The Building of the First Apiaceae Genome

Carrot (Daucus carota) is the most widely grown crop in the Apiaceae (Umbelliferae) family. Additionally, it is one of the most important root crops and a main source of provitamin A. To prepare a reference genome sequence of carrot, we sequenced the whole genome of a dihaploid carrot DH1, using primarily Illumina sequencing technology. The genome size is estimated as 473 Mb. After filtering out low quality reads, 88.2Gb of high quality genomic sequence corresponding to 186-fold nt coverage of the entire carrot genome, was used for assembly. The first draft of the carrot genome assembly covered 424 Mb representing 90.0% of the estimated genome size. The assembly consisted of 8,096 sequences greater than 500bp, with an N50 length of 787.2 kb and 1.8 kb for the scaffolds and contigs, respectively. Systematic integration of DH1 ordered BAC end sequences from 29,875 BAC clones and three linkage maps allowed us to assemble and anchor 57 scaffold and superscaffolds covering 362 Mb, to the nine carrot chromosomes increasing N50 of the assembly to 12 Mb. Annotation of repeat sequences revealed that 48% of the carrot genome is composed of repeated sequences. Sequencing of the carrot transcriptome from 20 different tissues and treatments using Illumina is ongoing. The carrot genome sequencing project includes gene annotation, gene family analysis, and comparative genome evolution.