Chloroplast genomes of six Colocasia species (Araceae) including taro

Chloroplast genome diversity in taro (Colocasia esculenta) and one other Colocasia species (C. formosana) was previously analysed using concatenated sequences produced by sequencing six polymorphic loci. Here we present complete chloroplast genome sequences for 19 samples (17 new) from six species of Colocasia (Araceae): C. esculenta, C. lihengieae, C. formosana, C. spongifolia, C. oresbia and C. fallax. Three different alignments of these sequences were prepared for a report entitled "Chloroplast capture and range extension after hybridization in taro (Colocasia esculenta)" (Matthews et al. 2024 in press). The alignments show that C. fallax is a distant outgroup and C. oresbia a near outgroup for C. esculenta (including wild and cultivated forms) and a group of closely related wild species (C. lihengiae, C. formosana, C. spongifolia).

The alignments may be useful for future studies involving (1) further populations of each species in the present study, and (2) Colocasia species not represented here.

This work was mainly carried out as part of a project entitled "Mapping Genetic Diversity in Taro to Test Domestication Theories" an international research project supported by the  Japan Society for the Promotion of Science (JSPS Kakenhi No. 17H04614, awarded to P. J. Matthews, with funding for the period 1st April 2017 -– 31st March 2021. Other funding sources for related work carried out before, during and after this period are also noted here.

Methods
Complete chloroplast genome sequences were obtained from 17 field samples representing six species of Colocasia (Araceae) The sequences were assembled and then aligned together with two previously-published sequences from taro (C. esculenta). The 17 new samples were sequenced using Illumina PE 150 run (Genwiz Life Sciences, China). Bioinformatic analyses, including sequencing-data quality checks, genome assembly, annotations, circularization and data curation, were done as reported previously. The previously-published taro sequences were from New Zealand (var. GP, triploid, JN105689 and var. RR, triploid, JN105690).

Using MAFFT in Geneious, sequence sets (see below) were aligned, and one copy of the inverted repeat (IRa) and all gaps (indels) were removed. Three different alignments were made for the sequences from (1) 19 sample, six species, (2) 18 samples, five species, and (3) 16 samples, four species. The alignments were used to prepare Maxium Likelihood (ML) trees shown in the full article. Individual complete genome sequences have been deposited in Genbank.