Comparative Transcriptomics of Root Development in Wild and Cultivated Carrots

Genes
Gabriela MachajDariusz Grzebelus

Abstract

The carrot is the most popular root vegetable worldwide. The genetic makeup underlying the development of the edible storage root are fragmentary. Here, we report the first comparative transcriptome analysis between wild and cultivated carrot roots at multiple developmental stages. Overall, 3285, 4637, and 570 genes were differentially expressed in the cultivated carrot in comparisons made for young plants versus developing roots, young plants versus mature roots, and developing roots versus mature roots, respectively. Of those, 1916, 2645, and 475, respectively, were retained after filtering out genes showing similar profiles of expression in the wild carrot. They were assumed to be of special interest with respect to the development of the storage root. Among them, transcription factors and genes encoding proteins involved in post-translational modifications (signal transduction and ubiquitination) were mostly upregulated, while those involved in redox signaling were mostly downregulated. Also, genes encoding proteins regulating cell cycle, involved in cell divisions, development of vascular tissue, water transport, and sugar metabolism were enriched in the upregulated clusters. Genes encoding components of photosystem I and ...Continue Reading

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Citations

Jun 19, 2020·International Journal of Molecular Sciences·Alicja Macko-PodgórniDariusz Grzebelus

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Methods Mentioned

BETA
electrophoresis
RNAseq
ubiquitination

Software Mentioned

RNAseq
StringTie
STAR
Bowtie
DESeq2
R
Trimmomatic
TransDecoder
EBSeq
Cuffmerge

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