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

• Published in: Scientific reports Vol. 11; no. 1; p. 4093
• Main Authors: Chialva, Constanza, Blein, Thomas, Crespi, Martin, Lijavetzky, Diego
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 18-02-2021; Nature Publishing Group; Nature Portfolio
• Subjects: 631/449/1659; 631/449/1870; 631/449/2491; Anthocyanins; Anthocyanins - biosynthesis; Anthocyanins - metabolism; Antisense RNA; Biochemistry, Molecular Biology; Biosynthesis; Botanics; Daucus carota; Daucus carota - genetics; Daucus carota - metabolism; Gene expression; Gene Expression Regulation, Plant - genetics; Genes, Plant - genetics; Genomics; Genotypes; Humanities and Social Sciences; Life Sciences; Metabolites; multidisciplinary; Non-coding RNA; Phloem - metabolism; Pigmentation; Plant Roots - metabolism; RNA, Long Noncoding - immunology; Science; Science (multidisciplinary); Storage organs; Transcriptome; Vegetal Biology; Xylem; Xylem - metabolism
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-021-83514-4

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.