Journal of Plant Biotechnology

The Korean Society of Plant Biotechnology (한국식물생명공학회)
권호 표지
DOI QR코드

DOI QR Code

Transcriptome analysis of a medicinal plant, Pistacia chinensis

  • Choi, Ki-Young (Department of Controlled Agriculture, Kangwon National University) ;
  • Park, Duck Hwan (Division of Bioresource Sciences, Kangwon National University) ;
  • Seong, Eun-Soo (Department of Medicinal Plants, Suwon Women's University) ;
  • Lee, Sang Woo (International Biological Material Research Center, KRIBB) ;
  • Hang, Jin (Yunnan Academy of Agricultural Sciences) ;
  • Yi, Li Wan (Yunnan Academy of Agricultural Sciences) ;
  • Kim, Jong-Hwa (Department of Horticulture, Kangwon National University) ;
  • Na, Jong-Kuk (Department of Controlled Agriculture, Kangwon National University)
  • Received : 2019.11.12
  • Accepted : 2019.12.02
  • Published : 2019.12.31
Download PDF
⟨ Previous Next ⟩

Abstract

Pistacia chinensis Bunge has not only been used as a medicinal plant to treat various illnesses but its young shoots and leaves have also been used as vegetables. In addition, P. chinensis is used as a rootstock for Pistacia vera (pistachio). Here, the transcriptome of P. chinensis was sequenced to enrich genetic resources and identify secondary metabolite biosynthetic pathways using Illumina RNA-seq methods. De novo assembly resulted in 18,524 unigenes with an average length of 873 bp from 19 million RNA-seq reads. A Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation tool assigned KO (KEGG orthology) numbers to 6,553 (36.2%) unigenes, among which 4,061 unigenes were mapped into 391 different metabolic pathways. For terpenoid backbone and carotenoid biosynthesis pathways, 44 and 22 unigenes encode enzymes corresponding to 30 and 16 entries, respectively. Twenty-two unigenes encode proteins for 16 entries of the carotenoid biosynthesis pathway. As for the phenylpropanoid and flavonoid biosynthesis pathways, 63 and 24 unigenes were homologous to 17 and 14 entry proteins, respectively. Mining of simple sequence repeat identified 2,599 simple sequence repeats from P. chinensis unigenes. The results of the present study provide a valuable resource for in-depth studies on comparative and functional genomics to unravel the underlying mechanisms of the medicinal properties of Pistacia L.

Keywords

References

  1. Akhtar N, Rashid A, Murad W, Bergmeier E (2013) Diversity and use of ethno-medicinal plants in the region of Swat, North Pakistan. Journal of Ethnobiology and Ethnomedicine 9(1):25. doi:10.1186/1746-4269-9-25
  2. Bae DY, Eum SM, Lee SW, Paik JH, Kim SY, Park M, Lee C, Tran TB, Do VH, Heo JY, Seong ES, Kim IS, Choi KY, Hong JS, Ramekar RV, Choi S, Na JK (2018) Enrichment of genomic resources and identification of simple sequence repeats from medicinally important Clausena excavata. 3 Biotech 8(133):1-10. doi:doi.org/10.1007/s13205-018-1162-x
  3. Batra P, Sharma AK (2013) Anti-cancer potential of flavonoids:recent trends and future perspectives. 3 Biotech 3(6):439-459. doi:10.1007/s13205-013-0117-5
  4. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114-2120. doi:10.1093/bioinformatics/btu170
  5. Bozorgi M, Memariani Z, Mobli M, Salehi Surmaghi MH, Shams-Ardekani MR, Rahimi R (2013) Five Pistacia species (P. vera, P. atlantica, P. terebinthus, P. khinjuk, and P. lentiscus): a review of their traditional uses, phytochemistry, and pharmacology. The Scientific World Journal 2013:219815. doi:10.1155/2013/219815
  6. Dong S, Liu Y, Xiong B, Jiang X, Zhang Z (2016) Transcriptomic Analysis of a Potential Bioenergy Tree, Pistacia chinensis Bunge, and Identification of Candidate Genes Involved in the Biosynthesis of Oil. BioEnergy Research 9(3):740-749. doi:10.1007/s12155-016-9716-4
  7. Eum SM, Kim S-Y, Hong JS, Roy NS, Choi S, Paik J, Lee SW, Tran TB, Do VH, Kim KS, Seong E-S, Park K-C, Yu CY, Eom SH, Choi K-Y, Kim J-H, Na J-K (2019) Transcriptome analysis and development of SSR markers of ethnobotanical plant Sterculia lanceolata. Tree Genetics & Genomes 15(3):37. doi:10.1007/s11295-019-1348-3
  8. Kotwal S, Kaul S, Sharma P, Gupta M, Shankar R, Jain M, Dhar MK (2016) De Novo Transcriptome Analysis of Medicinally Important Plantago ovata Using RNA-Seq. PloS one 11(3):e0150273. doi:10.1371/journal.pone.0150273
  9. Lee BY, Kim HS, Choi BS, Hwang DS, Choi AY, Han J, Won EJ, Choi IY, Lee SH, Om AS, Park HG, Lee JS (2015) RNA-seq based whole transcriptome analysis of the cyclopoid copepod Paracyclopina nana focusing on xenobiotics metabolism. Comparative biochemistry and physiology Part D, Genomics & proteomics 15:12-19. doi:10.1016/j.cbd.2015.04.002
  10. Liu JJ, Geng CA, Liu XK (2008) A new pyrrolidone derivative from Pistacia chinensis. Chinese Chemical Letters 19(1):65-67. doi:https://doi.org/10.1016/j.cclet.2007.10.037
  11. Loke KK, Rahnamaie-Tajadod R, Yeoh CC, Goh HH, Mohamed-Hussein ZA, Mohd Noor N, Zainal Z, Ismail I (2016) RNA-seq analysis for secondary metabolite pathway gene discovery in Polygonum minus. Genomics data 7:12-13. doi:10.1016/j.gdata.2015.11.003
  12. Nishimura S, Taki M, Takaishi S, Iijima Y, Akiyama T (2000) Structures of 4-aryl-coumarin (neoflavone) dimers isolated from Pistacia chinensis BUNGE and their estrogen-like activity. Chemical & pharmaceutical bulletin 48(4):505-508. doi:10.1248/cpb.48.505
  13. Rai A, Yamazaki M, Takahashi H, Nakamura M, Kojoma M, Suzuki H, Saito K (2016) RNA-seq Transcriptome Analysis of Panax japonicus, and Its Comparison with Other Panax Species to Identify Potential Genes Involved in the Saponins Biosynthesis. Frontiers in plant science 7:481. doi:10.3389/fpls.2016.00481
  14. Rashed K, Said A, Abdo A, Selim S (2016) Antimicrobial activity and chemical composition of Pistacia chinensis Bunge leaves. International Food Research Journal 23(1): 316-321 (2016) 23(1):316-321
  15. Rauf A, Patel S, Uddin G, Siddiqui BS, Ahmad B, Muhammad N, Mabkhot YN, Hadda TB (2017) Phytochemical, ethnomedicinal uses and pharmacological profile of genus Pistacia. Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie 86:393-404. doi:10.1016/j.biopha.2016.12.017
  16. Shi Q, Zuo C (1992) Chemical components of the leaves of Pistacia chinensis Bge. Zhongguo Zhong Yao Za Zhi 17:422-423
  17. Spinelli F, Speakman J-B, Rademacher W, Halbwirth H, Stich K, Costa G (2005) Luteoforol, a flavan 4-ol, is induced in pome fruits by prohexadione-calciumand shows phytoalexin-like properties against Erwinia amylovoraand other plant pathogens. European Journal of Plant Pathology 112(2):133-142. doi:10.1007/s10658-005-2192-x
  18. Tang M, Zhang P, Zhang L, Li M, Wu L (2012) A potential bioenergy tree: Pistacia chinensis Bunge. Energy Procedia 16:737-746 https://doi.org/10.1016/j.egypro.2012.01.119
  19. Zaloglu S, Kafkas S, Dogan Y, Guney M (2015) Development and characterization of SSR markers from pistachio (Pistacia vera L.) and their transferability to eight Pistacia species. Scientia Horticulturae 189:94-103. doi:https://doi.org/10.1016/j.scienta.2015.04.006
  20. Zeng L, Tu X-L, Dai H, Han F-M, Lu B-S, Wang M-S, Nanaei HA, Tajabadipour A, Mansouri M, Li X-L, Ji L-L, Irwin DM, Zhou H, Liu M, Zheng H-K, Esmailizadeh A, Wu D-D (2019) Whole genomes and transcriptomes reveal adaptation and domestication of pistachio. Genome Biology 20(1):79. doi:10.1186/s13059-019-1686-3
  21. Zhang Z, Xie W, Zhao Y, Zhang J, Wang N, Ntakirutimana F, Yan J, Wang Y (2019) EST-SSR marker development based on RNA-sequencing of E. sibiricus and its application for phylogenetic relationships analysis of seventeen Elymus species. BMC Plant Biology 19(1):235. doi:10.1186/s12870-019-1825-8
  22. Ziya Motalebipour E, Kafkas S, Khodaeiaminjan M, Coban N, Gozel H (2016) Genome survey of pistachio (Pistacia vera L.) by next generation sequencing: Development of novel SSR markers and genetic diversity in Pistacia species. BMC genomics 17(1):998-998. doi:10.1186/s12864-016-3359-x