https://orcid.org/0000-0003-2948-6051
Abstract
Michelia balansae var. balansae (Aug. Candolle) Dandy is a timber and spices species in Magnoliaceae, native to China and Vietnam. In this paper, the complete chloroplast genome (cpDNA) and basic annotated information were reported and its phylogenetic relationship with other species in Magnoliaceae was analyzed. The size of chloroplast genome of M. balansae var. balansae is 160,134 bp, which exhibited a typical quadripartite structure comprising a large single-copy (LSC) region of 88,161 bp and a small single-copy (SSC) region of 18,845 bp separated by a pair identical inverted repeat regions (IRs) of 26,564 bp each. The chloroplast genome contains 131 genes, including 86 protein-coding genes (PCGs), 37 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes. The phylogenetic analysis indicated that M. balansae var. balansae is most affinal to M. montana and they form a nomophyletic group with other 14 Michelia species. This Michelia clade is sister to the Aromadendron clade with high support. All genera mentioned in this analysis are nomophyletic under the system of Magnoliaceae by Sima and Lu.
Michelia balansae (Aug. Candolle) Dandy is the type species of Michelia sect. Dichlamys Dandy in the family Magnoliaceae (Dandy Citation1974). It has two varieties, var. balansae (Aug. Candolle) Dandy and var. appressipubescens Y. W. Law. The latter variety occurs in Guizhou, Hainan and Yunnan of China (Law Citation1985; Law and Wu Citation1996; Sima and Lu Citation2009). Michelia balansae var. balansae (Aug. Candolle) Dandy is native to China (Fujian, Guangdong, Guangxi, Hainan, Yunnan) and Vietnam (Bac Ha, Cao Bang, Ha Giang, Ha Tay, Hanoi, Hoa Binh, Lao Cai, Nghe An, Phu Tho, Quang Binh, Son La, Thai Nguyen, Thanh Hoa, Tuyen Quang, Vinh Phuc, Yen Bai) (Law Citation1985; Law and Wu Citation1996; Sima and Lu Citation2009; Tran Citation2012; Vu and Xia Citation2012), and cultivated as an ornamental tree species in Southern China (Ma and Jiao Citation2008; Wang et al. Citation2013). It is a good tree species for timber and spices in tropical region and used for medicinal purpose (Nguyen et al. Citation2005; Tran Citation2012; Vu and Xia Citation2012). However, there has been no report on chloroplast genome information of Michelia balansae var. balansae (Aug. Candolle) Dandy until now.
The complete sequence of chloroplast genome of Michelia balansae var. balansae (Aug. Candolle) Dandy was reported in this study. The fresh leaf of Michelia balansae var. balansae (Aug. Candolle) Dandy was collected from Kunming Arboretum, Yunnan Academy of Forestry & Grassland Science (formerly Yunnan Academy of Forestry), Yunnan Province of China (25°9′4″N, 102°44′45″E). The sheets of vouchered specimen, Y. K. Sima & S. Y. Chen 99275, are stored at the herbaria, YAF and YCP. Total genomic DNA was extracted from fresh leaves using DNA Plantzol Reagent (Invitrogen, Carlsbad, CA, USA) to construct chloroplast DNA libraries. The extracted DNA was sequenced by Illumina HiSeq Sequencing System (Illumina, San Diego, CA) and shotgun library was constructed. About 1.7 Gb pair-end (150 bp) raw reads were obtained and the low-quality sequences were filtered using CLC Genomics Workbench v8.0 (CLC Bio, Aarhus, Denmark) to get high-quality clean reads. NOVOPlasty software (Dierckxsens et al. Citation2017) was used to align and assemble cp genome with Pachylarnax sinica (Y. W. Law) N. H. Xia & C. Y. Wu (JX280400) served as the reference. The complete chloroplast genome of Michelia balansae var. balansae (Aug. Candolle) Dandy was automatically annotated using CpGAVAS2 (Shi et al. Citation2019) and then adjusted and confirmed with Geneious 9.1 (Kearse et al. Citation2012). The sequence data were deposited into GenBank. Then, the complete chloroplast genome was submitted to the GenBank under the accession number of MT654130.
The size of chloroplast genome of Michelia balansae var. balansae (Aug. Candolle) Dandy is 160,134 bp, which exhibited a typical quadripartite structure comprising a large single-copy (LSC) region of 88,161 bp and a small single-copy (SSC) region of 18,845 bp separated by a pair of identical inverted repeat regions (IRs) of 26,564 bp each. The chloroplast genome contains 131 genes, including 86 protein-coding genes (PCGs), 37 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes.
In order to determine the phylogenetic position of M. balansae var. balansae (Aug. Candolle) Dandy, 24 complete chloroplast genome sequences of the family Magnoliaceae from NCBI were aligned using MAFFT v. 7 (Sima and Lu Citation2012; Katoh and Standley Citation2013; Sima, Yu, et al. Citation2020). Based on the system of Magnoliaceae by Sima and Lu (Citation2012), four species of the tribe magnolieae, Kmeria septentrionalis (HM775382), Pachylarnax sinica (JX280400), P. yunnanensis (KF753638) and P. omeiensis (MK728935) were served as the outgroup. A phylogenetic tree was built using MrBayes v3.2.7 (Ronquist et al. Citation2012) with a single priori GTR + GAMMA model and bootstrap values were calculated from 1000 replicates.
The results of phylogenetic analysis indicated that Michelia balansae var. balansae (Aug. Candolle) Dandy is most affinal to Michelia montana Blume (MN990614) and they form a nomophyletic group with other 14 species of the genus Michelia Linnaeus (). This clade of the genus Michelia Linnaeus is sister to the clade of the genus Aromadendron Blume with high support and it is the same as those results of other studies (Chen, Wu, Fu, et al. Citation2020; Chen, Wu, Ma, et al. Citation2020; Sima, Li, et al. Citation2020; Sima, Wu, et al. 2020). All genera mentioned in this analysis are nomophyletic under the system of Magnoliaceae by Sima and Lu (Citation2012) and it is consistent with the findings of other analyses (Chen, Wu, Fu, et al. Citation2020; Chen, Wu, Ma, et al. Citation2020; Luo et al. Citation2020; Sima, Li, et al. Citation2020; Sima, Wu, et al. Citation2020). The determination of the complete chloroplast genome sequence provided new molecular data to illuminate the genus Michelia Linnaeus in Magnoliaceae evolution.
Figure 1. The phylogenetic tree inferred from the complete chloroplast genome sequences in the family Magnoliaceae. Bootstrap values (1000 replicates) are shown at the nodes.
Disclosure statement
No potential conflict of interest was reported by the authors.
Data availability statement
The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at (https://www.ncbi.nlm.nih.gov) under the accession no. MT654130. The associated BioProject, SRA, and Bio-Sample numbers are PRJN682272, SRR13201444, and SAMN16984752 respectively.
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References
- Chen SY, Wu T, Fu YP, Hao JB, Ma HF, Zhu YF, Sima YK. 2020. Complete chloroplast genome sequence of Michelia champaca var. champaca Linnaeus, an ornamental tree species of Magnoliaceae. Mitochondrial DNA Part B. 5(3):2845–2847.
- Chen SY, Wu T, Ma HF, Fu YP, Zhu YF, Hao JB, Jiang H, Sima YK. 2020. The complete chloroplast genome sequence of Lirianthe hodgsonii, a tree species of Magnoliaceae as least concern. Mitochondrial DNA Part B. 5(3):3082–3084.
- Dandy JE. 1974. Magnoliaceae Juss. taxonomy. In: Nilsson S, editor. World pollen and spore flora, Vol. 3. Stockholm: Almqvist & Wiksell; p. 2–5.
- Dierckxsens N, Mardulyn P, Smits G. 2017. Novoplasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 45(4):e18.
- Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30(4):772–780.
- Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, et al. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 28(12):1647–1649.
- Law YW. 1985. Taxa nova Magnoliacearum. Bull Bot Res. 5(3):121–131.
- Law YW, Wu YF. 1996. Magnoliaceae. In: Flora Reipublicae Popularis Sinicae. Tomus Vol. 30(1). Beijing: Science Press; p. 82–198.
- Luo W, Li ZR, Sima YK, Xu T. 2020. The complete chloroplast genome sequence of the Manglietia longirostrata Sima, a rare and endemic species to China. Mitochondrial DNA Part B. 5 (3):2872–2891.
- Ma XY, Jiao GL. 2008. Study on photosynthetic characteristics of Michelia crassipes and Michelia balansae. Guangdong Forest Sci Technol. 24(2):10–13.
- Nguyen AD, Tran DT, Nguyen XD. 2005. Chemical composition of the leaf oil of Michelia balansae (A. DC.) Dandy from Vietnam. J Essent Oil-Bearing Plant. 8(1):11–14.
- Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hohna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 61(3):539–542.
- Shi LC, Chen HM, Jiang M, Wang LQ, Wu X, Wang LF, Liu C. 2019. CPGAVAS2, an integrated plastome sequence annotator and analyzer. Nucleic Acids Res. 47(W1):W65–73.
- Sima YK, Li YQ, Yuan XL, Wang Y. 2020. The complete chloroplast genome sequence of Michelia chapensis Dandy: an endangered species in China. Mitochondrial DNA Part B. 5 (2):1594–1595.
- Sima YK, Lu SG. 2012. A new system for the family Magnoliaceae. In: Xia NH, Zeng QW, Xu FX, Wu QG, editors. Proceedings of the Second International Symposium on the Family Magnoliaceae. Wuhan: Huazhong University Science & Technology Press; p. 55–71.
- Sima YK, Lu SG. 2009. Magnoliaceae. In: Shui YM, Sima YK, Wen J, Chen WH, editors. Vouchered flora of Southeast Yunnan. Vol. 1. Kunming: Yunnan Science & Technology Press; p. 16–67.
- Sima YK, Wu T, Fu YP, Hao JB, Chen SY. 2020. Complete chloroplast genome sequence of Lirianthe coco (Loureiro). N. H. Xia & C. Y. Wu (Magnoliaceae), a popular ornamental species. Mitochondrial DNA Part B. 5(3):2410–2412.
- Sima YK, Yu H, Ma HF, Hao JB, Chen SY, Li SW, Fu YP. 2020. New combinations in Magnoliaceae. J West China Forest Sci. 49(4):29–40.
- Tran CK. 2012. Plants used as medicines and spices of the family Magnoliaceae in Vietnam. In: Xia NH, Zeng QW, Xu FX, Wu QG, editors. Proceedings of the Second International Symposium on the Family Magnoliaceae. Wuhan: Huazhong University Science & Technology Press; p. 86–94.
- Vu QN, Xia NH. 2012. Taxonomy and biogeography of the family Magnoliaceae from Vietnam. In: Xia NH, Zeng QW, Xu FX, Wu QG, editors. Proceedings of the Second International Symposium on the Family Magnoliaceae. Wuhan: Huazhong University Science & Technology Press; p. 95–115.
- Wang MY, Sima YK, Wu SB, Chen SY, Hao JB. 2013. Leaf variation of Michelia balansae, an ornamental species. Guangdong Agri Sci. 40(7):49–53.