CarrotDB: a genomic and transcriptomic database for carrot

Abstract

Carrot (Daucus carota L.) is an economically important vegetable worldwide and is the largest source of carotenoids and provitamin A in the human diet. Given the importance of this vegetable to humans, research and breeding communities on carrot should obtain useful genomic and transcriptomic information. The first whole-genome sequences of ‘DC-27’ carrot were de novo assembled and analyzed. Transcriptomic sequences of 14 carrot genotypes were downloaded from the Sequence Read Archive (SRA) database of National Center for Biotechnology Information (NCBI) and mapped to the whole-genome sequence before assembly. Based on these data sets, the first Web-based genomic and transcriptomic database for D. carota (CarrotDB) was developed (database homepage: http://apiaceae.njau.edu.cn/car rotdb). CarrotDB offers the tools of Genome Map and Basic Local Alignment Search Tool. Using these tools, users can search certain target genes and simple sequence repeats along with designed primers of ‘DC-27’. Assembled transcriptomic sequences along with fragments per kilobase of transcript sequence per millions base pairs sequenced information (FPKM) information of 14 carrot genotypes are also provided. Users can download de novo assembled whole-genome sequences, putative gene sequences and putative protein sequences of ‘DC-27’. Users can also download transcriptome sequence assemblies of 14 carrot genotypes along with their FPKM information. A total of 2826 transcription factor (TF) genes classified into 57 families were identified in the entire genome sequences. These TF genes were embedded in CarrotDB as an interface. The ‘GERMPLASM’ part of CarrotDB also offers taproot photos of 45 carrot genotypes and a table containing accession numbers, names, countries of origin and colors of cortex, phloem and xylem parts of taproots corresponding to each carrot genotype. CarrotDB will be continuously updated with new information.Database URL: http://apiaceae.njau.edu.cn/carrotdb/

A MYB transcription factor, DcMYB6, is involved in regulating anthocyanin biosynthesis in purple carrot taproots

“…AtPAP1 (AAG42001) was BLASTed against our CarrotDB: a genomic and transcriptomic database for carrot34 and the high-quality carrot genome which spans 421.5 Mb and accounts for ~90% of the estimated genome size (473 Mb)35. Two transcript contigs showing high sequence identity with AtPAP1 and with higher FPKM values in purple carrots than in non-purple carrots were identified in the transcriptomic database of CarrotDB.…”

Characterising genes associated with flowering time in carrot (Daucus carota L.) using transcriptome analysis

“…, ; Xu et al . ). In the present work, we investigated the effects of environmental factors on flowering and utilised RNA‐seq technology to characterise the carrot transcriptome and to identify flowering time genes such as COL , FLC and SOC1 .…”

Elevated Carbon Dioxide Altered Morphological and Anatomical Characteristics, Ascorbic Acid Accumulation, and Related Gene Expression during Taproot Development in Carrots

“…Based on the homologous sequences from Arabidopsis and other plant species, a total of 12 genes involved in AsA biosynthesis, degradation, and recycling were identified in CarrotDB (Xu et al, 2014; Wang G. L. et al, 2015). These genes included phosphoglucose isomerase ( DcPGI ), phosphomannose isomerase ( DcPMI ), GDP- D -manmose pyrophosphorylase ( DcGMP ), GDP- D -mannose- 3′ ,5 ′ -epimerase ( DcGME ), GDP- L -galactose phosphorylase ( DcGGP ), L -galactose-1- P phosphatase ( DcGPP ), myo -inositol oxygenase ( DcMIOX ), ascorbate oxidase ( DcAO ), ascorbic acid peroxidase ( DcAPX ), monodehydroascorbate reductase ( DcMDHAR ), dehydroascorbate reductase ( DcDHAR ), and glutathione reductase ( DcGR ).…”