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

Constanza Chialva,Diego Lijavetzky,Martin Crespi,Thomas Blein

doi:10.1038/s41598-021-83514-4

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.

Highlights

Anthocyanins are flavonoids, a class of phenolic compounds synthesized via the phenylpropanoid pathway, a late branch of the shikimic acid pathway[1]
In order to thoroughly identify and annotate long noncoding RNAs (lncRNAs) related to anthocyanin biosynthesis regulation in carrot roots, we performed a whole transcriptome RNA-seq analysis of specific tissues from the carrot genotypes ‘Nightbird’ and ‘Musica’ (Supplementary Figure S1)
Genetic analyses using model plant species like Arabidopsis, petunia and maize allowed the identification of most structural genes in the anthocyanin biosynthesis pathway as well as the main regulatory genes controlling pigment synthesis

Summary

Introduction

Anthocyanins are flavonoids, a class of phenolic compounds synthesized via the phenylpropanoid pathway, a late branch of the shikimic acid pathway[1]. The broad variation observed among purple carrot root genotypes, regarding both anthocyanin concentration and pigment distribution in the phloem and xylem tissues, suggests independent genetic regulation in these two root tissues[23]. In this sense, Xu et al.[16] found that the expression pattern of a R2R3–MYB TF, DcMYB6, is correlated with anthocyanin production in carrot roots and that the overexpression of this gene in Arabidopsis thaliana enhanced anthocyanin accumulation in vegetative and reproductive tissues in this heterologous system. Among these cis-lncRNAs, NATs are of special interest as they have been shown to provide a mechanism for locally regulating the transcription or translation of the target gene on the other strand, providing novel mechanisms involved in the regulation of key biological processes[39], plant development[40] and environmentally dependent gene expression[36,37]

Methods

Results

Conclusion