Complete chloroplast genome sequences of Dioscorea: Characterization, genomic resources, and phylogenetic analyses

Zhenyu Zhao; Xin Wang; Yi Yu; Subo Yuan; Dan Jiang; Yujun Zhang; Teng Zhang; Wenhao Zhong; Qingjun Yuan; Luqi Huang

doi:10.7717/peerj.6032

Complete chloroplast genome sequences of Dioscorea: Characterization, genomic resources, and phylogenetic analyses

PeerJ. 2018 Dec 4:6:e6032. doi: 10.7717/peerj.6032. eCollection 2018.

Authors

Zhenyu Zhao^#¹, Xin Wang^#^{1

2}, Yi Yu³, Subo Yuan⁴, Dan Jiang⁵, Yujun Zhang⁶, Teng Zhang¹, Wenhao Zhong¹, Qingjun Yuan¹, Luqi Huang¹

Affiliations

¹ State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
² Tianjin University of Traditional Chinese Medicine,Tianjin, China.
³ Infinitus (China) Company Ltd, Guangzhou, China.
⁴ Department of Immunology, Medical College, Wuhan University of Science and Technology, Wuhan, China.
⁵ School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China.
⁶ National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.

^# Contributed equally.

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.

Keywords: Chloroplast genome; Dioscorea; Phylogeny; Single sequence repeats; Variable marker.

Grants and funding

This work was funded by the National Natural Science Foundation of China (NSFC: 81325023 and 31671092), the National Key Research and Development Program of China (2017YFC1703700: 2017YFC1703704) and Key Project at Central Government Level: The Ability Establishment of Sustainable Use for Valuable Chinese Medicine Resources (2060302). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.