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CarrotDB: a genomic and transcriptomic database for carrot.

Zhi-Sheng Xu1, Hua-Wei Tan1, Feng Wang1

  • 1State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.

Database : the Journal of Biological Databases and Curation
|October 1, 2014
PubMed
Summary
This summary is machine-generated.

The first carrot genome database, CarrotDB, provides genomic and transcriptomic data for Daucus carota L. This resource aids researchers by offering gene information and germplasm data for carrot breeding and study.

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Area of Science:

  • * Plant Genomics
  • * Bioinformatics
  • * Molecular Biology

Background:

  • * Carrot (Daucus carota L.) is a globally significant vegetable crop, crucial for dietary carotenoids and provitamin A.
  • * Access to comprehensive genomic and transcriptomic data is vital for carrot research and breeding initiatives.
  • * Previous genomic resources for carrot were limited, hindering in-depth studies.

Purpose of the Study:

  • * To assemble and analyze the first whole-genome sequence of carrot ('DC-27').
  • * To develop a user-friendly, web-based database (CarrotDB) integrating genomic and transcriptomic data for Daucus carota L.
  • * To identify and incorporate transcription factor genes and germplasm information into the database.

Main Methods:

  • * De novo whole-genome sequencing and assembly of 'DC-27' carrot.
  • * Downloaded transcriptomic sequences from NCBI's SRA database for 14 carrot genotypes.
  • * Mapped transcriptomic data to the assembled whole-genome sequence.
  • * Developed CarrotDB with integrated tools for gene and SSR searching, and data download functionalities.

Main Results:

  • * Successfully assembled and analyzed the first whole-genome sequence of carrot.
  • * Developed CarrotDB, a comprehensive genomic and transcriptomic database for Daucus carota L.
  • * Identified 2826 transcription factor genes across 57 families within the carrot genome.
  • * Integrated taproot images and descriptive data for 45 carrot genotypes into the 'GERMPLASM' section.
  • * Provided downloadable whole-genome sequences, gene/protein sequences, and transcriptome assemblies with FPKM values.

Conclusions:

  • * CarrotDB serves as a foundational resource for genomic and transcriptomic exploration in Daucus carota L.
  • * The database facilitates research by providing integrated access to diverse carrot genetic and phenotypic data.
  • * CarrotDB will be continuously updated, promising ongoing advancements in carrot biology and breeding.