Complete chloroplast genome of Ilex dabieshanensis: Genome structure, comparative analyses with three traditional Ilex tea species, and its phylogenetic relationships within the family Aquifoliaceae

Ting Zhou; Kun Ning; Zhenghai Mo; Fan Zhang; Yanwei Zhou; Xinran Chong; Donglin Zhang; Yousry A El-Kassaby; Jian Bian; Hong Chen

doi:10.1371/journal.pone.0268679

Complete chloroplast genome of Ilex dabieshanensis: Genome structure, comparative analyses with three traditional Ilex tea species, and its phylogenetic relationships within the family Aquifoliaceae

PLoS One. 2022 May 19;17(5):e0268679. doi: 10.1371/journal.pone.0268679. eCollection 2022.

Authors

Ting Zhou¹, Kun Ning², Zhenghai Mo¹, Fan Zhang¹, Yanwei Zhou¹, Xinran Chong¹, Donglin Zhang³, Yousry A El-Kassaby⁴, Jian Bian⁵, Hong Chen¹

Affiliations

¹ Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China.
² College of Horticulture, Jinling Institute of Technology, Nanjing City, Jiangsu Province, P.R. China.
³ Department of Horticulture, University of Georgia, Athens, GA, United States of America.
⁴ Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada.
⁵ Jiangsu Yufeng Tourism Development Co. Ltd., Yancheng, China.

Abstract

Ilex dabieshanensis K. Yao & M. B. Deng is not only a highly valued tree species for landscaping, it is also a good material for making kuding tea due to its anti-inflammatory and lipid-lowering medicinal properties. Utilizing next-generation and long-read sequencing technologies, we assembled the whole chloroplast genome of I. dabieshanensis. The genome was 157,218 bp in length, exhibiting a typical quadripartite structure with a large single copy (LSC: 86,607 bp), a small single copy (SSC: 18,427 bp) and a pair of inverted repeat regions (IRA and IRB: each of 26,092 bp). A total of 121 predicted genes were encoded, including 113 distinctive (79 protein-coding genes, 30 tRNAs, and 4 rRNAs) and 8 duplicated (8 protein-coding genes) located in the IR regions. Overall, 132 SSRs and 43 long repeats were detected and could be used as potential molecular markers. Comparative analyses of four traditional Ilex tea species (I. dabieshanensis, I. paraguariensis, I. latifolia and I. cornuta) revealed seven divergent regions: matK-rps16, trnS-psbZ, trnT-trnL, atpB-rbcL, petB-petD, rpl14-rpl16, and rpl32-trnL. These variations might be applicable for distinguishing different species within the genus Ilex. Phylogenetic reconstruction strongly suggested that I. dabieshanensis formed a sister clade to I. cornuta and also showed a close relationship to I. latifolia. The generated chloroplast genome information in our study is significant for Ilex tea germplasm identification, phylogeny and genetic improvement.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Aquifoliaceae / genetics
Genome, Chloroplast*
Ilex* / genetics
Phylogeny
Tea

Substances

Tea

Grants and funding

This research work was funded by Jiangsu Institute of Botany Talent Fund (JIBTF202111) received by T, the Independent Research Project of Jiangsu Province (JSPKLB202036), Natural Science Foundation of Jiangsu Province for Distinguished Young Scholars (BK20170619), and Jiangsu Agricultural Science and Technology Independent Innovation Fund (CX(21)3020) received by H. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.