药学学报, 2019, 54(11): 2106-2112
引用本文:
乔永刚, 贺嘉欣, 王勇飞, 曹亚萍, 贾孟君, 张鑫瑞, 梁建萍, 宋芸. 药用植物苦参的叶绿体基因组及其特征分析[J]. 药学学报, 2019, 54(11): 2106-2112.
QIAO Yong-gang, HE Jia-xin, WANG Yong-fei, CAO Ya-ping, JIA Meng-jun, ZHANG Xin-rui, LIANG Jian-ping, SONG Yun. Analysis of chloroplast genome and its characteristics of medicinal plant Sophora flavescens[J]. Acta Pharmaceutica Sinica, 2019, 54(11): 2106-2112.

药用植物苦参的叶绿体基因组及其特征分析
乔永刚, 贺嘉欣, 王勇飞, 曹亚萍, 贾孟君, 张鑫瑞, 梁建萍, 宋芸
山西农业大学生命科学学院, 山西 太谷 030801
摘要:
为探究苦参叶绿体基因组特征及该属物种的系统进化发育关系,本研究利用高通量测序技术对苦参叶绿体基因组进行测序和功能注释。结果显示:苦参叶绿体基因组全长154 165 bp,呈典型的四段式结构。苦参叶绿体基因组共包含123个基因,包括77个蛋白编码基因、38个tRNA基因及8个rRNA基因。经序列分析鉴定出104个SSR位点,大部分重复由A和T组成。此外该叶绿体基因组密码子偏好性较弱,编码区偏向使用A和T碱基。对两个不同地区苦参叶绿体基因组进行比较分析发现了4个差异基因。基于最大似然法(ML)对苦参及其他16种豆科植物进行系统发育分析,发现苦参与其同属植物苦豆子的亲缘关系最近。本研究为苦参的遗传变异、育种以及系统发育分析等提供了重要的理论依据,具有一定的参考价值。
关键词:    苦参      叶绿体基因组      SSR      密码子偏好性      比较基因组学      系统发育分析     
Analysis of chloroplast genome and its characteristics of medicinal plant Sophora flavescens
QIAO Yong-gang, HE Jia-xin, WANG Yong-fei, CAO Ya-ping, JIA Meng-jun, ZHANG Xin-rui, LIANG Jian-ping, SONG Yun
College of Life Sciences, Shanxi Agricultural University, Taigu 030801, China
Abstract:
In order to explore the chloroplast genome characteristics of Sophora flavescens and the phylogenetic relationship of the genus, this study used high-throughput sequencing technology to sequence and functionally annotate the chloroplast genome of Sophora flavescens. The results showed that the full length 154 165 bp of Sophora flavescens chloroplast genome showed a typical four-stage structure. The chloroplast genome contains 123 genes, including 77 protein-coding genes, 38 tRNA genes and 8 rRNA genes. Sequence analysis revealed 104 SSR loci, most of which consisted of A and T. In addition, the chloroplast genome codon preference is weak, and the coding region is biased towards the use of A and T bases. A comparative analysis of two different regions of Sophora flavescens chloroplast genome revealed four differential genes. Based on the maximum likelihood method (ML) for phylogenetic analysis of Sophora flavescens and 16 other leguminous, it was found that the relationship between Sophora flavescens and the genus Sophora alopecuroides is the closest. This study provides an important theoretical basis for the genetic variation, breeding and phylogenetic analysis of Sophora flavescens, and has certain reference value.
Key words:    Sophora flavescens    chloroplast genome    SSR    codon preference    comparative genomics    phylogenetic analysis   
收稿日期: 2019-07-16
DOI: 10.16438/j.0513-4870.2019-0564
基金项目: 山西振东企业国际合作项目资助(2018ZDGH0101);山西省高等学校教学改革项目资助(J2015028,J2017031);山西省基础研究计划资助(201801D121204).
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参考文献:
[1] He TN. Gentianaceae in Flora Reipublicae Popularis Sinicae: Vol 73(中国植物志: 73卷)[M]. Beijing: Science Press, 1983.
[2] Chinese Pharmacopoeia Commission. Pharmacopoeia of the People’s Republic of China: Vol I (中华人民共和国药典: 一部)[S]. Beijing: China Medical Science Press, 2015: 202-203.
[3] Liu G, Dong J, Wang H, et al. Characterization of alkaloids in Sophora flavescens Ait. by high-performance liquid chromatography-electrospray ionization tandem mass spectrometry[J]. J Pharm Biomed Anal, 2011, 54: 1065-1072.
[4] Dong Y, Li YX, Yan X, et al. Protection effect of matrine against precancerous lesion of gastric cancer in model rats[J]. China Pharm (中国药房), 2010, 21: 1357-1359.
[5] Zhang JR. Effects of matrine on cisplatinum sensitivity of epithelial ovarian cancer and analysis of its potential mechanism[J]. Guide China Med (中国医药指南), 2010, 8: 26-28.
[6] Zhang JH, Zhao YY, Liu QX, et al. Studies on the chemical constituents from Sophora flavescens Ait[J]. China J Chin Mater Med (中国中药杂志), 2000, 25: 37-39.
[7] Meng J, Li XP, Li HT, et al. Comparative analysis of the complete chloroplast genomes of four aconitum medicinal species[J]. Molecules, 2018, 23: 1015-1017.
[8] Tonti-Filippini J, Nevill PG, Dixon K, et al. What can we do with 1000 plastid genomes?[J]. Plant J, 2017, 90: 808-818.
[9] Zhou J, Chen X, Cui Y, et al. Molecular structure and phylogenetic analyses of genomes of two aristolochia medicinal species[J]. Int J Mol Sci, 2017, 18: 1839.
[10] Yu XQ, Drew BT, Yang JB, et al. Comparative chloroplast genomes of eleven Schima (Theaceae) species: insights into DNA barcoding and phylogeny[J]. PLoS One, 2017, 12: e0178026.
[11] Xu C, Dong W, Li W, et al. Comparative analysis of six lagerstroemia complete chloroplast genomes[J]. Front Plant Sci, 2017, 8: 15.
[12] Gu C, Tembrock LR, Zheng S, et al. The complete chloroplast genome of Catha edulis: a comparative analysis of genome features with related species[J]. Int J Mol Sci, 2018, 19: 525.
[13] Shinozaki K, Ohme M, Tanaka M, et al. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression[J]. Plant Mol Biol Rep, 1986, 5: 2043-2049.
[14] 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.
[15] Mu XP, Wang PF, Du JJ, et al. The chloroplast genome of Cerasus humilis: genomic characterization and phylogenetic analysis[J]. PLoS One, 2018, 13: e0196473.
[16] Deng CY, Xin GL, Zhang JQ, et al. Characterization of the complete chloroplast genome of Dalbergia hainanensis (Leguminosae), a vulnerably endangered legume endemic to China[J]. Conserv Gen Res, 2018, 11: 105-108.
[17] Tao X, Ma L, Zhang Z, et al. Characterization of the complete chloroplast genome of alfalfa (Medicago sativa) (Leguminosae)[J]. Gene Rep, 2016, 6: 67-73.
[18] Sakai M, Kanazawa A, Fujii A, et al. Phylogenetic relationships of the chloroplast genomes in the genus Glycine inferred from four intergenic spacer sequences[J]. Plant System Evol, 2003, 239: 29-54.
[19] Zhang WL, Li L, Li GH. Characterization of the complete chloroplast genome of shrubby sophora (Sophora flavescens Ait.)[J]. Mitochondrial DNA Part B, 2018, 3: 1282-1283.
[20] Freyer R, Hoch B, Neckermann K, et al. RNA editing in maize chloroplasts is a processing step independent of splicing and cleavage to monocistronic mRNAs[J]. Plant J, 1993, 4: 621-629.
[21] Tillich M, Lehwark P, Pellizzer T, et al. GeSeq-versatile and accurate annotation of organelle genomes[J]. Nucleic Acids Res, 2017, 45: W6-W11.
[22] Lohse M, Drechsel O, Kahlau S, et al. Organellar Genome DRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets[J]. Nucleic Acids Res, 2013, 41: W575-W581.
[23] Thiel T, Michalek W, Varshney R, et al. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)[J]. Theo Appl Gen, 2003, 106: 411-422.
[24] Shields DC, Sharp PM. Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases[J]. Nucleic Acids Res, 1987, 15: 8023-8040.
[25] Tippmann HF. Analysis for free: comparing programs for sequence analysis[J]. Briefings Bioinf, 2004, 5: 82.
[26] Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets[J]. Mol Biol Evol, 2016, 33: 1870.
[27] Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads[J]. EMBnet J, 2011. DOI: org/10.14806/ej.17.1.200.
[28] Hu J, Gui S, Zhu Z, et al. Genome-wide identification of SSR and SNP markers based on whole-genome re-sequencing of a Thailand wild sacred lotus (Nelumbo nucifera)[J]. PLoS One, 2015, 10: e0143765.
[29] 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.
[30] Qian J, Song J, Gao H, et al. The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza[J]. PLoS One, 2013, 8: e57607.
[31] Li XY, Xiao BG, Gao YL, et al. SSR locus analysis of chloroplast genome and mitochondrial genome of tobacco[J]. Acta Bot Sin, 2011, 31: 2399-2405.
[32] Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system[J]. J Mol Biol, 1981, 151: 389-409.
[33] Sharp PM, Tuohy TMF, Mosurski KR. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes[J]. Nucleic Acids Res, 1986, 14: 5125-5143.
[34] Chumley TW, Palmer JD, Mower JP, et al. The complete chloroplast genome sequence of Pelargonium hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants[J]. Mol Biol Evol, 2006, 23: 2175-2190.
[35] Yang M, Zhang X, Liu G, et al. The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.)[J]. PLoS One, 2010, 5: e12762.