Abstract
Dioscorea L., the largest genus of the family Dioscoreaceae with over 600 species, is not only an important food but also a medicinal plant. The identification and classification of Dioscorea L. is a rather difficult task. In this study, we sequenced five Dioscorea chloroplast genomes, and analyzed with four other chloroplast genomes of Dioscorea species from GenBank. The Dioscorea chloroplast genomes displayed the typical quadripartite structure of angiosperms, which consisted of a pair of inverted repeats separated by a large single-copy region, and a small single-copy region. The location and distribution of repeat sequences and microsatellites were determined, and the rapidly evolving chloroplast genome regions (trnK-trnQ, trnS-trnG, trnC-petN, trnE-trnT, petG-trnW-trnP, ndhF, trnL-rpl32, and ycf1) were detected. Phylogenetic relationships of Dioscorea inferred from chloroplast genomes obtained high support even in shortest internodes. Thus, chloroplast genome sequences provide potential molecular markers and genomic resources for phylogeny and species identification.
Highlights
The identification of Dioscorea L. has presented a challenge to systematists because of its great morphological variations, especially the aerial parts, such as leaves (Wilkin et al, 2005)
Comparisons of chloroplast genomes provide additional effective resources for the development of variable markers, which are used for phylogeny or species identification (Dong et al, 2012)
Generation Sequencing (NGS) technique generates the large numbers of DNA sequences at relatively low cost and promptly extended gene-based phylogenetics to phylogenomics
Summary
The identification of Dioscorea L. has presented a challenge to systematists because of its great morphological variations, especially the aerial parts, such as leaves (Wilkin et al, 2005). For phylogenetic studies of Dioscorea, some chloroplast molecular markers (such as rbcL, matK, trnH-psbA, trnL-F), have been analyzed (Gao et al, 2008; Hsu et al, 2013; Wilkin et al, 2005). Further studies to seek high resolution molecular markers in the species level to the success of identification and phylogeny in Dioscorea is necessary. Comparisons of chloroplast genomes provide additional effective resources for the development of variable markers, which are used for phylogeny or species identification (Dong et al, 2012). The comparative analysis of nine complete Dioscorea chloroplast genomes was conducted to demonstrate the features and structural differentiation of the sequences, to provide valuable chloroplast molecular markers for further phylogenetic and species identification. We tested the feasibility of phylogeny reconstruction using chloroplast genome data
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