Full-length Transcriptome Analysis of a Homology of Medicine and Food of Pueraria thomsonii

doi:10.7668/hbnxb.20192213

Abstract

Abstract: In order to in-depth understand the overall level of transcriptome and the flavonoid biosynthesis pathway genes of Pueraria thomsonii Benth. The mixed sample of root, stem and leaf of Pueraria thomsonii was used as materials for sequencing analysis using the single-molecule long read sequencing technology(SMRT) of Pacific Biosciences Sequel platform. A total of 10 994 967 high quality reads and 384 072 full-length non-chimeric(FLNC) were obtained. Sequencing data after quality control, 90 856 isoforms were obtained. There were 85 239 isoforms annotated by NR, SwissProt, KOG, KEGG and GO databases, and the number of NR annotation was 84 675, accounting for 93.2%;In KEGG database, only 22 330 genes were annotated in 132 pathways, and 9 368 genes were distributed more in metabolic pathway, accounting for 41.95%. A total of 3 507 transcription factors(TF) were predicted, and bHLH TF family was the most annotated genes. Besides, 14 127 genes were assigned to 17 R gene classes, mainly RLP. 33 660 SSR sequences were detected, most of them were AG/CT type. By analyzing the biosynthesis pathway of flavonoids, 110 genes were found, including 26 genes encoding HCT, 3 genes encoding CHS and 7 genes encoding CHI. Compared with Illumina HiSeq^TM2500, PacBio platform obtained longer transcripts and higher annotation rates. This research intensively studied the Pueraria thomsonii at the full-length transcriptome level, which provided more reliable transcriptome data for molecular biology research and scientific basis for further development of molecular markers and mining excellent genes of Pueraria thomsonii.

Key words: Pueraria thomsonii, Homology of medicine and food, Full-length transcriptome, Breeding

CLC Number:

S567.19

MEI Yu, LI Xiangrong, CAI Shike, GU Yan, WANG Jihua. Full-length Transcriptome Analysis of a Homology of Medicine and Food of Pueraria thomsonii[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2021, 36(5): 10-17. doi: 10.7668/hbnxb.20192213.

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References

[1] 国家药典委员会. 2020中华人民共和国药典第一部中药[M].北京:中国医药科技出版社, 2020:302, 347.
National Pharmacopoeia Committee. The People's Republic of China pharmacopoeia(Part 1)[M].Beijing:China Medical Science and Technology Press, 2020:302, 347.
[2] 陈欣. 粉葛及其资源开发研究[D].成都:西南交通大学, 2011.
Chen X. The studies of Pueraria thomsonii radix and its resource[D].Chengdu:Southwest Jiaotong University, 2011.
[3] 尚小红, 曹升, 肖亮, 严华兵, 王颖, 曾文丹, 谢向誉, 陆柳英, 赖大欣. 广西葛种质资源调查与收集[J].植物遗传资源学报, 2020, 21(5):1301-1307.doi:10.13430/j.cnki.jpgr.20200301002.
Shang X H, Cao S, Xiao L, Yan H B, Wang Y, Zeng W D, Xie X Y, Lu L Y, Lai D X. Investigation and collection of Pueraria germplasm resources in Guangxi[J]. Journal of Plant Genetic Resources, 2020, 21(5):1301-1307.
[4] 吴志瑰, 邓可众, 葛菲, 吴波, 朱玉野, 胡生福, 林贵兵, 徐艳琴, 刘勇, 朱卫丰, 谢璐欣, 黄秋莲, 范崔生. 葛类中药的品种沿革、产区及功效考证[J].江西中医药大学学报, 2020, 32(1):1-4, 124.
Wu Z G, Deng K Z, Ge F, Wu B, Zhu Y Y, Hu S F, Lin G B, Xu Y Q, Liu Y, Zhu W F, Xie L X, Huang Q L, Fan C S. Herbal textual research of kudzuvine root on original plants, traditional functions, and resources distribution[J]. Journal of Jiangxi University of Traditional Chinese Medicine, 2020, 32(1):1-4, 124.
[5] 董彐倩, 梅瑜, 王继华, 黄能旭, 蔡时可. 药食同源植物葛根的研究进展[J].长江蔬菜, 2020, 2(5):43-47.doi:10.3865/j.issn.1001-3547.2020.02.014.
Dong X Q, Mei Y, Wang J H, Huang N X, Cai S K. Research progress on a medicinal and edible plant Radix puerariae[J]. Journal of Changjiang Vegetables, 2020, 2(5):43-47.
[6] Song W, Li Y J, Qiao X, Qian Y, Ye M. Chemistry of the Chinese herbal medicine Puerariae radix(Ge-Gen):A review[J]. Journal of Chinese Pharmaceutical Sciences, 2014, 23(6):347-360.
[7] 郭华, 王旭玲. 葛根素对糖尿病合并颈动脉硬化患者氧化应激和血液流变学的影响[J].世界中医药, 2018, 13(10):2526-2529.doi:10.3969/j.issn.1673-7202.2018.10.040.
Guo H, Wang X L. Effects of puerarin on oxidative stress and hemorheology of patients with diabetes mellitus combined with carotid atherosclerosis[J]. World Chinese Medicine, 2018, 13(10):2526-2529.
[8] 王瑞娴, 李川. 全长转录组测序技术在非模式植物转录组学研究中的应用[J].分子植物育种, 2019, 17(2):502-508.doi:10.13271/j.mpb.017.000502.
Wang R X, Li C. Application of full-length transcriptome sequencing in non-model plant transcriptome research[J]. Molecular Plant Breeding, 2019, 17(2):502-508.
[9] 毛俐慧, 刘建新, 丁华侨, 徐笑寒, 田丹青. 姜荷花全长转录组微卫星特征分析和引物设计[J].分子植物育种, 2018, 16(22):7407-7414.doi:10.13271/j.mpb.016.007407.
Mao L H, Liu J X, Ding H Q, Xu X H, Tian D Q. Microsatellite characterization analysis and primers design of the whole transcriptome of Curcuma alismatifolia[J]. Molecular Plant Breeding, 2018, 16(22):7407-7414.
[10] 徐志超. 基于联合测序技术的丹参活性成分生物合成及调控机制研究[D].北京:北京协和医学院, 2016.
Xu Z C. Study on biosynthesis and regulation of active compounds in Salvia miltiorrhiza by hybrid sequencing[D].Beijing:Peking Union Medical College Hospital, 2016.
[11] 贾鹏燕. 盐胁迫下苦苣菜的生理响应及转录组分析[D].杨凌:西北农林科技大学, 2017.
Jia P Y. Physiological and transcriotome study of Sonchus oleraceus L. response to salt stress[D].Yangling:Northwest A&F University, 2017.
[12] Gordon S P, Tseng E, Salamov A, Zhang J W, Meng X D, Zhao Z Y, Kang D W, Underwood J, Grigoriev I V, Figueroa M, Schilling J S, Chen F, Wang Z. Widespread polycistronic transcripts in fungi revealed by single-molecule mRNA sequencing[J]. PLoS One, 2015, 10(7):e0132628.doi:10.1371/journal.pone.0132628.
[13] Conesa A, Götz S, García-Gömez J M, Terol J, Talön M, Robles M. Blast2GO:a universal tool for annotation, visualization and analysis in functional genomics research[J]. Bioinformatics, 2005, 21(18):3674-3676.doi:10.1093/bioinformatics/bti610.
[14] Ye J, Fang L, Zheng H K, Zhang Y, Chen J, Zhang Z J, Wang J, Li S T, Li R Q, Bolund L, Wang J. WEGO:a web tool for plotting GO annotations[J]. Nucleic Acids Research, 2006, 34:W293-W297.doi:10.1093/nar/gkl031.
[15] 戴雨霖, 于珊珊, 张颖, 郝颖, 钟薇, 越皓, 刘淑莹. 葛花中异黄酮类化学成分的RRLC-Q-TOF MS/MS研究[J].高等学校化学学报, 2014, 35(7):1396-1402.doi:10.7503/cjcu20140168.
Dai Y L, Yu S S, Zhang Y, Hao Y, Zhong W, Yue H, Liu S Y. Studies on the isoflavone in extract of the flower of Pueraria Lobata by RRLC-Q-TOF MS/MS[J]. Chemical Journal of Chinese Universities, 2014, 35(7):1396-1402.
[16] 杨雪, 雒军, 王引权.调控植物黄酮类化合物生物合成的MYB转录因子研究进展[J].甘肃中医药大学学报, 2018, 35(6):77-81.doi:10.16841/j.issn1003-8450.2018.06.17.
Yang X, Luo J, Wang Y Q. MYB transcription factors involved in regulation of flavonoid biosynthesis of medicinal plants[J]. Journal of Gansu University of Chinese Medicine, 2018, 35(6):77-81.
[17] 莫文珠. 稻瘟病菌无毒基因AvrPit的遗传多样性[D].广州:华南农业大学, 2018.
Mo W Z. Genetic diversity of the AvrPit alleles in rice blast populations[D].Guangzhou:South China Agricultural University, 2018.
[18] 刘路贤. 菊花栽培品种遗传多样性的AFLP分析及SSR分子标记的开发[D].开封:河南大学, 2013.
Liu L X. Analyses of genetic diversity by using AFLP and development of SSR markers in Dendranthema×gradifolium[D].Kaifeng:Henan University, 2013.
[19] Xu Z C, Peters R J, Weirather J, Luo H M, Liao B S, Zhang X, Zhu Y J, Ji A J, Zhang B, Hu S N, Au K F, Song J Y, Chen S L. Full-length transcriptome sequences and splice variants obtained by a combination of sequencing platforms applied to different root tissues of Salvia miltiorrhiza and tanshinone biosynthesis[J]. The Plant Journal, 2015, 82(6):951-961.doi:10.1111/tpj.12865.
[20] 张雅雯, 邵东燕, 师俊玲, 朱静, 黄庆生, 杨慧. 山奈酚生物功能研究进展[J].生命科学, 2017, 29(4):400-405.doi:10.13376/j.cbls/2017053.
Zhang Y W, Shao D Y, Shi J L, Zhu J, Huang Q S, Yang H. A review on biological activities of kaempferol[J]. Chinese Bulletin of Life Sciences, 2017, 29(4):400-405.

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