药学学报, 2020, 55(1): 168-176
引用本文:
张明英, 王西芳, 高静, 刘阿萍, 颜永刚, 杨新杰, 张岗. 美丽芍药叶绿体全基因组解析及系统发育分析[J]. 药学学报, 2020, 55(1): 168-176.
ZHANG Ming-ying, WANG Xi-fang, GAO Jing, LIU A-ping, YAN Yong-gang, YANG Xin-jie, ZHANG Gang. Complete chloroplast genome of Paeonia mairei H. Lév.: characterization and phylogeny[J]. Acta Pharmaceutica Sinica, 2020, 55(1): 168-176.

美丽芍药叶绿体全基因组解析及系统发育分析
张明英, 王西芳, 高静, 刘阿萍, 颜永刚, 杨新杰, 张岗
陕西中医药大学药学院/陕西省秦岭中草药应用开发工程技术研究中心, 陕西 西安 712046
摘要:
本研究利用Illumina HiSeq X Ten测序平台对芍药属药用植物美丽芍药进行了叶绿体全基因组测序,通过生物信息学分析方法进行序列组装、注释和特征解析,并将其与芍药属其他11种植物的叶绿体全基因组进行了比较基因组学和系统发育分析。结果显示,美丽芍药叶绿体基因组全长152 731 bp,GC含量为38.4%,具有被子植物叶绿体基因组典型的四分体结构,包括一个大单拷贝区(large single copy,LSC)、一个小单拷贝区(small single copy,SSC)和一对反向重复区(inverted repeat sequence,IRa/IRb),长度分别为84 402、16 969和25 680 bp;共注释得到136个基因,包括90个蛋白编码基因,38个tRNA基因和8个rRNA基因,其中7个蛋白编码基因、7个tRNA基因和4个rRNA基因分别在反向重复区发生了一次重复;此外,在美丽芍药叶绿体基因组中共检测出28个散在重复序列(dispersed repeats)、10个串联重复序列(tandem repeats)和64个简单重复序列(simple sequence repeats,SSRs)。芍药属12个物种的叶绿体基因组在大小、基因组成和排列顺序、GC含量等方面高度保守;同时,非编码区(包括基因间区和内含子)序列的种间变异高于蛋白编码基因序列,LSC区和SSC区序列变异高于IR区。系统发育分析结果以100%的支持率支持美丽芍药与芍药、草芍药和川赤芍共同构成一个单系分支,并与芍药亲缘关系最近。本研究首次报道了美丽芍药叶绿体全基因组,对其序列变异及结构特征进行了解析,并基于叶绿体全基因组序列构建系统发育树,明确了美丽芍药在芍药属内的系统发育位置,研究结果将为美丽芍药的保护遗传学和资源开发利用等研究提供理论基础。
关键词:    芍药属      美丽芍药      叶绿体基因组      高通量测序      系统发育     
Complete chloroplast genome of Paeonia mairei H. Lév.: characterization and phylogeny
ZHANG Ming-ying, WANG Xi-fang, GAO Jing, LIU A-ping, YAN Yong-gang, YANG Xin-jie, ZHANG Gang
College of Pharmacy and Shaanxi Qinling Application Development and Engineering Center of Chinese Herbal Medicine, Shaanxi University of Chinese Medicine, Xi'an 712046, China
Abstract:
The whole chloroplast genome of the medicinal plant Paeonia mairei H. Lév. was sequenced using the Illumina HiSeq X Ten platform and then assembled, annotated, and characterized by bioinformatic methods in this study. The complete chloroplast genome of P. mairei is 152 731 bp in length with the typical quadripartite structure, which consists of a large single copy-region (LSC, 84 402 bp), a small single copy-region (SSC, 16 969 bp), and a pair of inverted repeat regions (IRa and IRb, 25 680 bp), with an overall GC content of 38.4%. A total of 136 predicted genes, including 90 protein-coding genes, 38 tRNA genes and eight rRNA genes were identified. Among these, seven protein-coding genes, seven tRNA genes and four rRNA genes were found duplicated in the IR regions. In addition, 28 dispersed repeats, 10 tandem repeats, and 64 simple sequence repeats were detected within the whole chloroplast genome of P. mairei. Comparative analyses between 12 Peaonia species showed that the chloroplast genomes are highly conserved in length, gene content, gene order, and GC content. Meanwhile, the noncoding sequences (intergenic regions and introns) show a higher variation than the protein coding sequences, and sequences from the LSC region and SSC region are more variable than those from the IR regions. P. mairei was inferred forming in a distinct clade with P. lactiflora, P. obovate, and P. anomala subsp. veitchii with a 100% bootstrap value and is phylogenetically closest to P. lactiflora. These results may provide a basis for further genetic studies and the development and utilization of medicinal P. mairei.
Key words:    Paeonia    Paeonia mairei H. Lév.    chloroplast genome    high throughput sequencing    phylogeny   
收稿日期: 2019-08-19
DOI: 10.16438/j.0513-4870.2019-0654
基金项目: 陕西省教育厅科学计划研究项目(18JK0221);陕西省自然科学基础研究计划(2019JQ-876);陕西中医药大学博士科研启动经费(104080001);陕西中医药大学"秦药"品质评价及资源开发学科创新团队项目(2019-QN01);陕西省高校青年杰出人才支持计划项目;陕西中医药大学"思邈学者项目".
通讯作者: 张岗,Tel:86-29-38185165,E-mail:jay_gumling2003@aliyun.com
Email: jay_gumling2003@aliyun.com
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参考文献:
[1] Neuhaus HE, Emes MJ. Nonphotosynthetic metabolism in plastids[J]. Annu Rev Plant Physiol Plant Mol Biol, 2000, 51:111-140.
[2] McFadden GI. Primary and secondary endosymbiosis and the origin of plastids[J]. J Phycol, 2001, 37:951-959.
[3] Corriveau JL, Coleman AW. Rapid screening method to detect potential biparental inheritance of plastid DNA and results for over 200 angiosperm species[J]. Am J Bot, 1988, 75:1443-1458.
[4] Jansen RK, Ruhlman TA. Plastid Genomes of Seed Plants, in Genomics of Chloroplasts and Mitochondria[M]. Dordrecht:Springer Netherlands, 2012.
[5] Sugiura M, Shinozaki K, Zaita N, et al. Clone bank of the tobacco (Nicotiana tabacum) chloroplast genome as a set of overlapping restriction endonuclease fragments:mapping of eleven ribosomal protein genes[J]. Plant Sci, 1986, 44:211-217.
[6] Ohyama K, Fukuzawa H, Kohchi T, et al. Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA[J]. Nature, 1986, 322:572-574.
[7] Chen SL, Song JY. Herbgenomics[J]. China J Chin Mater Med (中国中药杂志), 2016, 41:3881-3889.
[8] Zhang N, Erickson DL, Ramachandran P, et al. An analysis of Echinacea chloroplast genomes:implications for future botanical identification[J]. Sci Rep, 2017, 7:216.
[9] Zhu S, Niu Z, Xue Q, et al. Accurate authentication of Dendrobium officinale and its closely related species by comparative analysis of complete plastomes[J]. Acta Pharm Sin B, 2018, 8:969-980.
[10] Fu CN, Wu CS, Ye LJ, et al. Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide[J]. Sci Rep, 2019, 9:2773.
[11] Hong DY, Pan KY, Turland NJ. Paeoniaceae in Flora of China[M]. Beijing:Science Press/St. Louis:Missouri Botanical Garden Press, 2001.
[12] Editorial Committee of Chinese Materia Medica. Chinese Materia Medica (中华本草)[M]. Shanghai:Shanghai Science and Technology Press, 1999.
[13] Lee M, Park JH, Gil JS, et al. The complete chloroplast genome of Paeonia lactiflora Pall. (Paeoniaceae)[J]. Mitochondr DNA Part B Resour, 2019, 4:2715-2716.
[14] Zhang G, Sun J, Li YM, et al. The complete chloroplast genome of Paeonia anomala subsp. Veitchii[J]. Mitochondr DNA Part B Resour, 2016, 1:191-192.
[15] Guo S, Guo L, Zhao W, et al. Complete chloroplast genome sequence and phylogenetic analysis of Paeonia ostii[J]. Molecules, 2018, 23:246.
[16] Bai GQ, Guo HW, Zhao N, et al. The complete chloroplast genome of Paeonia rockii (Paeoniaceae), an endangered endemic species to China[J]. Conserv Genet Resour, 2018, 10:453-456.
[17] Chen YM, Zhou QJ, Sun LJ, et al. The chloroplast genome of Paeonia decomposita (Paeoniaceae), an endangered wild tree peony from Sichuan, China[J]. Conserv Genet Resour, 2019, 11:59-61.
[18] Zhou XJ, Song LL, Peng ZF, et al. The complete chloroplast genome sequence of Paeonia jishanensis (Paeoniaceae), a rare wild tree peony[J]. Mitochondr DNA Part B Resour, 2019, 4:503-504.
[19] Li HE, Guo QQ, Zheng WL. Characterization of the complete chloroplast genomes of two sister species of Paeonia:genome structure and evolution[J]. Conserv Genet Resour, 2018, 10:209-212.
[20] Stern FC. A Study of the Genus Paeonia[M]. London:The Royal Horticulture Society, 1946.
[21] Hong DY. Peonies of the World:Taxonomy and Phytogeography[M]. Richmond:Royal Botanic Gardens, 2010.
[22] Patel RK, Jain M. NGS QC Toolkit:a toolkit for quality control of next generation sequencing data[J]. PLoS One, 2012, 7:e30619.
[23] Jin JJ, Yu WB, Yang JB, et al. GetOrganelle:a simple and fast pipeline for de novo assembly of a complete circular chloroplast genome using genome skimming data[J]. BioRxiv, 2018:256479.
[24] Wick RR, Schultz MB, Zobel J, et al. Bandage:interactive visualization of de novo genome assemblies[J]. Bioinformatics, 2015, 31:3350-3352.
[25] Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2[J]. Nat Methods, 2012, 9:357-359.
[26] Qu XJ, Moore MJ, Li DZ, et al. PGA:a software package for rapid, accurate, and flexible batch annotation of plastomes[J]. Plant Methods, 2019, 15:50.
[27] Kearse M, Moir R, Wilson A, et al. Geneious Basic:an integrated and extendable desktop software platform for the organization and analysis of sequence data[J]. Bioinformatics, 2012, 28:1647-1649.
[28] Lowe TM, Chan PP. tRNAscan-SE on-line:integrating search and context for analysis of transfer RNA genes[J]. Nucleic Acids Res, 2016, 44:W54-W 57.
[29] Greiner S, Lehwark P, Boc R. OrganellarGenomeDRAW (OGDRAW) version 1.3.1:expanded toolkit for the graphical visualization of organellar genomes[J]. Nucleic Acids Res, 2019, 47:W59-W64.
[30] Kurtz S, Choudhuri JV, Ohlebusch E, et al. REPuter:the manifold applications of repeat analysis on a genomic scale[J]. Nucleic Acids Res, 2001, 29:4633-4642.
[31] Benson G. Tandem repeats finder:a program to analyze DNA sequences[J]. Nucleic Acids Res, 1999, 27:573-580.
[32] Beier S, Thiel T, Munch T, et al. MISA-web:a web server for microsatellite prediction[J]. Bioinformatics, 2017, 33:2583-2585.
[33] Frazer KA, Pachter L, Poliakov A, et al. VISTA:computational tools for comparative genomics[J]. Nucleic Acids Res, 2004, 32(suppl_2):W273-W279.
[34] Katoh K, Toh H. Parallelization of the MAFFT multiple sequence alignment program[J]. Bioinformatics, 2010, 26:1899-1900.
[35] Stamatakis A. RAxML version 8:a tool for phylogenetic analysis and post-analysis of large phylogenies[J]. Bioinformatics, 2014, 30:1312-1313.
[36] Wang S, Xie Y. China Species Eed List (中国物种红色名录)[M]. Beijing:Higher Education Press, 2004.
[37] Shi Y. Study on Chemical Compositions of Paeonia mairei Levl. and Their Bioactivities (美丽芍药化学成分及其生物活性分析)[D]. Xi'an:Shaanxi University of Science and Technology, 2015.
[38] Shen XF, Wu ML, Liao BS, et al. Complete chloroplast genome sequence and phylogenetic analysis of the medicinal plant Artemisia annua[J]. Molecules, 2017, 22:E1330.
[39] Guo HJ, Liu JS, Luo L, et al. Complete chloroplast genome sequences of Schisandra chinensis:genome structure, comparative analysis, and phylogenetic relationship of basal angiosperms[J]. Sci China C (中国科学:生命科学), 2017, 47:728-739.
[40] Yang QQ, Jiang M, Wang LQ, et al. Complete chloroplast genome of Allium chinense:comparative genomic and phylogenetic analysis[J]. Acta Pharm Sin (药学学报), 2019, 54:173-181.
[41] Zhang MY, Fritsch PW, Ma PF, et al. Plastid phylogenomics and adaptive evolution of Gaultheria series Trichophyllae (Ericaceae), a clade from sky islands of the Himalaya-Hengduan Mountains[J]. Mol Phylogenet Evol, 2017, 110:7-18.
[42] Du Q, Wang B, Wei Z, et al. Genetic diversity and population structure of Chinese white poplar (Populus tomentosa) revealed by SSR markers[J]. J Hered, 2012, 103:853-862.
[43] Chmielewski M, Meyza K, Chybicki I, et al. Chloroplast microsatellites as a tool for phylogeographic studies:the case of white oaks in Poland[J]. iForest, 2015, 8:765-771.
[44] Tian N, Han LM, Chen C, et al. The complete chloroplast genome sequence of Epipremnum aureum and its comparative analysis among eight Araceae species[J]. PLoS One, 2018, 13:e0192956.
[45] Kuang DY, Wu H, Wang YL, et al. Complete chloroplast genome sequence of Magnolia kwangsiensis (Magnoliaceae):implication for DNA barcoding and population genetics[J]. Genome, 2011, 54:663-673.
[46] Sun YL, Hong SK. Phylogenetic relationship and evolution analysis of the peony Paeonia species using multi-locus deoxyribonucleic acid (DNA) barcodes[J]. J Med Plants Res, 2012, 6:5048-5058.
[47] Sang T, Crawford DJ, Stuessy TF. Documentation of reticulate evolution in peonies (Paeonia) using internal transcribed spacer sequences of nuclear ribosomal DNA:implications for biogeography and concerted evolution[J]. Proc Natl Acad Sci U S A, 1995, 92:6813-6817.
[48] Sang T, Crawford D, Stuessy T. Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae)[J]. Am J Bot, 1997, 84:1120-1136.
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