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Mitochondrial DNA B Resour
Mitochondrial DNA B Resour
Mitochondrial DNA. Part B, Resources
2380-2359
Taylor & Francis

33366424
10.1080/23802359.2019.1696242
1696242
Version of Record
Research Article
Mitogenome Announcement
The complete chloroplast genome of an endangered plant-Nomocharis aperta
X. Chen et al.
Chen Xueda ab
Zhang Xiuhai b
Liu Yixin b
Gao Junlian b
Xing Zhen a
Du Yunpeng b
a Resources and Environment College, Tibet Agriculture and Animal Husbandry University, Nyingchi, China;
b Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Functional Flower Engineering Technology Research Center, Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
Xueda Chen and Xiuhai Zhang contributed equally to this work.

CONTACT Zhen Xing xztibetan@163.comResources and Environment College, Tibet Agriculture and Animal Husbandry University, Nyingchi, Tibet860000, China;
Yunpeng Du dyp_851212@126.comBeijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Functional Flower Engineering Technology Research Center, Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing100097, China
9 12 2019
2020
5 1 6566
© 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
2019
The Author(s)
https://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Nomocharis aperta is an endangered and endemic species with high ornamental value in China. In this study, we reported a complete chloroplast genome of N. aperta, which was de novo assembled using the next-generation sequencing data. The complete chloroplast genome is 152,845 in length, including a large single copy region of 70,506 bp and a small single copy region of 17,468 bp and two inverted repeat regions of 26,520 bp. A total of 130 functional genes were encoded, consisting of 84 protein-coding genes, 36 transfer RNA genes, and 8 ribosomal RNA genes. The overall AT content of the chloroplast genome is 63.00%. In addition, phylogenetic analysis with the reported chloroplast genomes showed that N. aperta is nested within Lilium and close to L. henricii, L. bakerianum and L. taliense. It indicates that the study on the relationship between Nomocharis and Lilium needs more Nomocharis and Lilium complete chloroplast genome, especially some key species like N. aperta.

Keywords

Nomocharis aperta
high-throughput sequence
complete chloroplast genome
phylogenetic analysis
Lilium-Nomocharis complex
National Natural Science Foundation of China10.13039/50110000180931601781 Youth Research Fund of Beijing Academy of Agriculture and ForestryQNJJ201910 This work was supported by the National Natural Science Foundation of China [Grant No. 31601781] and Youth Research Fund of Beijing Academy of Agriculture and Forestry [QNJJ201910].
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The genus Nomocharis was established by the famous French botanist Adrien Rene Franchet (1889) with Nomocharis pardanthina Franchet, based on material collected by Delavay in western Yunnan (Sealy 1983). However, it is still a problem about the classification of Nomocharis so far. Recent molecular phylogenetic analysis indicates that Nomocharis is nested within Lilium (Gao et al. 2012; Du, He, Wang, Wei, Li, et al. 2014; Du, He, Wang, Li, Wei, Yuan, et al. 2014). But several phylogenetic studies reported just use nuclear and chloroplast sequences, not complete genome. Now, we report the complete chloroplast genome of Nomocharis aperta in order to further study the classification of Nomocharis and solve the Lilium-Nomocharis complex deeply and completely.

Nomocharis aperta is an endangered species of Nomocharis (http://www.iplant.cn/rep/prot/Nomocharis%20aperta), samples of N. aperta were collected from Shangri-La (Geospatial coordinates: N：27°36′54″E：99°42′44″) in Northwest Yunnan, China, and DNA was stored at the herbarium of Institute of Botany, CAS (Herbarium number: BOP127294). Total genomic DNA was extracted from fresh leaves, according to the DNAsecure Plant Kit (Aidlab). A genomic DNA library was constructed using VAHTSTM Turbo DNA Library Prep Kit for IlluminaVR (Vazyme, Nanjing City, China). High-throughput sequencing was performed with pair-end reads on the HiSeq4000 Sequencing System at Novogene (http://www.novogene.com/index.php). The raw reads were quality-trimmed by NGSQC Toolkit v2.3.3 and assembled by SPAdes v3.6.1 (Bankevich et al. 2012). Assembled chloroplast genome was annotated using Dual Organellar GenoMe Annotator (http://dogma.ccbb.utexas.edu/) (Wyman et al. 2004). The gene map of the chloroplast genome was drawn in OGDraw v1.2 (Lohse et al. 2013).

The complete chloroplast genome of N. aperta (Genbank accession number: MN509269) is 152,845 bp in length, including a large single copy (LSC) region of 70,506 bp and a small single copy (SSC) region of 17,468 bp and two inverted repeat (IR) regions of 26,520 bp. The complete cp-DNA encodes 130 genes, comprising 84 protein-coding genes, 36 transfer RNA genes, and 8 ribosomal RNA genes. Among these genes, 15 genes (trnK-UUU, rps16, atpF, rpoC1, trnL-UAA, trnV-UAC, rps12, petB, petD, rpl16, rpl2, ndhB, trnL-GAU, ndhA, trnA-UGC) contained one intron, 2 genes (ycf3, clpP) contained two introns and 6 genes (trnL-GAU, trnA-UGC, ndhB, rpl2, rps12, trnL-GAU) were located in IR region. The nucleotide composition of N. aperta has high A + T content of 63.00%, and the corresponding values of the SSC, LSC, and IR regions were 69.40%, 65.30%, and 57.50%, respectively.

In order to analyze phylogenetic relationship between N. aperta and its related species, a maximum-likelihood (ML) phylogenetic tree was constructed with CIPRES (http://www.phylo.org/) (Miller et al. 2010). The complete chloroplast genome of 16 representative species from genera Nomocharis, Lilium, Fritillaria, Notholirion, and Cardiocrinum (later three genera as outgroups) were selected to perform the ML analysis. In the ML tree, Fritillaria, Notholirion, and Cardiocrinum were three separate monophyletic groups with the bootstrap values 100% (Figure 1). Nomocharis aperta was close to N. pardanthina (Liu et al. 2018) but nested within Lilium. It indicates that the phylogenetic position of Nomocharis needs a further study. So this report provides essential genetic data for further study on Lilium-Nomocharis complex. Meanwhile, it also contributes to conserve the genetic diversity of this endangered species.

Figure 1. Phylogenetic relationships of 11 species in the Nomocharis and Lilium with the outgroups of 1 Notholirion species, 2 Cardiocrinum species and 2 Fritillaria species constructed by complets chloroplast genome with the maximum likelihood (ML) analyses. The bootstrap values were based on 1000 replicates.

Disclosure statement

No potential conflict of interest was reported by the authors.
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