IMR Press / FBL / Volume 27 / Issue 1 / DOI: 10.31083/j.fbl2701009
Open Access Original Research
Study of the genus Torreya (Taxaceae) based on chloroplast genomes
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1 Anhui Provincial Engineering Laboratory of Wetland Ecosystem Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, 230601 Hefei, Anhui, China
2 Bioinformatic Department, Shanghai Winnerbio Technology Co., Ltd., 201403 Shanghai, China
3 Institute of Chinese Medicine Resources, Anhui College of Traditional Chinese Medicine, 241000 Wuhu, Anhui, China
4 Shanghai Majorbio Bio-pharm Technology Co., Ltd., 201203 Shanghai, China
5 Department of Environmental Engineering, College of Chemistry and Materials Engineering, Quzhou University, 324000 Quzhou, Zhejiang, China
*Correspondence: hongxin@ahu.edu.cn (Xin Hong); ljh976128@163.com (Jian-Hui Li)
These authors contributed equally.
Academic Editor: Changsoo Kim
Front. Biosci. (Landmark Ed) 2022, 27(1), 009; https://doi.org/10.31083/j.fbl2701009
Submitted: 26 May 2021 | Revised: 10 December 2021 | Accepted: 15 December 2021 | Published: 10 January 2022
Copyright: © 2022 The Author(s). Published by IMR Press.
This is an open access article under the CC BY 4.0 license.
Abstract

Background: Species of the genus Torreya are similar in morphology, and their morphological taxonomic characteristics are not stable because of environmentally induced changes. Therefore, morphology is insufficient for understanding their relationships. Chloroplast genome sequencing technology provides a powerful tool for molecular analysis to get more infomation for classification and identification of Torreya genus. Methods: A total of 4 chloroplast genome of Torreya, including T. Parvifolia, T. nucifera, T. fargesii var. Yunnanensis and T. grandis var. jiulongshanensis, were sequenced and annotated. Campartive genome and phylogenetic tree were provided for variation analysis. Results: The chloroplast genome size of the four samples is about 137 kb, the inverted repeat (IR) regions are identified in the genus Torreya. Genome comparison using mVISTA showed high sequence similarity among different species. Regions with divergence in exon regions include accD, ndhB, ndhF, psbA, psbJ, rpl2, rps3, rps16, rps18, ycf1, and ycf2. The phylogenetic tree based on 73 single-copy genes showed a clearer relationships among different species of Torreya. Conclusions: All genomes of the four Torreya species consist of two short IR regions, and results of the phylogenetic analysis concluded that T. parvifolia should be considered as T. fargesii var. yunnanensis or treated as a sister species. T. grandis var. jiulongshanensis should be treated as a variety of T. grandis according to molecular evidence, supporting the originally published proposal.

Keywords
Torreya
Chloroplast genome
Phylogeny
Single-copy orthologous genes
Molecular ecology
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