36th International Carrot Conference Abstract

The building of the first Apiaceae Genome

Massimo Iorizzo¹, Douglas Senalik^1,2, Shelby Ellison¹, Pablo Cavagnaro³, Allen Van Deynze⁴ and Philipp Simon^1,2

¹ Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706. USA

² USDA-Agricultural Research Service, Vegetable Crops Research Unit, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA

³ CONICET, Fac. Ciencias Agrarias – Universidad Nacional de Cuyo, and INTA EEA La Consulta, CC8 La Consulta (5567), Mendoza, Argentina

⁴ Seed Biotechnology Center, University of California, 1 Shields Ave, Davis, CA, 95616-8816, USA

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 442 Mb representing 93.4% of the estimated genome size. The assembly consisted of 8,096 sequences greater than 500bp, with an N50 length of 750 kb and 29 kb for the scaffolds and contigs, respectively. Systematic integration of DH1 ordered BAC end sequences from 29,875 BAC clones and five linkage maps allowed us to assemble and anchor 371 scaffold and superscaffolds covering 365 Mb, to the nine carrot chromosomes increasing N50 of the assembly to 1.4 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 will include gene annotation, gene family analysis, and comparative genome evolution.

Last updated Friday, 26-Jul-2013 08:11:00 CDT