Nantaise transcriptome assembly Arias et al. 2020

Resource Type: 
Analysis
Name: 
Nantaise transcriptome assembly Arias et al. 2020
Description: 

Plants of commercially acquired carrot (Daucus carota L.) cultivar Nantaise were harvested 8 weeks after sowing.

RNA was sequenced by OMIC Solution (Santiago, Chile) using the Ion Torrent PGM technology (chip P1.1.17) with IonXpress RNA kit (Thermo Fisher Scientific) after library profile analysis using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA). Adapter sequences were removed, and a de novo transcriptome assembly was carried out following CLC Genomics Workbench default parameters including a quimera analysis.

The assembly contains 63,164 contigs, from which 18,488 genes are differentially expressed (DEG) between the two experimental conditions light and dark.

Publication: 
Arias D, Maldonado J, Silva H, Stange C. A de novo transcriptome analysis revealed that photomorphogenic genes are required for carotenoid synthesis in the dark-grown carrot taproot.. Molecular genetics and genomics : MGG. 2020 Nov; 295(6):1379-1392.
Relationship: 
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Relationships
The analysis, Nantaise transcriptome assembly Arias et al. 2020 blast to DCARv2, is a part of analysis, Nantaise transcriptome assembly Arias et al. 2020.
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Program, Pipeline, Workflow or Method Name: 
CLC Genomics Workbench + quimera
Program Version: 
not specified
Date Performed: 
Sunday, July 12, 2020 - 00:00
Data Source: 
Source Name
: Publication supplemental table S9
Source URI
: https://link.springer.com/article/10.1007/s00438-020-01707-4
Organism: 
NameCommon NameComment
Carrot
For a general overview of carrot, see the Carrot Facts Page
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Biomaterial: 
NameDescription
Carrot roots cultivated in dark (R/D) or in light (R/L).
Carrot roots cultivated in dark (R/D) or in light (R/L).
Carrot roots cultivated in dark (R/D) or in light (R/L).
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Project: 
NameDescription
Daucus carota (carrot) is one of the few plant species that synthesize and accumulate carotenoids in the storage root that grows in darkness. Contrary to other plants, light inhibits secondary root growth and carotenoid accumulation, suggesting the existence of new mechanisms repressed by light that regulate both processes. In order to identify genes induced by dark and repressed by light that regulate carotenoid synthesis and carrot root development, we performed RNA-Seq analysis from dark and light-grown carrot roots.
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Data Source File: 
438_2020_1707_MOESM1_ESM.xlsx