Resource Type:
Phylogenetic Tree
Accession:
S16441
Name:
TreeBASE Tree Tr78026
Phylotree Type:
RNA
Analysis:
Publication:
Rong J, Lammers Y, Strasburg JL, Schidlo NS, Ariyurek Y, de Jong TJ, Klinkhamer PG, Smulders MJ, Vrieling K. New insights into domestication of carrot from root transcriptome analyses.. BMC genomics. 2014 Oct 14; 15:895.
File:
| File | Type |
|---|---|
| TreeBASE study S16441 tree Tr78026 | newick |
Tree View:
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TreeBASE Tree Tr78026 from study S16441. The root transcriptomes of widely differing cultivated and wild carrots were sequenced. A method accounting for sequencing errors was introduced to optimize SNP (single nucleotide polymorphism) discovery. 11,369 SNPs were identified. Of these, 622 (out of 1000 tested SNPs) were validated and used to genotype a large set of cultivated carrot, wild carrot and other wild Daucus carota subspecies, primarily of European origin.
This tree is presented as figure 3 in the publication.
Phylogenetic analysis was based on the combined datasets of 622-SNP and 89-SNP. Different Daucus species were used as outgroup to D. carota. Sample names beginning with “W” are wild species and those with “C” are cultivars; the middle name of each sample indicates species name (for outgroup) or subspecies name of wild species, or root type/accession name of cultivars; the sampling country is indicated at the end.