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

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 char...

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Autores principales:	Constanza Chialva, Thomas Blein, Martin Crespi, Diego Lijavetzky
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ca9b8d87686a434b99741dd404bc6406
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spelling	oai:doaj.org-article:ca9b8d87686a434b99741dd404bc64062021-12-02T14:03:46ZInsights into long non-coding RNA regulation of anthocyanin carrot root pigmentation10.1038/s41598-021-83514-42045-2322https://doaj.org/article/ca9b8d87686a434b99741dd404bc64062021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-83514-4https://doaj.org/toc/2045-2322Abstract 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 linked to the DcMYB7 key anthocyanin biosynthetic transcription factor suggested how the regulation of this pathway may have evolved between genotypes.Constanza ChialvaThomas BleinMartin CrespiDiego LijavetzkyNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Constanza Chialva Thomas Blein Martin Crespi Diego Lijavetzky Insights into long non-coding RNA regulation of anthocyanin carrot root pigmentation
description	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 linked to the DcMYB7 key anthocyanin biosynthetic transcription factor suggested how the regulation of this pathway may have evolved between genotypes.
format	article
author	Constanza Chialva Thomas Blein Martin Crespi Diego Lijavetzky
author_facet	Constanza Chialva Thomas Blein Martin Crespi Diego Lijavetzky
author_sort	Constanza Chialva
title	Insights into long non-coding RNA regulation of anthocyanin carrot root pigmentation
title_short	Insights into long non-coding RNA regulation of anthocyanin carrot root pigmentation
title_full	Insights into long non-coding RNA regulation of anthocyanin carrot root pigmentation
title_fullStr	Insights into long non-coding RNA regulation of anthocyanin carrot root pigmentation
title_full_unstemmed	Insights into long non-coding RNA regulation of anthocyanin carrot root pigmentation
title_sort	insights into long non-coding rna regulation of anthocyanin carrot root pigmentation
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/ca9b8d87686a434b99741dd404bc6406
work_keys_str_mv	AT constanzachialva insightsintolongnoncodingrnaregulationofanthocyanincarrotrootpigmentation AT thomasblein insightsintolongnoncodingrnaregulationofanthocyanincarrotrootpigmentation AT martincrespi insightsintolongnoncodingrnaregulationofanthocyanincarrotrootpigmentation AT diegolijavetzky insightsintolongnoncodingrnaregulationofanthocyanincarrotrootpigmentation
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Insights into long non-coding RNA regulation of anthocyanin carrot root pigmentation

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