophytes, haptophytes, stramenopiles, dinoflagellates, and chromerids (<xref rid="B14" ref-type="bibr">14</xref>). The oxygen sensitivity of LIPOR (<xref rid="B15" ref-type="bibr">15</xref>) may at least partially explain such multiple independent losses of LIPOR genes in response to the increased level of atmospheric oxygen since the origins of eukaryotic algae.</p><sec id="s1"><title>Nucleotide sequence accession number.</title><p>The assembled chloroplast genome sequence of <italic>C. tetramitiformis</italic> has been archived at GenBank with the accession number <ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/nuccore/KX013545">KX013545</ext-link>.</p></sec></sec></body><back><fn-group><fn fn-type="other"><p><bold>Citation</bold> Satjarak A, Paasch AE, Graham LE, Kim E. 2016. 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