DNA sequences for six chloroplast loci concatenated, representing haplotypes found in Colocasia esculenta, and closely related Araceae

As an ancient clonal root and leaf crop, taro (Colocasia esculenta) is highly polymorphic with uncertain genetic and geographic origins. We explored chloroplast DNA variation in wild and cultivated taros and other Colocasia species, and found cultivated taro to be polyphyletic, with tropical and temperate clades originating in Southeast Asia. A third clade was found exclusively in wild populations from Southeast Asia to Australia and Papua New Guinea. Our findings do not support the hypothesis of taro domestication in Papua New Guinea.

Methods
These data were collected in a survey of wild and cultivated forms of Colocasia esculenta, and near relatives, mainly in Asia and the Pacific. Sequencing was carried out at six chloroplast loci defined by the six primer sets ACECP005, ACECP016, ACECP018, ACRP026, ACECP035, and ACECP039. Before concatenation, sequences were edited to manually determine ambiguous nucleotide reads, remove indels, align, and trim read ends.

ACECP refers to Ahmed, Colocasia esculenta, Chloroplast.

The primers were chosen because they were previously shown to amplify variable loci within the taro chloroplast genome. See:

Ahmed, I., Biggs P. J., Matthews P. J., Collins L. J., Hendy M. D., & Lockhart P. J.  Mutational dynamics of aroid chloroplast genomes. Genome Biol. Evol. 4, 1316–1323 (2012)

Ahmed, I., Matthews, P. J., Biggs, P. J., Naeem, M., McLenachan, P. A. & Lockhart, P. J.  Identification of chloroplast genome loci suitable for high-resolution phylogeographic studies of Colocasia esculenta (L.) Schott (Araceae) and closely related taxa. Mol. Ecol. Resour. 13, 929–937 (2013).