Nantaise transcriptome assembly Arias et al. 2020

Resource Type:

Analysis

Name:

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.

File:


File	Type
Nantaise transcriptome assembly Arias et al. 2020 FASTA file	FASTA format

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:

There is 1 relationship.
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.

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:


Name	Common Name	Comment
Daucus carota subsp. sativus	Carrot	For a general overview of carrot, see the Carrot Facts Page

Biomaterial:


Name	Description
SAMN14648295	Carrot roots cultivated in dark (R/D) or in light (R/L).
SAMN14648296	Carrot roots cultivated in dark (R/D) or in light (R/L).
SAMN14648297	Carrot roots cultivated in dark (R/D) or in light (R/L).

Project:


Name	Description
Daucus carota subsp. sativus cultivar:Nantaise: Transcriptome from dark and light-grown carrot roots (Daucus carota subsp. sativus )	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.

Data Source File:

438_2020_1707_MOESM1_ESM.xlsx