De novo transcriptome sequencing in Bixa orellana to identify genes involved in methylerythritol phosphate, carotenoid and bixin biosynthesis
Identifieur interne : 000836 ( Main/Exploration ); précédent : 000835; suivant : 000837De novo transcriptome sequencing in Bixa orellana to identify genes involved in methylerythritol phosphate, carotenoid and bixin biosynthesis
Auteurs : Yair Cárdenas-Conejo ; Víctor Carballo-Uicab ; Meric Lieberman [États-Unis] ; Margarita Aguilar-Espinosa ; Luca Comai [États-Unis] ; Renata Rivera-MadridSource :
- BMC Genomics [ 1471-2164 ] ; 2015.
Abstract
Bixin or annatto is a commercially important natural orange-red pigment derived from lycopene that is produced and stored in seeds of
In order to investigate the MEP, carotenoid, and bixin pathways genes, total RNA from young leaves and two different developmental stages of seeds from
The identification and qRT-PCR quantification of cDNAs involved in annatto production suggest a hypothetical model for bixin biosynthesis that involve coordinated activation of some MEP, carotenoid and bixin pathway genes. These findings provide a better understanding of the mechanisms regulating these pathways and will facilitate the genetic improvement of
The online version of this article (doi:10.1186/s12864-015-2065-4) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-015-2065-4
PubMed: 26511010
PubMed Central: 4625570
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en"><italic>De novo</italic> transcriptome sequencing in <italic>Bixa orellana</italic> to identify genes involved in methylerythritol phosphate, carotenoid and bixin biosynthesis</title><author><name sortKey="Cardenas Conejo, Yair" sort="Cardenas Conejo, Yair" uniqKey="Cardenas Conejo Y" first="Yair" last="Cárdenas-Conejo">Yair Cárdenas-Conejo</name><affiliation><nlm:aff id="Aff1">Centro de Investigación Científica de Yucatán, A. C. Calle 43 No. 130, Col. Chuburná de Hidalgo, 97200 Mérida, Yucatán Mexico</nlm:aff><wicri:noCountry code="subfield">Yucatán Mexico</wicri:noCountry></affiliation></author><author><name sortKey="Carballo Uicab, Victor" sort="Carballo Uicab, Victor" uniqKey="Carballo Uicab V" first="Víctor" last="Carballo-Uicab">Víctor Carballo-Uicab</name><affiliation><nlm:aff id="Aff1">Centro de Investigación Científica de Yucatán, A. C. Calle 43 No. 130, Col. Chuburná de Hidalgo, 97200 Mérida, Yucatán Mexico</nlm:aff><wicri:noCountry code="subfield">Yucatán Mexico</wicri:noCountry></affiliation></author><author><name sortKey="Lieberman, Meric" sort="Lieberman, Meric" uniqKey="Lieberman M" first="Meric" last="Lieberman">Meric Lieberman</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Plant Biology and Genome Center, University of California, Davis, CA 95616 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Plant Biology and Genome Center, University of California, Davis</wicri:cityArea></affiliation></author><author><name sortKey="Aguilar Espinosa, Margarita" sort="Aguilar Espinosa, Margarita" uniqKey="Aguilar Espinosa M" first="Margarita" last="Aguilar-Espinosa">Margarita Aguilar-Espinosa</name><affiliation><nlm:aff id="Aff1">Centro de Investigación Científica de Yucatán, A. C. Calle 43 No. 130, Col. Chuburná de Hidalgo, 97200 Mérida, Yucatán Mexico</nlm:aff><wicri:noCountry code="subfield">Yucatán Mexico</wicri:noCountry></affiliation></author><author><name sortKey="Comai, Luca" sort="Comai, Luca" uniqKey="Comai L" first="Luca" last="Comai">Luca Comai</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Plant Biology and Genome Center, University of California, Davis, CA 95616 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Plant Biology and Genome Center, University of California, Davis</wicri:cityArea></affiliation></author><author><name sortKey="Rivera Madrid, Renata" sort="Rivera Madrid, Renata" uniqKey="Rivera Madrid R" first="Renata" last="Rivera-Madrid">Renata Rivera-Madrid</name><affiliation><nlm:aff id="Aff1">Centro de Investigación Científica de Yucatán, A. C. Calle 43 No. 130, Col. Chuburná de Hidalgo, 97200 Mérida, Yucatán Mexico</nlm:aff><wicri:noCountry code="subfield">Yucatán Mexico</wicri:noCountry></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26511010</idno><idno type="pmc">4625570</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4625570</idno><idno type="RBID">PMC:4625570</idno><idno type="doi">10.1186/s12864-015-2065-4</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000594</idno><idno type="wicri:Area/Pmc/Curation">000593</idno><idno type="wicri:Area/Pmc/Checkpoint">000641</idno><idno type="wicri:Area/Ncbi/Merge">001D76</idno><idno type="wicri:Area/Ncbi/Curation">001D76</idno><idno type="wicri:Area/Ncbi/Checkpoint">001D76</idno><idno type="wicri:Area/Main/Merge">000836</idno><idno type="wicri:Area/Main/Curation">000836</idno><idno type="wicri:Area/Main/Exploration">000836</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main"><italic>De novo</italic> transcriptome sequencing in <italic>Bixa orellana</italic> to identify genes involved in methylerythritol phosphate, carotenoid and bixin biosynthesis</title><author><name sortKey="Cardenas Conejo, Yair" sort="Cardenas Conejo, Yair" uniqKey="Cardenas Conejo Y" first="Yair" last="Cárdenas-Conejo">Yair Cárdenas-Conejo</name><affiliation><nlm:aff id="Aff1">Centro de Investigación Científica de Yucatán, A. C. Calle 43 No. 130, Col. Chuburná de Hidalgo, 97200 Mérida, Yucatán Mexico</nlm:aff><wicri:noCountry code="subfield">Yucatán Mexico</wicri:noCountry></affiliation></author><author><name sortKey="Carballo Uicab, Victor" sort="Carballo Uicab, Victor" uniqKey="Carballo Uicab V" first="Víctor" last="Carballo-Uicab">Víctor Carballo-Uicab</name><affiliation><nlm:aff id="Aff1">Centro de Investigación Científica de Yucatán, A. C. Calle 43 No. 130, Col. Chuburná de Hidalgo, 97200 Mérida, Yucatán Mexico</nlm:aff><wicri:noCountry code="subfield">Yucatán Mexico</wicri:noCountry></affiliation></author><author><name sortKey="Lieberman, Meric" sort="Lieberman, Meric" uniqKey="Lieberman M" first="Meric" last="Lieberman">Meric Lieberman</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Plant Biology and Genome Center, University of California, Davis, CA 95616 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Plant Biology and Genome Center, University of California, Davis</wicri:cityArea></affiliation></author><author><name sortKey="Aguilar Espinosa, Margarita" sort="Aguilar Espinosa, Margarita" uniqKey="Aguilar Espinosa M" first="Margarita" last="Aguilar-Espinosa">Margarita Aguilar-Espinosa</name><affiliation><nlm:aff id="Aff1">Centro de Investigación Científica de Yucatán, A. C. Calle 43 No. 130, Col. Chuburná de Hidalgo, 97200 Mérida, Yucatán Mexico</nlm:aff><wicri:noCountry code="subfield">Yucatán Mexico</wicri:noCountry></affiliation></author><author><name sortKey="Comai, Luca" sort="Comai, Luca" uniqKey="Comai L" first="Luca" last="Comai">Luca Comai</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Plant Biology and Genome Center, University of California, Davis, CA 95616 USA</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Plant Biology and Genome Center, University of California, Davis</wicri:cityArea></affiliation></author><author><name sortKey="Rivera Madrid, Renata" sort="Rivera Madrid, Renata" uniqKey="Rivera Madrid R" first="Renata" last="Rivera-Madrid">Renata Rivera-Madrid</name><affiliation><nlm:aff id="Aff1">Centro de Investigación Científica de Yucatán, A. C. Calle 43 No. 130, Col. Chuburná de Hidalgo, 97200 Mérida, Yucatán Mexico</nlm:aff><wicri:noCountry code="subfield">Yucatán Mexico</wicri:noCountry></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Bixin or annatto is a commercially important natural orange-red pigment derived from lycopene that is produced and stored in seeds of <italic>Bixa orellana</italic> L. An enzymatic pathway for bixin biosynthesis was inferred from homology of putative proteins encoded by differentially expressed seed cDNAs. Some activities were later validated in a heterologous system. Nevertheless, much of the pathway remains to be clarified. For example, it is essential to identify the methylerythritol phosphate (MEP) and carotenoid pathways genes.</p></sec><sec><title>Results</title><p>In order to investigate the MEP, carotenoid, and bixin pathways genes, total RNA from young leaves and two different developmental stages of seeds from <italic>B. orellana</italic> were used for the construction of indexed mRNA libraries, sequenced on the Illumina HiSeq 2500 platform and assembled de novo using Velvet, CLC Genomics Workbench and CAP3 software. A total of 52,549 contigs were obtained with average length of 1,924 bp. Two phylogenetic analyses of inferred proteins, in one case encoded by thirteen general, single-copy cDNAs, in the other from carotenoid and MEP cDNAs, indicated that <italic>B. orellana</italic> is closely related to sister Malvales species cacao and cotton. Using homology, we identified 7 and 14 core gene products from the MEP and carotenoid pathways, respectively. Surprisingly, previously defined bixin pathway cDNAs were not present in our transcriptome. Here we propose a new set of gene products involved in bixin pathway.</p></sec><sec><title>Conclusion</title><p>The identification and qRT-PCR quantification of cDNAs involved in annatto production suggest a hypothetical model for bixin biosynthesis that involve coordinated activation of some MEP, carotenoid and bixin pathway genes. These findings provide a better understanding of the mechanisms regulating these pathways and will facilitate the genetic improvement of <italic>B. orellana</italic>.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12864-015-2065-4) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Da Dendy, V" uniqKey="Da Dendy V">V DA Dendy</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bohm, F" uniqKey="Bohm F">F Böhm</name></author><author><name sortKey="Edge, R" uniqKey="Edge R">R Edge</name></author><author><name sortKey="Truscott, Tg" uniqKey="Truscott T">TG Truscott</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zeevaart, Jad" uniqKey="Zeevaart J">JAD 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name="États-Unis"><region name="Californie"><name sortKey="Lieberman, Meric" sort="Lieberman, Meric" uniqKey="Lieberman M" first="Meric" last="Lieberman">Meric Lieberman</name></region><name sortKey="Comai, Luca" sort="Comai, Luca" uniqKey="Comai L" first="Luca" last="Comai">Luca Comai</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a OrangerV1
| This area was generated with Dilib version V0.6.25. |  |