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Research Article

De novo assembly and characterization of the transcriptome and development of microsatellite markers in a Chinese endemic Euphorbia kansui

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Pages 562-574 | Received 15 Jan 2020, Accepted 22 Jun 2020, Published online: 08 Jul 2020

References

  • Chinese Pharmacopeia Committee. Phamacopoeia of the People’s Republic of China. Beijing: Chinese Medical Science Press, 2010, 81.
  • Whelan LC, Ryan MF. Ethanolic extracts of Euphorbia and other ethnobotanical species as inhibitors of human tumour cell growth. Phytomedicine. 2003;10(1):53–58.
  • Zheng WF. Study on in vivo antiviral activity of four diterpenoids from ethanol extracts of Euphorbia kansui. Chin Tradi Herbal Drugs. 2004;35:65–68.
  • Wang LY, Wang NL, Yao XS, et al. Diterpenes from the roots of Euphorbia kansui and their in vitro effects on the cell division of Xenopus. J Nat Prod. 2002;65(9):1246–1251.
  • Wang L-Y, Wang N-L, Yao X-S, et al. Euphane and tirucallane triterpenes from the roots of Euphorbia kansui and their in vitro effects on the cell division of Xenopus. J Nat Prod. 2003;66(5):630–633.,
  • Han XY. The clinical research of Kansui roots and its anti-fertility effects. J Med Res. 1980;5:8–11.
  • Dang QL, Choi YH, Choi GJ, et al. Pesticidal activity of ingenane diterpenes isolated from Euphorbia kansui against Nilaparvata lugens and Tetranychus urticae. J Asia-Pac Entomol. 2010;13(1):51–54.
  • Chan AP, Crabtree J, Zhao Q, et al Draft genome sequence of the oilseed species Ricinus communis. Nat Biotechnol. 2010;28(9):951–956.
  • Sato S, Hirakawa H, Isobe S, et al. Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L. DNA Res. 2011;18(1):65–76.
  • Rahman AY, Usharraj AO, Misra BB, et al. Draft genome sequence of the rubber tree Hevea brasiliensis. BMC Genomics. 2013;14:75. [23375136]
  • Zhao XY, Si JJ, Miao Y, et al. Comparative proteomics of Euphorbia kansui Liou milky sap at two different developmental stages. Plant Physiol Biochem. 2014;79:60–65.
  • Morozova O, Marra MA. Applications of next-generation sequencing technologies in functional genomics. Genomics. 2008;92(5):255–264.
  • Grabherr MG, Haas BJ, Yassour M, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29(7):644–652.
  • Wang W, Wang Y, Zhang Q, et al. Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencing. BMC Genomics. 2009;10:465 [cited 2019 Dec 10]
  • Wang G, Du XL, Ji J, et al. De novo characterization of the Lycium chinense Mill. leaf transcriptome and analysis of candidate genes involved in carotenoid biosynthesis. Gene. 2015;555(2):458–463.
  • Tautz D, Renz M. Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res. 1984;12(10):4127–4138.
  • Ellegren H. Microsatellites: simple sequences with complex evolution. Nat Rev Genet. 2004;5(6):435–445.
  • Jiang B, Xie DS, Liu WR, et al De novo assembly and characterization of the transcriptome, and development of SSR markers in Wax Gourd (Benicasa hispida)). PLoS One. 2013;8(8):e71054.
  • Sathyanarayana N, Pittala RK, Tripathi PK, et al. Transcriptomic resources for the medicinal Legume Mucuna pruriens: de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers. BMC Genomics. 2017;18(1):409.
  • Xu M, Liu X, Wang J, et al. Transcriptome sequencing and development of novel genic SSR markers for Dendrobium officinale. Mol Breeding. 2017;37(2):18.
  • Yan XH, Fang MF, Qian ZQ, et al. Isolation and characterization of polymorphic microsatellites in the perennial herb Euphorbia kansui using paired-end Illumina shotgun sequencing. Conserv Genet Resour. 2014;6(4):841–843.
  • Chen C, Xu M, Wang C, et al. Characterization of the Lycium barbarum fruit transcriptome and development of EST-SSR markers. PLoS One. 2017;12(11):e0187738.
  • He CT, Li ZL, Zhou Q, et al. Transcriptome profiling reveals specific patterns of paclitaxel synthesis in a new Taxus yunnanensis cultivar. Plant Physiol Biochem. 2018;122:10–18.
  • Mudalkar S, Golla R, Ghatty S, et al De novo transcriptome analysis of an imminent biofuel crop, Camelina sativa L. using Illumina GAIIX sequencing platform and identification of SSR markers. Plant Mol Biol. 2014;84(1-2):159–171.
  • Jiang NH, Zhang GH, Zhang JJ, et al. Analysis of the transcriptome of Erigeron breviscapus uncovers putative scutellarin and chlorogenic acids biosynthetic genes and genetic markers. PLoS One. 2014;9(6):e100357.
  • Lu XY, Kim H, Zhong SL, et al. De novo transcriptome assembly for rudimentary leaves in Litchi chinesis Sonn. and identification of differentially expressed genes in response to reactive oxygen species. BMC Genomics. 2014;15:805.
  • Chen XM, Li JK, Xiao SJ, et al. De novo assembly and characterization of foot transcriptome and microsatellite marker development for Paphia textile. Gene. 2016;576(1 Pt 3):537–543.
  • Li YL, Yuan D, Xu X, et al. Studies on macrocyclic jatrophan diterpenes of Euphorbia kansui. Chin J Chin Mate Med. 2008;33:1836–1839.
  • Cao XY, Jiang JH, Liu Q, et al. Cloning and analysis of a cDNA encoding key enzyme gene (hmgr) of the MVA pathway in medicinal plant Euphorbia pekinensis. J Wuhan Bot Res. 2007;25:123–126.
  • Sando T, Takaoka C, Mukai Y, et al. Cloning and characterization of mevalonate pathway genes in a natural rubber producing plant, Hevea brasiliensis. Biosci Biotech Bioch. 2008;72:2019–2060.
  • Chai J, Wang D, Peng Y, et al. Molecular cloning, expression and immunolocalization analysis of diphosphomevalonate decarboxylase involved in terpenoid biosynthesis from Euphorbia helioscopia L. Biotechnol Biotechnol Equip. 2017;31(6):1106–1115.
  • Zhao XY, Zhang Y, Wang M, et al Comparative proteomic analysis of latex from Euphorbia kansui laticifers at different development stages with and without UV-B treatment via iTRAQ-coupled two-dimensional liquid chromatography-MS/MS. Funct Plant Biol. 2019;47(1):67–79.
  • He YF, Gao W, Liu TS, et al. Research advances of diterpene synthase. Acta Pharm Sinica. 2011;46:1019–1025.
  • Kirby J, Nishimoto M, Park JG, et al. Cloning of casbene and neocembrene synthases from Euphorbiaceae plants and expression in Saccharomyces cerevisiae. Phytochemistry. 2010;71(13):1466–1473.
  • Dueber MT, Adolf W, West CA. Biosynthesis of the diterpene phytoalexin casbene: partial purification and characterization of casbene synthetase from Ricinis communis. Plant Physiol. 1978;62(4):598–603.
  • Mau CJ, West CA. Cloning of casbene synthase cDNA: evidence for conserved structural features among terpenoid cyclases in plants. Proc Natl Acad Sci USA. 1994;91(18):8497–8501.
  • Liu HW, Tang Q, Yang YF, et al. Casbene synthase gene cloned from Euphorbia fischeriana Steud. Mol Plant Breed. 2012;10:62–66.
  • Zalapa JE, Cuevas H, Zhu H, et al. Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. Am J Bot. 2012;99(2):193–208.
  • Xing W, Liao J, Cai M, et al. De novo assembly of transcriptome from Rhododendron latoucheae Franch. using Illumina sequencing and development of new EST-SSR markers for genetic diversity analysis in Rhododendron. Tree Genet Genomes. 2017;13:53.
  • Han Z, Ma X, Wei M, et al. SSR marker development and intraspecific genetic divergence exploration of Chrysanthemum indicum based on transcriptome analysis. BMC Genomics. 2018;19(1):291
  • Raji AA, Anderson JV, Kolade OA, et al. Gene-based microsatellites for cassava (Manihot esculenta Crantz): prevalence, polymorphisms, and cross-taxa utility. BMC Plant Biol. 2009;9:118.
  • Kumar B, Kumar U, Yadav HK. Identification of EST-SSRs and molecular diversity analysis in Mentha piperita. Crop J. 2015;3(4):335–342.
  • Torales SL, Rivarola M, Pomponio MF, et al. De novo assembly and characterization of leaf transcriptome for the development of functional molecular markers of the extremophile multipurpose tree species Prosopis alba. BMC Genomics. 2013;14:705
  • Hu Z, Zhang T, Gao XX, et al. De novo assembly and characterization of the leaf, bud, and fruit transcriptome from the vulnerable tree Juglans mandshurica for the development of 20 new microsatellite markers using Illumina sequencing. Mol Genet Genomics. 2016;291(2):849–862.
  • Varshney PK, Graner A, Sorrells ME. Genic microsatellite markers in plants: features and applications. Trends Biotechnol. 2005;23(1):48–55.
  • Barbara T, Palma-Silva C, Paggi GM, et al. Cross-species transfer of nuclear microsatellite markers: potential and limitations. Mol Ecol. 2007;16(18):3759–3767.
  • Yan Z, Wu F, Luo K, et al. Cross-species transferability of EST-SSR markers developed from the transcriptome of Melilotus and their application to population genetics research. Sci Rep. 2017;7(1):59–79.
  • Yadav HK, Ranjan A, Asif MH, et al. EST-derived SSR markers in Jatropha curcas development, characterization, polymorphism, and transferability across the species/genera. Tree Genet Genomes. 2011;7(1):207–219.