De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity.

ABSTRACT:

Background

Among next generation sequence technologies, platforms such as Illumina and SOLiD produce short reads but with higher coverage and lower cost per sequenced nucleotide than 454 or Sanger. A challenge now is to develop efficient strategies to use short-read length platforms for de novo assembly and marker development. The scope of this study was to develop a de novo assembly of carrot ESTs from multiple genotypes using the Illumina platform, and to identify polymorphisms.

Results

A de novo assembly of transcriptome sequence from four genetic backgrounds produced 58,751 contigs and singletons. Over 50% of these assembled sequences were annotated allowing detection of transposable elements and new carrot anthocyanin genes. Presence of multiple genetic backgrounds in o

SUBMITTER: Iorizzo M 

PROVIDER: S-EPMC3224100 | biostudies-literature | 2011 Aug

REPOSITORIES: biostudies-literature