Data from: Development of an ultra-dense genetic map of the sunflower genome

AbstractThe development of ultra-dense genetic maps has the potential to facilitate detailed comparative genomic analyses and whole genome sequence assemblies. Here we describe the use of a custom Affymetrix GeneChip containing nearly 2.4 million features (25 bp sequences) targeting 86,023 unigenes from sunflower (Helianthus annuus L.) and related species to test for single-feature polymorphisms (SFPs) in a recombinant inbred line (RIL) mapping population derived from a cross between confectionery and oilseed sunflower lines (RHA280 x RHA801). We then employed an existing genetic map derived from this same population to rigorously filter out low quality data and place 67,486 features corresponding to 22,481 unigenes on the sunflower genetic map. The resulting map contains a substantial fraction of all sunflower genes and will thus facilitate a number of downstream applications, including genome assembly and the identification of candidate genes underlying QTL or traits of interest., Usage notesHelianthus Genespace Est AssemblyAll genotyping was performed using a custom Affymetrix GeneChip (Affymetrix, CA, USA) designed from Helianthus expressed-sequence tags (ESTs). A total of 283,605 Sanger ESTs from 7 sunflower species (GenBank numbers: AJ318230-AJ318330, AJ412174-AJ412667, AJ437699-AJ437975, AJ539583-AJ540226, AJ541055-AJ541795, AJ542101-AJ542392, AJ827751-AJ829440, BG734514-BG734530, BG874297-BG874313, BG891021-BG891022, BQ909263-BQ917261, BQ965129-BQ980049, BU015365-BU036497, BU671782-BU672110, CD845604-CD858495, CF076145-CF099271, CX943504-CX948070, DY903733-DY959228, EE605695-EE627562, EE628472-EE661299, EL412382-EL492411, EL511146-EL515442, EL772988) were assembled using TGICL [11]. These sequences included 94,017 ESTs from H. annuus; 35,704 from H. argophyllus; 21,589 from H. ciliaris; 33,959 from H. exilis; 30,504 from H. paradoxus; 27,479 from H. petiolaris; and 40,353 from H. tuberosus. The final assembly included 87,237 “unigenes” corresponding to 27,587 contigs and 59,650 singletons.Sunflower_EST_assembly.txt