3 Biotech

, 8:133 | Cite as

Enrichment of genomic resources and identification of simple sequence repeats from medicinally important Clausena excavata

  • Doo Young Bae
  • Sang Mi Eum
  • Sang Woo Lee
  • Jin-Hyub Paik
  • Soo-Yong Kim
  • Mihyun Park
  • Changyoung Lee
  • The Bach Tran
  • Van Hai Do
  • Jae-Yun Heo
  • Eun-Soo Seong
  • Il-Seop Kim
  • Ki-Young Choi
  • Jin Sung Hong
  • Rahul Vasudeo Ramekar
  • Sangho Choi
  • Jong-Kuk Na
Original Article
  • 3 Downloads

Abstract

To broaden and delve into the genomic information of Clausena excavata, an important medicinal plant in many Asian countries, RNA sequencing (RNA-seq) analysis was performed and a total of 16,638 non-redundant unigenes (≥ 300 bp) with an average length of 755 bp were generated by de novo assembly from 17,580,456 trimmed clear reads. The functional categorization of the identified unigenes by a gene ontology (GO) term resulted in 2305 genes in the cellular component, 5577 in the biological processes, and 8056 in the molecular functions, respectively. The top sub-category in biological processes was the metabolic process with 4374 genes. Among annotated genes, 3006 were mapped to 123 metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis tool. The search for simple sequence repeats (SSRs) resulted in 845 SSRs from 749 SSR-containing unigenes and the most abundant SSR motifs was AAG/CTT with 179 occurrences. Twelve SSR markers were tested for cross transferability among five Clausena species; eight of them exhibited polymorphism. Taken together, these data provide valuable resources for genomic or genetic studies of Clausena species and other relative studies. The transcriptome shotgun assembly data have been deposited at DDBJ/EMBL/GenBank under the accession GGEM00000000.

Keywords

RNA-seq Medicinal plant Clausena species SSR marker 

Notes

Acknowledgements

This work was supported by a grant from the National Foundation for Science and Technology Development of ROK (NRF-2016K1A1A8A01939075) and by 2017 research grant from Kangwon National University.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interests.

Supplementary material

13205_2018_1162_MOESM1_ESM.docx (226 kb)
Supplementary material 1 (DOCX 226 kb)

References

  1. Arbab IA, Abdul AB, Aspollah M, Abdullah R, Abdelwahab SI, Ibrahim MY, Ali LZ (2012) A review of traditional uses, phytochemical and pharmacological aspects of selected members of Clausena genus (Rutaceae). J Med Plants Res 6(38):5107–5118CrossRefGoogle Scholar
  2. Asari N, Ramaswamy M, Subbian E, Palliyarakkal M, Malhotra SK, Karun A (2014) Standalone EST microsatellite mining and analysis tool (SEMAT): for automated EST-SSR analysis in plants. Tree Genet Genom 10(6):1755–1757.  https://doi.org/10.1007/s11295-014-0785-2 CrossRefGoogle Scholar
  3. Atanasov AG, Waltenberger B, Pferschy-Wenzig EM, Linder T, Wawrosch C, Uhrin P, Temml V, Wang L, Schwaiger S, Heiss EH, Rollinger JM, Schuster D, Breuss JM, Bochkov V, Mihovilovic MD, Kopp B, Bauer R, Dirsch VM, Stuppner H (2015) Discovery and resupply of pharmacologically active plant-derived natural products: a review. Biotechnol Adv 33(8):1582–1614.  https://doi.org/10.1016/j.biotechadv.2015.08.001 CrossRefGoogle Scholar
  4. Bayer RJ, Mabberley DJ, Morton C, Miller CH, Sharma IK, Pfeil BE, Rich S, Hitchcock R, Sykes S (2009) A molecular phylogeny of the orange subfamily(Rutaceae: Aurantioideae) using nine cpDNA sequences. Am J Bot 96(3):668–685.  https://doi.org/10.3732/ajb.0800341 CrossRefGoogle Scholar
  5. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32(3):314–331Google Scholar
  6. Chen C, Zhou P, Choi YA, Huang S, Gmitter FG Jr (2006) Mining and characterizing microsatellites from citrus ESTs. TAG. TAG Theor Appl Genet Theoretische und angewandte Genetik 112(7):1248–1257.  https://doi.org/10.1007/s00122-006-0226-1 CrossRefGoogle Scholar
  7. Chen S, Yao H, Han J, Liu C, Song J, Shi L, Zhu Y, Ma X, Gao T, Pang X, Luo K, Li Y, Li X, Jia X, Lin Y, Leon C (2010) Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS One 5(1):e8613.  https://doi.org/10.1371/journal.pone.0008613 CrossRefGoogle Scholar
  8. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18):3674–3676.  https://doi.org/10.1093/bioinformatics/bti610 CrossRefGoogle Scholar
  9. Garcia-Ortega LF, Martinez O (2015) How many genes are expressed in a transcriptome? Estimation and results for RNA-Seq. PLoS One 10(6):e0130262.  https://doi.org/10.1371/journal.pone.0130262 CrossRefGoogle Scholar
  10. Hao D-C, Chen S-L, Xiao P-G, Liu M (2012) Application of high-throughput sequencing in medicinal plant transcriptome studies. Drug Dev Res 73(8):487–498.  https://doi.org/10.1002/ddr.21041 CrossRefGoogle Scholar
  11. He H, Zhu W, Shen Y, Yang X, Zuo G, Ha X (2000) Flavonoid glycosides from Clausena excavata. Acta Botanica Yunnanica 23(2):256–260Google Scholar
  12. Ito C, Itoigawa M, Katsuno S, Omura M, Tokuda H, Nishino H, Furukawa H (2000) Chemical constituents of Clausena excavata: isolation and structure elucidation of novel furanone-coumarins with inhibitory effects for tumor-promotion. J Nat Prod 63(9):1218–1224CrossRefGoogle Scholar
  13. Jung H, Yoon BH, Kim WJ, Kim DW, Hurwood DA, Lyons RE, Salin KR, Kim HS, Baek I, Chand V, Mather PB (2016) optimizing hybrid de novo transcriptome assembly and extending genomic resources for giant freshwater prawns (Macrobrachium rosenbergii): the identification of genes and markers associated with reproduction. Int J Mol Sci 17 (5).  https://doi.org/10.3390/ijms17050690
  14. Khanna D, Sethi G, Ahn KS, Pandey MK, Kunnumakkara AB, Sung B, Aggarwal A, Aggarwal BB (2007) Natural products as a gold mine for arthritis treatment. Curr Opin Pharmacol 7(3):344–351.  https://doi.org/10.1016/j.coph.2007.03.002 CrossRefGoogle Scholar
  15. 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.  https://doi.org/10.1371/journal.pone.0150273 CrossRefGoogle Scholar
  16. Kumar R, Saha A, Saha D (2012) A new antifungal coumarin from Clausena excavata. Fitoterapia 83(1):230–233.  https://doi.org/10.1016/j.fitote.2011.11.003 CrossRefGoogle Scholar
  17. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33(7):1870–1874.  https://doi.org/10.1093/molbev/msw054 CrossRefGoogle Scholar
  18. 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. Comp Biochem Physiol D Genom Proteom 15:12–19.  https://doi.org/10.1016/j.cbd.2015.04.002 Google Scholar
  19. Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22(13):1658–1659.  https://doi.org/10.1093/bioinformatics/btl158 CrossRefGoogle Scholar
  20. Liu SR, Li WY, Long D, Hu CG, Zhang JZ (2013) Development and characterization of genomic and expressed SSRs in citrus by genome-wide analysis. PLoS One 8(10):e75149.  https://doi.org/10.1371/journal.pone.0075149 CrossRefGoogle Scholar
  21. 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. Genom Data 7:12–13.  https://doi.org/10.1016/j.gdata.2015.11.003 CrossRefGoogle Scholar
  22. Luro FL, Costantino G, Terol J, Argout X, Allario T, Wincker P, Talon M, Ollitrault P, Morillon R (2008) Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping. BMC Genom 9:287.  https://doi.org/10.1186/1471-2164-9-287 CrossRefGoogle Scholar
  23. Moreton J, Dunham SP, Emes RD (2014) A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome. Front in Genet 5:190.  https://doi.org/10.3389/fgene.2014.00190 CrossRefGoogle Scholar
  24. Morton CM, Grant M, Blackmore S (2003) Phylogenetic relationships of the Aurantioideae inferred from chloroplast DNA sequence data. Am J Bot 90(10):1463–1469.  https://doi.org/10.3732/ajb.90.10.1463 CrossRefGoogle Scholar
  25. Ollitrault F, Terol J, Pina JA, Navarro L, Talon M, Ollitrault P (2010) Development of SSR markers from Citrus clementina (Rutaceae) BAC end sequences and interspecific transferability in Citrus. Am J Bot 97(11):e124–129.  https://doi.org/10.3732/ajb.1000280 CrossRefGoogle Scholar
  26. 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. Front Plant Sci 7:481.  https://doi.org/10.3389/fpls.2016.00481 Google Scholar
  27. Samuel R, Ehrendorfer F, Chase MW, Greger H (2001) Phylogenetic analyses of Aurantioideae (Rutaceae) based on non-coding plastid DNA sequences and phytochemical features. Plant Biol 3(1):77–87.  https://doi.org/10.1055/s-2001-11747 CrossRefGoogle Scholar
  28. Schulz MH, Zerbino DR, Vingron M, Birney E (2012) Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28(8):1086–1092.  https://doi.org/10.1093/bioinformatics/bts094 CrossRefGoogle Scholar
  29. Sharif N, Mustahil N, Mohd Noor N, Sukari M, Rahmani M, Taufiq-Yap Y, Ee G (2011) Cytotoxic constituents of Clausena excavata. Afr J Biotech 10(72):16337–16341Google Scholar
  30. Sterck L, Rombauts S, Vandepoele K, Rouzé P, Van de Peer Y (2007) How many genes are there in plants (… why are they there)? Curr Opin Plant Biol 10(2):199–203CrossRefGoogle Scholar
  31. Sunthitikawinsakul A, Kongkathip N, Kongkathip B, Phonnakhu S, Daly JW, Spande TF, Nimit Y, Napaswat C, Kasisit J, Yoosook C (2003a) Anti-HIV-1 limonoid: first isolation from Clausena excavata. Phytother Res PTR 17(9):1101–1103.  https://doi.org/10.1002/ptr.1381 CrossRefGoogle Scholar
  32. Sunthitikawinsakul A, Kongkathip N, Kongkathip B, Phonnakhu S, Daly JW, Spande TF, Nimit Y, Rochanaruangrai S (2003b) Coumarins and carbazoles from Clausena excavata exhibited antimycobacterial and antifungal activities. Planta Med 69(2):155–157.  https://doi.org/10.1055/s-2003-37716 CrossRefGoogle Scholar
  33. Tang X, Xiao Y, Lv T, Wang F, Zhu Q, Zheng T, Yang J (2014) High-throughput sequencing and De Novo assembly of the Isatis indigotica transcriptome. PLoS One 9(9):e102963.  https://doi.org/10.1371/journal.pone.0102963 CrossRefGoogle Scholar
  34. Vargas P, Baldwin BG, Constance L (1998) Nuclear ribosomal DNA evidence for a western North American origin of Hawaiian and South American species of Sanicula (Apiaceae). Proc Natl Acad Sci USA 95(1):235–240CrossRefGoogle Scholar
  35. Wang S, Gribskov M (2017) Comprehensive evaluation of de novo transcriptome assembly programs and their effects on differential gene expression analysis. Bioinformatics 33(3):327–333.  https://doi.org/10.1093/bioinformatics/btw625 Google Scholar
  36. White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis N, Gelfand D, Sninsky J, White T (eds) PCR protocols: a guide to methods and applications. Academic Press Inc., New York, pp 315–322Google Scholar
  37. Wu CC, Ko FN, Wu TS, Teng CM (1994) Antiplatelet effects of clausine-D isolated from Clausena excavata. Biochem Biophys Acta 1201(1):1–6CrossRefGoogle Scholar
  38. Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, Wang J (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34((Web Server issue)):W293–W297.  https://doi.org/10.1093/nar/gkl031 CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Doo Young Bae
    • 1
  • Sang Mi Eum
    • 1
  • Sang Woo Lee
    • 1
  • Jin-Hyub Paik
    • 1
  • Soo-Yong Kim
    • 1
  • Mihyun Park
    • 1
  • Changyoung Lee
    • 1
  • The Bach Tran
    • 2
  • Van Hai Do
    • 2
  • Jae-Yun Heo
    • 3
    • 4
  • Eun-Soo Seong
    • 5
  • Il-Seop Kim
    • 6
  • Ki-Young Choi
    • 7
  • Jin Sung Hong
    • 8
  • Rahul Vasudeo Ramekar
    • 9
  • Sangho Choi
    • 1
  • Jong-Kuk Na
    • 7
  1. 1.International Biological Material Research CenterKorea Research Institute of Bioscience and BiotechnologyDaejeonRepublic of Korea
  2. 2.IEBR, Vietnam Academy of Science and Technology (VAST)Ha NoiVietnam
  3. 3.Agriculture and Life Sciences Research InstituteKangwon National UniversityChuncheonRepublic of Korea
  4. 4.Department of Plant ScienceGangneung-Wonju UniversityChuncheonRepublic of Korea
  5. 5.Department of Medicinal PlantsSuwon Women’s UniversitySuwonRepublic of Korea
  6. 6.Department of HorticultureKangwon National UniversityChuncheonRepublic of Korea
  7. 7.Department of Controlled AgricultureKangwon National UniversityChuncheonRepublic of Korea
  8. 8.Division of Bioresource SciencesKangwon National UniversityChuncheonRepublic of Korea
  9. 9.Department of of Applied Plant SciencesKangwon National UniversityChuncheonRepublic of Korea

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