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Insights into long non-coding RNA regulation of anthocyanin carrot root pigmentation

View ORCID ProfileConstanza Chialva, View ORCID ProfileThomas Blein, View ORCID ProfileMartin Crespi, View ORCID ProfileDiego Lijavetzky
doi: https://doi.org/10.1101/2020.10.27.356964
Constanza Chialva
1Instituto de Biología Agrícola de Mendoza (IBAM) UNCuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
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Thomas Blein
2Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Saclay and University of Paris Batiment 630, Gif Sur Yvette, France
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Martin Crespi
2Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Saclay and University of Paris Batiment 630, Gif Sur Yvette, France
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  • For correspondence: dlijavetzky@conicet.gov.ar martin.crespi@ips2.universite-paris-saclay.fr
Diego Lijavetzky
1Instituto de Biología Agrícola de Mendoza (IBAM) UNCuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
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  • For correspondence: dlijavetzky@conicet.gov.ar martin.crespi@ips2.universite-paris-saclay.fr
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ABSTRACT

Carrot (Daucus carota L.) is one of the most cultivated vegetable in the world and of great importance in the human diet. Its storage organs can accumulate large quantities of anthocyanins, metabolites that confer the purple pigmentation to carrot tissues and whose biosynthesis is well characterized. Long non-coding RNAs (lncRNAs) play critical roles in regulating gene expression of various biological processes in plants. In this study, we used a high throughput stranded RNA-seq to identify and analyze the expression profiles of lncRNAs in phloem and xylem root samples using two genotypes with a strong difference in anthocyanin production. We discovered and annotated 8484 new genes, including 2095 new protein-coding and 6373 non-coding transcripts. Moreover, we identified 639 differentially expressed lncRNAs between the phenotypically contrasted genotypes, including certain only detected in a particular tissue. We then established correlations between lncRNAs and anthocyanin biosynthesis genes in order to identify a molecular framework for the differential expression of the pathway between genotypes. A specific natural antisense transcript (NAT) linked to the DcMYB7 key anthocyanin biosynthetic transcription factor suggested how the regulation of this pathway may have evolved between genotypes.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • The Title of the manuscript modified; Section on Results "The differential expression of DcMYB6 and DcMYB7 and their lncNATs was validated by RT-qPCR" added; Section "RNA-seq data mining, identification and annotation of anthocyanin-related lncRNAs" updated with conservation information on new and known lncRNAs and mRNAs

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted January 11, 2021.
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Insights into long non-coding RNA regulation of anthocyanin carrot root pigmentation
Constanza Chialva, Thomas Blein, Martin Crespi, Diego Lijavetzky
bioRxiv 2020.10.27.356964; doi: https://doi.org/10.1101/2020.10.27.356964
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Insights into long non-coding RNA regulation of anthocyanin carrot root pigmentation
Constanza Chialva, Thomas Blein, Martin Crespi, Diego Lijavetzky
bioRxiv 2020.10.27.356964; doi: https://doi.org/10.1101/2020.10.27.356964

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