Transcriptome Analysis for Medicinal Plant Anisodus tanguticus

doi:10.7525/j.issn.1673-5102.2020.03.018

Abstract

Abstract: The transcriptome sequencing analysis of Anisodus tanguticus was carried out by high throughput sequencing technology to understand resource plant A.tanguticus deeply. The 71 463 Unigenes were obtained after processing. By comparing with several databases,we classified and analyzed the genes, and finally succeeded in annotating 47 624 genes. The 13 110 genes with 26 subclasses were annotated after comparing with KOG protein library.Compared with NR library, 39 621unigenes were annotated.The transcripts were compared with Swissprot and TrEMBL to obtain GO functional annotations. The 29 309 unigenes obtained from the annotations could be divided into three categories:molecular function, biological process, and cellular components, with 62 subcategories.Referring to the KEGG database, 3 679 genes were annotated. The metabolic pathways involved can be classified into four categories:metabolic related pathways, genetic information processing,cellular processes, and environmental information processing. Among them,metabolic related pathways are the most, accounting for about half of all metabolic pathways.Statistical results of metabolic pathways and related unigenes of the active ingredients of A.tanguticus showed that the number of metabolic pathways related to alkaloids was the most, and the number of unigenes corresponding to terpenoids and phenylpropanoids was the most.In addition, 31 382 SNP loci and 6 SSR repeat types were detected. Among them, single base repeat types accounted for the highest proportion, with 56.52 SSR repeats per million bases, accounting for 45.30%.These results enrich the transcriptome information of A.tanguticus and lay a foundation for the study of the molecular biology, which contribute to the further development and utilization of A.tanguticus.

Key words: Anisodus tanguticus, transcriptome, high throughput sequencing technology, gene annotation

CLC Number:

Q949.777.7

ZHANG Yu, XIA Ming-Ze, ZHANG Fa-Qi. Transcriptome Analysis for Medicinal Plant Anisodus tanguticus[J]. Bulletin of Botanical Research, 2020, 40(3): 458-467.

References

[1] 中国科学院西北高原生物研究所.藏药志[M].西宁:青海人民出版社,1991:142.Institute of Northwest Plateau Biology,Chinese Academy of Sciences.Tibetan pharmacology[M].Xining:Qinghai People's Publishing House,1991:142.
[2] 北京医学院.中草药化学成分学[M].北京:人民卫生出版社,1983:117-124.Beijing Medical College.Chemical constituents of Chinese herbal medicines[M].Beijing:People's Medical Publishing House,1983:117-124.
[3] 孙凯,杨丽敏.山莨菪碱的药理和临床研究进展[J].世界临床药物,2010,31(3):182-186.Sun K,Yang L M.Advance in pharmacological and clinical research of anisodamine[J].World Clinical Drugs,2010,31(3):182-186.
[4] 岳茂兴,李成林,赵尔增,等.山莨菪碱及地塞米松对MODS时微循环及免疫病理学改变的实验研究[J].中华外科杂志,1997,35(7):392-394.Yue M X,Li C L,Zhao E Z,et al.The effect of anisodaminum and dexamethasone on microcirculation,TNF,LPO and pathology in MODS[J].Chinese Journal of Surgery,1997,35(7):392-394.
[5] 师生波,李惠梅,王学英,等.青藏高原几种典型高山植物的光合特性比较[J].植物生态学报,2006,30(1):40-46.Shi S B,Li H M,Wang X Y,et al.Comparative studies of photosynthetic characteristics in typical alpine plants of the Qinghai-Tibet Plateau[J].Journal of Plant Ecology,2006,30(1):40-46.
[6] 张晓峰,王环.山莨菪植物体内4种莨菪烷类生物碱含量的变化[J].西北植物学报,2002,22(3):630-634.Zhang X F,Wang H.The variation of the contents of four tropane alkaloids in Anisodus tanguticus[J].Acta Botanica Boreali-Occidentalia Sinica,2002,22(3):630-634.
[7] 赵文吉,贾囯夫,陈太星,等.青藏高原特有药用植物山莨菪苗期生物量积累与分配特征[J].西南农业学报,2018,31(10):2092-2097.Zhao W J,Jia G F,Chen T X,et al.Biomass accumulation and allocation of seedling of Qinghai-Tibet Plateau endemic medicinal plants Anisodus tanguticus[J].Southwest China Journal of Agricultural Sciences,2018,31(10):2092-2097.
[8] 段元文,张挺峰,刘建全.山莨菪(茄科)的传粉生物学[J].生物多样性,2017,15(6):584-591.Duan Y W,Zhang T F,Liu J Q.Pollination biology of Anisodus tanguticus(Solanaceae)[J].Biodiversity Science,2007,15(6):584-591.
[9] 张盾,任梦云,张银东,等.基于ISSR分子标记的野生山莨菪遗传多样性研究[J].中草药,2018,49(1):219-226.Zhang D,Ren M Y,Zhang Y D,et al.Genetic diversity research on Anisodus tanguticus based on ISSR molecular markers[J].Chinese Traditional and Herbal Drugs,2018,49(1):219-226.
[10] Zheng W,Wang L Y,Meng L H,et al.Genetic variation in the endangered Anisodus tanguticus(Solanaceae),an alpine perennial endemic to the Qinghai-Tibetan Plateau[J].Genetica,2008,132(2):123-129.
[11] 祁云霞,刘永斌,荣威恒.转录组研究新技术:RNA-Seq及其应用[J].遗传,2011,33(11):1191-1202.Qi Y X,Liu Y B,Rong W H.RNA-Seq and its applications:a new technology for transcriptomics[J].Hereditas(Beijing),2011,33(11):1191-1202.
[12] 洪奇阳,毕行建,王大宁,等.转录组测序技术研究进展[J].中国生化药物杂志,2017,37(6):443-448.Hong Q Y,Bi X J,Wang D N,et al.Research progress on RNA-Seq technology[J].Chinese Journal of Biochemical and Pharmaceuticals,2017,37(6):443-448.
[13] Hrdlickova R,Toloue M,Tian B.RNA-Seq methods for transcriptome analysis[J].WIREs RNA,2017,8(1):e1364.
[14] 李智奕,宁维,陈利平,等.新一代测序技术及其在植物转录组研究中的应用[J].河南农业科学,2013,42(12):1-5.Li Z Y,Ning W,Chen L P,et al.The next generation sequencing technology and its application in plant T ranscriptome[J].Journal of Henan Agricultural Sciences,2013,42(12):1-5.
[15] 李东.热胁迫下丹参次生代谢比较转录组学研究[D].成都:四川农业大学,2011.Li D.Research of secondary metabolism comparative transcriptomicsin heat stress of Salvia miltiorrhiza[D].Chengdu:Sichuan Agricultural University,2011.
[16] 李依民,彭亮,杨冰月,等.基于高通量测序技术的黄三七根茎转录组数据分析[J].中草药,2018,49(21):4983-4990.Li Y M,Peng L,Yang B Y,et al.Transcriptomic data analyses of rhizome of Souliea vaginata via Illumina high-throughput sequencing technology[J].Chinese Traditional and Herbal Drugs,2018,49(21):4983-4990.
[17] 李太强,刘雄芳,万友名,等.基于高通量测序的极小种群野生植物长梗杜鹃转录组分析[J].植物研究,2017,37(6):825-834.Li T Q,Liu X F,Wan Y M,et al.Transcriptome analysis Rhododendron longipedicellatum(plant species with extremely small populations) based on high throughput sequencing[J].Bulletin of Botanical Research,2017,37(6):825-834.
[18] Chen J H,Zhang D Z,Zhang C,et al.Physiological characterization,transcriptomic profiling,and microsatellite marker mining of Lycium ruthenicum[J].Journal of Zhejiang University-SCIENCE B,2017,18(11):1002-1021.
[19] 刘雄芳,李太强,张序,等.重要食药同源植物余甘子转录组微卫星特征分析[J].植物研究,2019,39(2):294-302.Liu X F,Li T Q,Zhang X,et al.Characteristic analysis of microsatellites in the transcriptome of Phyllanthus emblica,an important edible and medicinal plant[J].Bulletin of Botanical Research,2019,39(2):294-302.
[20] 安文燕,孙君灵,龚文芳,等.陆地棉矮化突变体Ari1327茎尖的转录组分析[J].植物遗传资源学报,2014,15(5):1046-1052.An W Y,Sun J L,Gong W F,et al.Transcriptome analysis of stem apex of an upland cotton dwarf mutant Ari1327[J].Journal of Plant Genetic Resources,2014,15(5):1046-1052.
[21] Conesa A,Götz S,Garcia-Gomez J M,et al.Blast2GO:a universal tool for annotation,visualization and analysis in functional genomics research[J].Bioinformatics,2005,21(18):3674-3676.
[22] Ye J,Fang L,Zheng H K,et al.WEGO:a web tool for plotting GO annotations[J].Nucleic Acids Research,2006,34(S2):W293-W297.
[23] Kanehisa M.The KEGG database[M].//Bock G,Goodej A.‘In silico’ simulation of biological processes:novartis foundation symposium.New York:John Wiley,2002:91.
[24] 魏利斌,苗红梅,张海洋.芝麻发育转录组分析[J].中国农业科学,2012,45(7):1246-1256.Wei L B,Miao H M,Zhang H Y.Transcriptomic analysis of sesame development[J].Scientia AgriculturaSinica,2012,45(7):1246-1256.
[25] 江香梅,伍艳芳,肖复明,等.樟树5种化学类型叶片转录组分析[J].遗传,2014,36(1):58-68.Jiang X M,Wu Y F,Xiao F M,et al.Transcriptome analysis for leaves of five chemical types in Cinnamomum camphora[J].Hereditas,2014,36(1):58-68.
[26] 杜方.百合不同器官转录组分析及SSR标记开发应用[D].杭州:浙江大学,2014.Du F.Transcriptome analysis of different lily organs and development and application of SSR markers[D].Hangzhou:Zhejiang University,2014.
[27] 吴超,彭娟,向林,等.基于高通量测序的铁皮石斛叶片转录组分析[J].分子植物育种,2016,14(12):3334-3346.Wu C,Peng J,Xiang L,et al.Sequencing and analysis of the transcriptome of Dendrobium officinale[J].Molecular Plant Breeding,2016,14(12):3334-3346.
[28] 杜慧霞.仿刺参(Apostichopus japonicus)转录组分析与遗传图谱构建[D].青岛:中国海洋大学,2013.Du H X.Transcriptome characterization and genetic map construction for Apostichopus japonicus[D].Qingdao:Ocean University of China,2013.