De novo transcriptome sequencing facilitates genomic resource generation in Tinospora cordifolia

Functional and Integrative Genomics

Volumn 16, Issue 5, 2016, Pages 581-591

  Singh, Rakesh ^a   Kumar, Rajesh ^a   Mahato, Ajay Kumar ^b   Paliwal, Ritu ^a   Singh, Amit Kumar ^a   Kumar, Sundeep ^a   Marla, Soma S ^a   Kumar, Ashok ^a   Singh, Nagendra K ^b  

^a NATIONAL BUREAU OF PLANT GENETIC RESOURCES   (India)

^b NATIONAL RESEARCH CENTRE ON PLANT BIOTECHNOLOGY   (India)

Author keywords

EST SSR; Terpenes; Tinospora; Transcription factor; Transcriptome

Indexed keywords

BASIC HELIX LOOP HELIX TRANSCRIPTION FACTOR; DEOXYXYLULOSE 5 PHOSPHATE SYNTHASE; ISOPENTENYL DIPHOSPHATE DELTA ISOMERASE; METHYLERYTHRITOL 4 PHOSPHATE; MEVALONIC ACID; TERPENOID; TRANSCRIPTION FACTOR; TRANSCRIPTOME; UNCLASSIFIED DRUG; MICROSATELLITE DNA;

ALLELE; ARABIDOPSIS; ARTICLE; CACAO; CONTIG MAPPING; DATA MINING; EXPRESSED SEQUENCE TAG; FRAGARIA; GENE LOCUS; GENE ONTOLOGY; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GERMPLASM; GRAPE; ISOMERIZATION; MALUS; NONHUMAN; NUCLEOTIDE MOTIF; NUCLEOTIDE REPEAT; PHYLOGENETIC TREE; PLANT LEAF; PLANT STEM; POLYMERIZATION; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN PRENYLATION; PROTEIN SYNTHESIS; PYROSEQUENCING; SEGMENTAL DUPLICATION; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SIMPLE SEQUENCE REPEAT; TINOSPORA CORDIFOLIA; TRANSCRIPTOMICS; GENETIC DATABASE; GENETIC VARIATION; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; MOLECULAR GENETICS; TINOSPORA;

DATABASES, GENETIC; EXPRESSED SEQUENCE TAGS; GENETIC VARIATION; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE ANNOTATION; TINOSPORA; TRANSCRIPTOME;

EID: 84979996112     PISSN: 1438793X     EISSN: 14387948     Source Type: Journal    
DOI: 10.1007/s10142-016-0508-x     Document Type: Article

References (38)

1. Aggarwal RK, Hendre PS, Varshney RK, Bhat PR, Krishnakumar V, Singh L (2007) Identification, characterization and utilization of EST-derived genic microsatellite markers for genomic analyses of coffee and related species. Theor Appl Genet 114:359–372
2. Ahmad SM, Verma V, Qazi PH, Ganaie MM, Bakshi SK, Qazi GN (2006) Molecular phylogeny in Indian Tinospora species by DNA based molecular markers. Plant Syst Evol 256:75–87
3. Ahmad SM, Verma V, Qazi PH, Hoot SB (2009) Phylogenetic patterns and genetic diversity of Indian Tinospora species based on chloroplast sequence data and cytochrome P450 polymorphisms. Plant Syst Evol 28:87–96
4. Asthana JG, Jain S, Mishra A, Vijaykant MS (2001) Evaluation of antileprotic herbal drug combinations and their combination with Dapsone. Indian Drugs 38:82–86
5. Bozhko M, Riegel R, Schubert R, Müller-Starck G (2003) A cyclophilin gene marker confirming geographic differentiation of Norway spruce populations and indicating viability selection on excess soil-born salinity. Mol Ecol 12:3147–3155
6. Dutta S, Kumawat G, Singh B, Gupta D, Singh S et al (2011) Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanuscajan (L.) Millspaugh]. BMC Plant Biol 11:17
7. Estévez JM, Cantero A, Reindl A, Reichler S, León P (2001) 1-Deoxy-D-xylulose-5-phosphate synthase, a limiting enzyme for plastidic isoprenoid biosynthesis in plants. J of Biol Chem 276(25):22901–22909
8. Gaitan-Solis E, Duque MC, Edwards KJ, Tohme J (2002) Microsatellite repeats in common bean (Phaseolus vulgaris): isolation, characterization and cross-species amplification in Phaseolus ssp. Crop Sci 42(6):2128–2136
9. Jeyachandran R, Xavier TF, Anand SP (2003) Antibacterial activity of stem extraxts of Tinosporacordifolia (Willd.). Ancient Science life 23:40–44
10. Kalpesh I, Mohan JSS (2009) Assessment of genetic diversity in the medicinal climber Tinosporacordifolia (Willd.) Miers (Menispermaceae) from Gujarat India. African J Biotechnol 8:6499–6505
11. Kantety RV, Rota ML, Matthews DE, Sorrells ME (2002) Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol 48:501–510
12. Kumpatla S, Mukhopadhyay S (2005) Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species. Genome 48(6):985–998
13. Larota M, Kantety RV, Yu JK, Sorrells ME (2005) Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley. BMC Genomics 6:23–35
14. Luro F, 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 Genomics 9:1–13
15. Mishra A, Kumar S, Pandey AK (2013) Scientific validation of the medicinal efficacy of Tinosporacordifolia. Sci World J 2013:292934, 8 pages. doi:10.1155/2013/292934
16. Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with non-repetitive DNA in plant genomes. Nat Genet 30:194–200
17. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35:W182–W185
18. Natarajan P, Parani M (2011) De novo assembly and transcriptome analysis of five major tissues of Jatropha curcasL. using GS FLX titanium platform of 454 pyrosequencing. BMC Genomics 12:191–203
19. Ohyama K, Suzuki M, Masuda K, Yoshida S, Muranaka T (2007) Chemical phenotypes of the hmg1 and hmg2 mutants of Arabidopsis demonstrates the in-planta role of HMG-CoA reductase in triterpene biosynthesis. Chem Pharm Bulletin 55(10):1518–1521
20. Paliwal R, Singh R, Singh AK, Kumar S, Kumar A, Majumdar RS (2013) Molecular characterization of giloe (TinosporacordifoliaWilld. Miers ex Hook. F. and Thoms.) accessions using Start Codon Targeted (SCoT) Markers. Int J Med Arom Plants 3(4):413–422
21. Rajalakshmi M, Eliza J, Priya CE, Nirmala A, Daisy P (2009) Anti-diabetic properties of Tinosporacordifolia stem extracts on streptozotocin-induced diabetic rats. African J of Pharm and Pharmaco 3:171–180
22. Rohlf FJ (2000) NTSYS-pc: numerical taxonomy and multivariate analysis system, version 2.1. Exeter Software, Applied Biostatistics Inc, NY, USA
23. Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 81(24):8014–8018
24. Scott KD, Eggler P, Seaton G et al (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100:723–726
25. Shinde VM, Dhaliwal K (2010) DNA fingerprinting of Tinosporacordifolia using RAPD analysis. J Global Pharma Tech 2(2):38–42
26. Sneath PH, Sokal RR (1973) Numerical taxonomy: the principal and practice of numerical classification. Freeman, San Francisco
27. Spandana U, Ali SL, Nirmala T, Santhi M, Sipaibabu SD (2013) A review on Tinosporacordifolia. Int J Current Pharma Rev Res 4(2):61–68
28. Suzuki M, Kamide Y, Nagata N et al (2004) Loss of function of 3‐hydroxy‐3‐methylglutaryl coenzyme a reductase 1 (HMG1) in Arabidopsis leads to dwarfing, early senescence and male sterility, and reduced sterol levels. The Plant J37(5):750–761
29. Thatte UM, Dhanukar SA, Rao SGA (1989) Tinospora induces colony stimulating activity in serum. J Postgrad Med 40:202–203
30. Thimmappa R, Geisler K, Louveau T, O’Maille P, Osbourn A (2014) Triterpene biosynthesis in plants. Ann Rev Plant Biol 65:225–257
31. Tholl D, Lee S (2011) Terpene specialized metabolism in Arabidopsis thaliana. Arabidopsis Book/American Society of Plant Biologists 9, e0143
32. Toth G, Gaspari Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10(7):967–981
33. Upadhyay AK, Kumar K, Kumar A, Mishra HS (2010) Tinosporacordifolia (Willd.) Hook.f. and Thoms. (Guduchi)—validation of the Ayurvedic pharmacology through experimental and clinical studies. Int J Ayurveda Res 1(2):112–121
34. Usha D, Thatte UM, Joshi DS, Dhanukar SA (1994) Flow cytometric evaluation of bone marrow proliferation induced by Tinosporacordifolia. Update Ayurveda 94:38–42
35. Varshney RK, Thiel T, Stein N, Langridge P, Graner A (2002) In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell Mol Biol Lett 7:537–546
36. Vranová E, Coman D, Gruissem W (2012) Structure and dynamics of the isoprenoid pathway network. Mol Plant 5(2):318–333
37. You FM, Huo NX, Gu YQ et al (2008) BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 9:253
38. Zeng S, Xiao G, Guo J et al (2010) Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimediumsagittatum (Sieb. Et zucc.) Maxim. BMC Genomics 11:94