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

Citation

Matthews, Peter J. et al. (2020), DNA sequences for six chloroplast loci concatenated, representing haplotypes found in Colocasia esculenta, and closely related Araceae, Dryad, Dataset, https://doi.org/10.5061/dryad.nvx0k6dpj

Abstract

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).

Usage Notes

Original sequence data for Colocasia esculenta and other taxa with the haplotypes submitted here (see below) can be found in Genbank, under the name of Ahmed, et al. In the paper submitted to Molecular Ecology, the haplotypes ("types") found in individual plant samples are listed in Supplementary Table S1. These include unique haplotypes found in only one plant sample. For these haplotypes, the Dryad sequences begin with the sample code name (an alphanumeric that begins with a three letter code representing the genus and species).

CES = C. esculenta, CAF = C. affinis, CFA = C. fallax, RVI = Remusatia vivipara, RSP = Remusatia sp., SSP = Steudnera sp.

A minority of sequences have missing values. The CESNZ04 haplotype was excluded from final analysis due to its extreme long‐branch position, which was later traced to a data‐handling error (the sequence of one of the concatenated loci appears to be from Alocasia sp.)

Funding

Higher Education Commission, Pakistan (Ahmed), Award: NA

MEXT Grant-in-Aid (Matthews), Award: 16405019

JSPS KAKENHI (Matthews), Award: 23405004

JSPS KAKENHI (Matthews)*, Award: 25257416

JSPS KAKENHI (Matthews), Award: 25257416

Vietnam National Foundation for Science & Technology Development (NAFOSTED)*, Award: 106.03-2019.322

MEXT Grant-in-Aid (Matthews), Award: 16405019

JSPS KAKENHI (Matthews), Award: 23405004