Transcriptome analysis of root response to citrus blight based on the newly assembled Swingle citrumelo draft genome
Identifieur interne : 000019 ( Main/Exploration ); précédent : 000018; suivant : 000020Transcriptome analysis of root response to citrus blight based on the newly assembled Swingle citrumelo draft genome
Auteurs : Yunzeng Zhang [États-Unis] ; Gary Barthe [États-Unis] ; Jude W. Grosser [États-Unis] ; Nian Wang [États-Unis]Source :
- BMC Genomics [ 1471-2164 ] ; 2016.
Abstract
Citrus blight is a citrus tree overall decline disease and causes serious losses in the citrus industry worldwide. Although it was described more than one hundred years ago, its causal agent remains unknown and its pathophysiology is not well determined, which hampers our understanding of the disease and design of suitable disease management.
In this study, we sequenced and assembled the draft genome for Swingle citrumelo, one important citrus rootstock. The draft genome is approximately 280 Mb, which covers 74 % of the estimated Swingle citrumelo genome and the average coverage is around 15X. The draft genome of Swingle citrumelo enabled us to conduct transcriptome analysis of roots of blight and healthy Swingle citrumelo using RNA-seq. The RNA-seq was reliable as evidenced by the high consistence of RNA-seq analysis and quantitative reverse transcription PCR results (R2 = 0.966). Comparison of the gene expression profiles between blight and healthy root samples revealed the molecular mechanism underneath the characteristic blight phenotypes including decline, starch accumulation, and drought stress. The JA and ET biosynthesis and signaling pathways showed decreased transcript abundance, whereas SA-mediated defense-related genes showed increased transcript abundance in blight trees, suggesting unclassified biotrophic pathogen was involved in this disease.
Overall, the Swingle citrumelo draft genome generated in this study will advance our understanding of plant biology and contribute to the citrus breeding. Transcriptome analysis of blight and healthy trees deepened our understanding of the pathophysiology of citrus blight.
The online version of this article (doi:10.1186/s12864-016-2779-y) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-016-2779-y
PubMed: 27391971
PubMed Central: 4938905
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Transcriptome analysis of root response to citrus blight based on the newly assembled Swingle citrumelo draft genome</title><author><name sortKey="Zhang, Yunzeng" sort="Zhang, Yunzeng" uniqKey="Zhang Y" first="Yunzeng" last="Zhang">Yunzeng Zhang</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred</wicri:cityArea></affiliation></author><author><name sortKey="Barthe, Gary" sort="Barthe, Gary" uniqKey="Barthe G" first="Gary" last="Barthe">Gary Barthe</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Citrus Research and Education Center, Department of Horticultural Sciences, University of Florida, Lake Alfred, FL USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>Citrus Research and Education Center, Department of Horticultural Sciences, University of Florida, Lake Alfred</wicri:cityArea></affiliation></author><author><name sortKey="Grosser, Jude W" sort="Grosser, Jude W" uniqKey="Grosser J" first="Jude W." last="Grosser">Jude W. Grosser</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Citrus Research and Education Center, Department of Horticultural Sciences, University of Florida, Lake Alfred, FL USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>Citrus Research and Education Center, Department of Horticultural Sciences, University of Florida, Lake Alfred</wicri:cityArea></affiliation></author><author><name sortKey="Wang, Nian" sort="Wang, Nian" uniqKey="Wang N" first="Nian" last="Wang">Nian Wang</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred</wicri:cityArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27391971</idno><idno type="pmc">4938905</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4938905</idno><idno type="RBID">PMC:4938905</idno><idno type="doi">10.1186/s12864-016-2779-y</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000606</idno><idno type="wicri:Area/Pmc/Curation">000605</idno><idno type="wicri:Area/Pmc/Checkpoint">000014</idno><idno type="wicri:Area/Ncbi/Merge">002105</idno><idno type="wicri:Area/Ncbi/Curation">002105</idno><idno type="wicri:Area/Ncbi/Checkpoint">002105</idno><idno type="wicri:Area/Main/Merge">000019</idno><idno type="wicri:Area/Main/Curation">000019</idno><idno type="wicri:Area/Main/Exploration">000019</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Transcriptome analysis of root response to citrus blight based on the newly assembled Swingle citrumelo draft genome</title><author><name sortKey="Zhang, Yunzeng" sort="Zhang, Yunzeng" uniqKey="Zhang Y" first="Yunzeng" last="Zhang">Yunzeng Zhang</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred</wicri:cityArea></affiliation></author><author><name sortKey="Barthe, Gary" sort="Barthe, Gary" uniqKey="Barthe G" first="Gary" last="Barthe">Gary Barthe</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Citrus Research and Education Center, Department of Horticultural Sciences, University of Florida, Lake Alfred, FL USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>Citrus Research and Education Center, Department of Horticultural Sciences, University of Florida, Lake Alfred</wicri:cityArea></affiliation></author><author><name sortKey="Grosser, Jude W" sort="Grosser, Jude W" uniqKey="Grosser J" first="Jude W." last="Grosser">Jude W. Grosser</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Citrus Research and Education Center, Department of Horticultural Sciences, University of Florida, Lake Alfred, FL USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>Citrus Research and Education Center, Department of Horticultural Sciences, University of Florida, Lake Alfred</wicri:cityArea></affiliation></author><author><name sortKey="Wang, Nian" sort="Wang, Nian" uniqKey="Wang N" first="Nian" last="Wang">Nian Wang</name><affiliation wicri:level="2"><nlm:aff id="Aff1">Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL USA</nlm:aff><country>États-Unis</country><placeName><region type="state">Floride</region></placeName><wicri:cityArea>Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred</wicri:cityArea></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Citrus blight is a citrus tree overall decline disease and causes serious losses in the citrus industry worldwide. Although it was described more than one hundred years ago, its causal agent remains unknown and its pathophysiology is not well determined, which hampers our understanding of the disease and design of suitable disease management.</p></sec><sec><title>Results</title><p>In this study, we sequenced and assembled the draft genome for Swingle citrumelo, one important citrus rootstock. The draft genome is approximately 280 Mb, which covers 74 % of the estimated Swingle citrumelo genome and the average coverage is around 15X. The draft genome of Swingle citrumelo enabled us to conduct transcriptome analysis of roots of blight and healthy Swingle citrumelo using RNA-seq. The RNA-seq was reliable as evidenced by the high consistence of RNA-seq analysis and quantitative reverse transcription PCR results (R<sup>2</sup> = 0.966). Comparison of the gene expression profiles between blight and healthy root samples revealed the molecular mechanism underneath the characteristic blight phenotypes including decline, starch accumulation, and drought stress. The JA and ET biosynthesis and signaling pathways showed decreased transcript abundance, whereas SA-mediated defense-related genes showed increased transcript abundance in blight trees, suggesting unclassified biotrophic pathogen was involved in this disease.</p></sec><sec><title>Conclusions</title><p>Overall, the Swingle citrumelo draft genome generated in this study will advance our understanding of plant biology and contribute to the citrus breeding. Transcriptome analysis of blight and healthy trees deepened our understanding of the pathophysiology of citrus blight.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12864-016-2779-y) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Albrigo, Lg" uniqKey="Albrigo L">LG Albrigo</name></author><author><name sortKey="Young, Rh" uniqKey="Young R">RH Young</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cohen, M" uniqKey="Cohen M">M Cohen</name></author><author><name sortKey="Pelosi, Rr" uniqKey="Pelosi R">RR Pelosi</name></author><author><name sortKey="Brlansky, Rh" uniqKey="Brlansky R">RH Brlansky</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Derrick, Ks" uniqKey="Derrick K">KS 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Li</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Floride</li></region></list><tree><country name="États-Unis"><region name="Floride"><name sortKey="Zhang, Yunzeng" sort="Zhang, Yunzeng" uniqKey="Zhang Y" first="Yunzeng" last="Zhang">Yunzeng Zhang</name></region><name sortKey="Barthe, Gary" sort="Barthe, Gary" uniqKey="Barthe G" first="Gary" last="Barthe">Gary Barthe</name><name sortKey="Grosser, Jude W" sort="Grosser, Jude W" uniqKey="Grosser J" first="Jude W." last="Grosser">Jude W. Grosser</name><name sortKey="Wang, Nian" sort="Wang, Nian" uniqKey="Wang N" first="Nian" last="Wang">Nian Wang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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