小檗科科尔切斯淫羊藿叶绿体全基因组研究

doi:10.11913/PSJ.2095-0837.2022.10039

摘要
图/表
参考文献(0)
相关文章 (1)

全文: PDF (2160 KB) HTML (1 KB)
输出: BibTeX | EndNote (RIS)

摘要

小檗科科尔切斯淫羊藿（Epimedium pinnatum Fisch.ex DC.）是分布于高加索地区的一种具有观赏和药用价值的多年生草本植物。本研究首次报道了科尔切斯淫羊藿的叶绿体全基因组序列。结果显示：科尔切斯淫羊藿叶绿体基因组全长为156 155 bp，GC含量为38.82%；由一个大的单拷贝区（LSC，89 425 bp）、一个小的单拷贝区（SSC，16 284 bp）和一对反向重复区（IRa和IRb，25 223 bp）组成。叶绿体基因组包含112个基因，其中蛋白质编码基因78个，tRNA基因30个，rRNA基因4个。系统发育分析结果表明，Rhizophyllum亚属的科尔切斯淫羊藿与Epimedium亚属的Macroceras组最先聚为一支，并与Epimedium亚属的Diphyllon组形成的一支分开。

	服务

	把本文推荐给朋友
	加入我的书架
	加入引用管理器
	E-mail Alert
	RSS
	作者相关文章
	于淑霞
	梁琼
	罗惠
	黄若琪
	李永
	张燕君

关键词 ：科尔切斯淫羊藿, 叶绿体基因组, 小檗科

Abstract：

Epimedium pinnatum Fisch. ex DC.(Berberidaceae) is a perennial herb with ornamental and medicinal value distributed in the Caucasus region. In this study, the Illumina NovaSeq 6000 sequencing system was used to assemble the complete chloroplast genome sequence of E. pinnatum for the first time. Results showed that the total length of the chloroplast genome was 156 155 bp with 38.82% GC content, comprising a large single-copy region (LSC, 89 425 bp), small single-copy region (SSC, 16 284 bp), and pair of inverted repeat regions (IRa and IRb, 25 223 bp). The chloroplast genome of E. pinnatum contained 112 genes, including 78 protein-coding genes, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. Phylogenetic analysis showed that E. pinnatum subgen. Epimedium and sect. Macroceras was clustered on a branch, which was separated from the branch composed of species from sect. Diphyllon, subgen. Epimedium. These results suggest that further study is needed to clarify the natural system of Epimedium based on more data.

Key words： Epimedium pinnatum Chloroplast genome Berberidaceae

收稿日期: 2021-05-06

ZTFLH:

Q943.2

基金资助:

国家自然科学基金（31670346，32071675）；中国科学院武汉植物园重点科研人才项目（Y855281A05）；武汉市科学技术局应用基础前沿项目（2019020701011435）。

通讯作者: 李永,liyongrui1@126.com;张燕君,yanjunzhang@wbgcas.cn E-mail: liyongrui1@126.com;yanjunzhang@wbgcas.cn

作者简介: 于淑霞(1994-),女,硕士研究生,研究方向为植物学(E-mail:601648604@qq.com)。

引用本文:

于淑霞, 梁琼, 罗惠, 黄若琪, 李永, 张燕君. 小檗科科尔切斯淫羊藿叶绿体全基因组研究[J]. 植物科学学报, 2022, 40(1): 39-46. Yu Shu-Xia, Liang Qiong, Luo Hui, Huang Ruo-Qi, Li Yong, Zhang Yan-Jun. Complete chloroplast genome of Epimedium pinnatum Fisch. ex DC.(Berberidaceae). Plant Science Journal, 2022, 40(1): 39-46.

链接本文:

http://www.plantscience.cn/CN/10.11913/PSJ.2095-0837.2022.10039 或 http://www.plantscience.cn/CN/Y2022/V40/I1/39

[1] Ying TS, Boufford DE, Brach AR. Epimedium L.[M]//Wu ZY, Raven PH, Hong DY, eds. Flora of China:Vol. 19. Beijing:Science Press? St. Louis:Missouri Botanical Garden Press, 2011:787-799.
[2] 郭宝林, 肖培根. 中药淫羊藿主要种类评述[J]. 中国中药杂志, 2003, 28(4):303-307. Guo BL, Xiao PG. Comment on main species of herba epimedii[J]. China Journal of Chinese Materia Medica, 2003, 28(4):303-307.
[3] Kim DR, Lee JE, Shim KJ, Cho JH, Lee CH, et al. Effects of herbal Epimedium on the improvement of bone metabolic disorder through the induction of osteogenic differentiation from bone marrow-derived mesenchymal stem cells[J]. Mol Med Rep, 2016, 15(1):125-130.
[4] Wu H, Lien EJ, Lien LL. Chemical and pharmacological investigations of Epimedium species:a survey[J]. Prog Drug Res, 2003, 60:1-57.
[5] Ma HP, He XR, Yang Y, Li MX, Hao DJ, Jia ZP. The genus Epimedium:an ethnopharmacological and phytochemical review[J]. J Ethnopharmacol, 2011, 134(3):519-541.
[6] Ban Y, Honda C, Hatsuyama Y, Igarashi M, Bessho H, Moriguchi T. Isolation and functional analysis of a MYB transcription factor gene that is a key regulator for the development of red coloration in apple skin[J]. Plant Cell Physiol, 2007, 48(7):958-970.
[7] Takos AM, Jaffé FW, Jacob SR, Bogs J, Robinson SP, Walker AR. Lightinduced expression of a MYB gene regulates anthocyanin biosynthesis in red apples[J]. Plant Physiol, 2006, 142(3):1216-1232.
[8] 袁航, 曹树萍, 陈抒云, 过立农, 郑健, 林瑞超. 淫羊藿的化学成分及质量控制研究进展[J]. 中草药, 2014, 45(24):3630-3640. Yuan H, Cao SP, Chen SY, Guo LN, Zheng J, Lin RC. Research progress on chemical constituents and quality control of Epimedii Folium[J]. Chinese Traditional and Herbal Drugs, 2014, 45(24):3630-3640.
[9] Chen JJ, Xu YQ, Wei GY, Wang ZL, He JB, et al. Chemotypic and genetic diversity in Epimedium sagittatum from different geographical regions of China[J]. Phytochemistry, 2015, 116:180-187.
[10] He CY, Wang Z, Shi JS. Pharmacological effects of icariin[J]. Adv Pharmacol, 2020, 87:179-203.
[11] Xu SJ, Yu JJ, Yang L, Zhu YL. Comparative pharmacokinetics and bioavailability of epimedin C in rat after intramuscular administration of epimedin C, a combination of four flavonoid glycosides and purified herba epimedii extract[J]. J Anal Methods Chem, 2016, 2016:5093537.
[12] Lubell JD, Brand MH. Division size and timing influence propagation of four species of Epimedium L.[J] HortScience, 2005, 40:1444-1447.
[13] Zhang YJ, Huang RQ, Wu L, Wang Y, Jin T, Liang Q. The complete chloroplast genome of Epimedium brevicornu Maxim (Berberidaceae), a traditional Chinese medicine herb[J]. Mitochondrial DNA B, 2020, 5(1):588590.
[14] Stearn WT. Genus Epimedium and Other Herbaceous Berberidaceae[M]. Portland:Timber Press, 2002:1-202.
[15] Zhang YX, Liu X, Yao Y, Luo YJ, Zhang C, et al. The complete chloroplast genome of Epimedium pudingense (Berberidaceae), a narrowly distributed plant species in China[J]. Mitochondrial DNA B, 2020, 5(3):2631-2633.
[16] Jansen RK, Raubeson LA, Boore JL, Depamphilis CW, Cui L, et al. Methods for obtaining and analyzing whole chloroplast genome sequences[J]. Method Enzymol, 2005, 395:348-84.
[17] Raubeson LA, Jansen RK. Chloroplast genomes of plants[M]//Henry RJ, ed. Plant Diversity and Evolution:Genotypic and Phenotypic Variation in Higher Plants. Wallingford:CABI Publishing, 2005:45-68.
[18] 张立娜, 曹桂兰, 韩龙植. 利用SSR标记揭示中国粳稻地方品种遗传多样性[J]. 中国农业科学, 2012, 45(3):405-413. Zhang LN, Cao GL, Han LZ. Analysis of genetic diversity of japonica rice landrace in China with microsatellite marker[J]. Scientia Agricultura Sinica, 2012, 45(3):405-413.
[19] Doyle JJ, Doyle JL. A rapid DNA isolation procedure for small quantities of fresh leaf tissue[J]. Phytochem Bull, 1987, 19(1):11-15.
[20] Jin JJ, Yu WB, Yang JB, Song Y, de Pamphilis CW, et al. GetOrganelle:a fast and versatile toolkit for accurate de novo assembly of organelle genomes[J]. Genome Biol, 2020, 21(1):241-241.
[21] Shi L, Chen H, Jiang M, Wang L, Wu X, et al. CPGAVAS2, an integrated plastome sequence annotator and analyser[J]. Nucleic Acids Res, 2019, 47(W1):65-73.
[22] Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, et al. Geneious basic:an integrated and extendable desktop software platform for the organization and analysis of sequence data[J]. Bioinformatics, 2012, 28(12):1647-1649.
[23] Burland TG. DNASTAR's Lasergene sequence analysis software[J]. Methods Mol Biol, 2000, 132:71-91.
[24] Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R. REPuter:the manifold applications of repeat analysis on a genomic scale[J]. Nucleic Acids Res, 2001, 29(22):4633-4642.
[25] Beier S, Thiel T, Münch T, Scholz U, Mascher M. MISA-web:a web server for microsatellite prediction[J]. Bioinformatics, 2017, 33(16):2583-2585.
[26] Thiel T, Michalek W, Varshney R, Graner A. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)[J]. Theor Appl Genet, 2003, 106:411-422.
[27] Katoh K, Rozewicki J, Yamada KD. MAFFT online service:multiple sequence alignment, interactive sequence choice and visualization[J]. Brief Bioinform, 2019, 20(4):1-7.
[28] Hall TA. Bioedit:a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT[J]. Nucleic Acids Symp Ser, 1999, 41(41):95-98.
[29] Silvestro D, Michalak I. RaxmlGUI:a graphical front-end for RAxML[J]. Org Divers Evol, 2012, 12(4):335-337.
[30] Nguyen P, Kim JS, Kim JH. The complete chloroplast genome of colchicine plants (Colchicum autumnale L. and Gloriosa superba L.) and its application for identifying the genus[J]. Planta, 2015, 242(1):223-237.
[31] Felsenstein J. Confidence limits on phylogenies:an approach using the bootstrap[J]. Evolution, 1985, 39(4):783-791.
[32] Hillis DM, Bull JJ. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis[J]. Syst Biol, 1993, 42(2):182-192.
[33] 倪梁红, 赵志礼, 米玛. 药用植物叶绿体基因组研究进展[J]. 中药材, 2015, 38(9):1990-1994. Ni LH, Zhao ZL, Mi M. Research progress of medicinal plant chloroplast genome[J]. Journal of Chinese Medicinal Materials, 2015, 38(9):1990-1994.
[34] De Smet Y, Goetghebeur P, Wanke S, Asselman P, Marie-Stéphanie S. Additional evidence for recent divergence of Chinese Epimedium (Berberidaceae) derived from AFLP, chloroplast and nuclear data supplemented with characterisation of leaflet pubescence[J]. Plant Ecol Evol, 2012, 145(1):121-126.
[35] Zhang ML, Uhink CH, Kadereit JW. Phylogeny and biogeography of Epimedium/Vancouveria (Berberidaceae):western north American-east Asian disjunctions, the origin of European mountain plant taxa and east Asian specific diversity[J]. Syst Bot, 2007, 32(1):81-92.
[36] Zhang YJ, Yang LL, Chen JJ, Sun W, Wang Y. Taxonomic and phylogenetic analysis of Epimedium L. based on amplified fragment length polymorphisms[J]. Sci Hortic, 2014, 170:284-292.