The complete nucleotide sequence of the coffee (Coffea arabica L.) chloroplast genome: organization and implications for biotechnology and phylogenetic relationships amongst angiosperms
Identifieur interne : 001102 ( Pmc/Checkpoint ); précédent : 001101; suivant : 001103The complete nucleotide sequence of the coffee (Coffea arabica L.) chloroplast genome: organization and implications for biotechnology and phylogenetic relationships amongst angiosperms
Auteurs : Nalapalli Samson [États-Unis] ; Michael G. Bausher [États-Unis] ; Seung-Bum Lee [États-Unis] ; Robert K. Jansen [États-Unis] ; Henry Daniell [États-Unis]Source :
- Plant biotechnology journal [ 1467-7644 ] ; 2007.
Abstract
The chloroplast genome sequence of
Url:
DOI: 10.1111/j.1467-7652.2007.00245.x
PubMed: 17309688
PubMed Central: 3473179
Affiliations:
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L.) chloroplast genome: organization and implications for biotechnology and phylogenetic relationships amongst angiosperms</title>
<author><name sortKey="Samson, Nalapalli" sort="Samson, Nalapalli" uniqKey="Samson N" first="Nalapalli" last="Samson">Nalapalli Samson</name>
<affiliation wicri:level="1"><nlm:aff id="A1">University of Central Florida, Department of Molecular Biology and Microbiology, Biomolecular Science, Building #20, Orlando, FL 32816-2364, USA</nlm:aff>
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<wicri:regionArea>University of Central Florida, Department of Molecular Biology and Microbiology, Biomolecular Science, Building #20, Orlando, FL 32816-2364</wicri:regionArea>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The complete nucleotide sequence of the coffee (<italic>Coffea arabica</italic>
L.) chloroplast genome: organization and implications for biotechnology and phylogenetic relationships amongst angiosperms</title>
<author><name sortKey="Samson, Nalapalli" sort="Samson, Nalapalli" uniqKey="Samson N" first="Nalapalli" last="Samson">Nalapalli Samson</name>
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<author><name sortKey="Lee, Seung Bum" sort="Lee, Seung Bum" uniqKey="Lee S" first="Seung-Bum" last="Lee">Seung-Bum Lee</name>
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<series><title level="j">Plant biotechnology journal</title>
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<front><div type="abstract" xml:lang="en"><title>Summary</title>
<p id="P1">The chloroplast genome sequence of <italic>Coffea arabica</italic>
L., the first sequenced member of the fourth largest family of angiosperms, Rubiaceae, is reported. The genome is 155 189 bp in length, including a pair of inverted repeats of 25 943 bp. Of the 130 genes present, 112 are distinct and 18 are duplicated in the inverted repeat. The coding region comprises 79 protein genes, 29 transfer RNA genes, four ribosomal RNA genes and 18 genes containing introns (three with three exons). Repeat analysis revealed five direct and three inverted repeats of 30 bp or longer with a sequence identity of 90% or more. Comparisons of the coffee chloroplast genome with sequenced genomes of the closely related family Solanaceae indicated that coffee has a portion of <italic>rps19</italic>
duplicated in the inverted repeat and an intact copy of <italic>infA</italic>
. Furthermore, whole-genome comparisons identified large indels (> 500 bp) in several intergenic spacer regions and introns in the Solanaceae, including <italic>trnE</italic>
(UUC)–<italic>trnT</italic>
(GGU) spacer, <italic>ycf4</italic>
–<italic>cemA</italic>
spacer, <italic>trnI</italic>
(GAU) intron and <italic>rrn5</italic>
–<italic>trnR</italic>
(ACG) spacer. Phylogenetic analyses based on the DNA sequences of 61 protein-coding genes for 35 taxa, performed using both maximum parsimony and maximum likelihood methods, strongly supported the monophyly of several major clades of angiosperms, including monocots, eudicots, rosids, asterids, eurosids II, and euasterids I and II. <italic>Coffea</italic>
(Rubiaceae, Gentianales) is only the second order sampled from the euasterid I clade. The availability of the complete chloroplast genome of coffee provides regulatory and intergenic spacer sequences for utilization in chloroplast genetic engineering to improve this important crop.</p>
</div>
</front>
</TEI>
<pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<pmc-dir>properties manuscript</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-journal-id">101201889</journal-id>
<journal-id journal-id-type="pubmed-jr-id">31826</journal-id>
<journal-id journal-id-type="nlm-ta">Plant Biotechnol J</journal-id>
<journal-id journal-id-type="iso-abbrev">Plant Biotechnol. J.</journal-id>
<journal-title-group><journal-title>Plant biotechnology journal</journal-title>
</journal-title-group>
<issn pub-type="ppub">1467-7644</issn>
<issn pub-type="epub">1467-7652</issn>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">17309688</article-id>
<article-id pub-id-type="pmc">3473179</article-id>
<article-id pub-id-type="doi">10.1111/j.1467-7652.2007.00245.x</article-id>
<article-id pub-id-type="manuscript">NIHMS411187</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>The complete nucleotide sequence of the coffee (<italic>Coffea arabica</italic>
L.) chloroplast genome: organization and implications for biotechnology and phylogenetic relationships amongst angiosperms</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Samson</surname>
<given-names>Nalapalli</given-names>
</name>
<xref ref-type="aff" rid="A1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Bausher</surname>
<given-names>Michael G.</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Lee</surname>
<given-names>Seung-Bum</given-names>
</name>
<xref ref-type="aff" rid="A1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Jansen</surname>
<given-names>Robert K.</given-names>
</name>
<xref ref-type="aff" rid="A3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Daniell</surname>
<given-names>Henry</given-names>
</name>
<xref ref-type="aff" rid="A1">1</xref>
<xref ref-type="corresp" rid="cor1">*</xref>
</contrib>
</contrib-group>
<aff id="A1"><label>1</label>
University of Central Florida, Department of Molecular Biology and Microbiology, Biomolecular Science, Building #20, Orlando, FL 32816-2364, USA</aff>
<aff id="A2"><label>2</label>
USDA-ARS, Horticultural Research Laboratory, Fort Pierce, FL 34945-3030, USA</aff>
<aff id="A3"><label>3</label>
Section of Integrative Biology and Institute of Cellular and Molecular Biology, Patterson Laboratories 141, University of Texas, Austin, TX 78712, USA</aff>
<author-notes><corresp id="cor1"><label>*</label>
<italic>Correspondence</italic>
(fax 407-823-0956; <email>daniell@mail.ucf.edu</email>
)</corresp>
</author-notes>
<pub-date pub-type="nihms-submitted"><day>2</day>
<month>10</month>
<year>2012</year>
</pub-date>
<pub-date pub-type="ppub"><month>3</month>
<year>2007</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>17</day>
<month>10</month>
<year>2012</year>
</pub-date>
<volume>5</volume>
<issue>2</issue>
<fpage>339</fpage>
<lpage>353</lpage>
<permissions><copyright-statement>© 2007 Blackwell Publishing Ltd</copyright-statement>
<copyright-year>2007</copyright-year>
</permissions>
<abstract><title>Summary</title>
<p id="P1">The chloroplast genome sequence of <italic>Coffea arabica</italic>
L., the first sequenced member of the fourth largest family of angiosperms, Rubiaceae, is reported. The genome is 155 189 bp in length, including a pair of inverted repeats of 25 943 bp. Of the 130 genes present, 112 are distinct and 18 are duplicated in the inverted repeat. The coding region comprises 79 protein genes, 29 transfer RNA genes, four ribosomal RNA genes and 18 genes containing introns (three with three exons). Repeat analysis revealed five direct and three inverted repeats of 30 bp or longer with a sequence identity of 90% or more. Comparisons of the coffee chloroplast genome with sequenced genomes of the closely related family Solanaceae indicated that coffee has a portion of <italic>rps19</italic>
duplicated in the inverted repeat and an intact copy of <italic>infA</italic>
. Furthermore, whole-genome comparisons identified large indels (> 500 bp) in several intergenic spacer regions and introns in the Solanaceae, including <italic>trnE</italic>
(UUC)–<italic>trnT</italic>
(GGU) spacer, <italic>ycf4</italic>
–<italic>cemA</italic>
spacer, <italic>trnI</italic>
(GAU) intron and <italic>rrn5</italic>
–<italic>trnR</italic>
(ACG) spacer. Phylogenetic analyses based on the DNA sequences of 61 protein-coding genes for 35 taxa, performed using both maximum parsimony and maximum likelihood methods, strongly supported the monophyly of several major clades of angiosperms, including monocots, eudicots, rosids, asterids, eurosids II, and euasterids I and II. <italic>Coffea</italic>
(Rubiaceae, Gentianales) is only the second order sampled from the euasterid I clade. The availability of the complete chloroplast genome of coffee provides regulatory and intergenic spacer sequences for utilization in chloroplast genetic engineering to improve this important crop.</p>
</abstract>
<kwd-group><kwd>chloroplast genetic engineering</kwd>
<kwd>chloroplast genome</kwd>
<kwd>coffee</kwd>
<kwd>phylogeny</kwd>
<kwd>Rubiaceae</kwd>
</kwd-group>
<funding-group><award-group><funding-source country="United States">National Institute of General Medical Sciences : NIGMS</funding-source>
<award-id>R01 GM063879 || GM</award-id>
</award-group>
</funding-group>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>États-Unis</li>
</country>
</list>
<tree><country name="États-Unis"><noRegion><name sortKey="Samson, Nalapalli" sort="Samson, Nalapalli" uniqKey="Samson N" first="Nalapalli" last="Samson">Nalapalli Samson</name>
</noRegion>
<name sortKey="Bausher, Michael G" sort="Bausher, Michael G" uniqKey="Bausher M" first="Michael G." last="Bausher">Michael G. Bausher</name>
<name sortKey="Daniell, Henry" sort="Daniell, Henry" uniqKey="Daniell H" first="Henry" last="Daniell">Henry Daniell</name>
<name sortKey="Jansen, Robert K" sort="Jansen, Robert K" uniqKey="Jansen R" first="Robert K." last="Jansen">Robert K. Jansen</name>
<name sortKey="Lee, Seung Bum" sort="Lee, Seung Bum" uniqKey="Lee S" first="Seung-Bum" last="Lee">Seung-Bum Lee</name>
</country>
</tree>
</affiliations>
</record>
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