De Novo Assembly and Characterization of Developing Spikes Transcriptome of Finger Millet (Eleusine coracana): a Minor Crop Having Nutraceutical Properties

Plant Molecular Biology Reporter

Volumn 33, Issue 4, 2015, Pages 905-922

  Kumar, Anil ^a   Gaur, Vikram Singh ^a   Goel, Anshita ^a   Gupta, Atul Kumar ^a  

^a G B PANT UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (India)

Author keywords

De novo assembly; Finger millet; Illumina; Transcriptome sequencing; Trinity

Indexed keywords

ELEUSINE CORACANA;

EID: 84938741043     PISSN: 07359640     EISSN: 15729818     Source Type: Journal    
DOI: 10.1007/s11105-014-0802-5     Document Type: Article

References (48)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410
2. Annadurai RS, Jayakumar V, Mugasimangalam RC et al (2012) Next generation sequencing and de novo transcriptome analysis of Costus pictus D. Don, a non-model plant with potent anti-diabetic properties. BMC Genomics 13:663
3. Campbell MA, Zhu W, Jiang N et al (2007) Identification and characterization of lineage-specific genes within the Poaceae. Plant Physiol 145:1311–1322
4. Carels N, Bernardi G (2000) Two classes of genes in plants. Genetics 154:1819–1825
5. Carels N, Hatey P, Jabbari K, Bernardi G (1998) Compositional properties of homologous coding sequences from plants. J Mol Evol 46:45–53
6. Chethan S, Malleshi NG (2007) Finger millet polyphenols: characterization and their nutraceutical potential. Am J Food Technol 2(7):582–592
7. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, 1000 Genomes Project Analysis Group (2011) The variant call format and VCF tools. Bioinformatics 27(15):2156–2158
8. Doraiswamy TR, Singh N, Daniel VA (1969) Effects of supplementing ragi (Eleusine coracana) diets with lysine or leaf protein on the growth and nitrogen metabolism of children. Br J Nutr 23:737–743
9. Egan AN, Schlueter J, Spooner DM (2012) Applications of next-generation sequencing in plant biology. Am J Bot 99(2):175–185
10. Fakrudin B, Shashidhar HE, Kulkarni RS, Hittalmani S (2004) Genetic diversity assessment of finger millet, Eleusine coracana (Gaertn.), germplasm through RAPD analysis. PGR Newsl 138:50–54
11. Garg R, Patel RK, Tyagi AK, Jain M (2011) De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res 18:53–63
12. Goel A, Gaur VS, Arora S, Gupta S, Kumar A (2012) In silico analysis of expression data for identification of genes involved in spatial accumulation of calcium in developing seeds of rice. OMICS 16:402–413
13. Grabherr MG, Haas BJ, Yassour M et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29(7):644–652
14. Gupta P, Goel R, Pathak S, Srivastava A, Singh SP, Sangwan RS, Asif MH, Trivedi PK (2013) De novo assembly, functional annotation and comparative analysis of Withania somnifera leaf and root transcriptomes to identify putative genes involved in the withanolides biosynthesis. PLoS One 8(5):e62714
15. 2+ transport: who’s directing the traffic? Trends Plant Sci 6:100–104
16. Iorizzo M, Senalik DA, Grzebelus D, Bowman M, Cavagnaro PF, Matvienko M, Ashrafi H, Van Deynze A, Simon PW (2011) De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity. BMC Genomics 12:389
17. Jehan T, Lakhanpaul S (2006) Single nucleotide polymorphism (SNP)—methods and applications in plant genetics: a review. Indian J Biotechnol 5:435–459
18. Joshi HC, Katoch KK (1990) Nutritive value of millets: a comparison with cereals and pseudocereals. Himal Res Dev 9:26–28
19. Kudapa H, Bharti AK, Cannon SB, Farmer AD, Mulaosmanovic B, Kramer R, Bohra A, Weeks NT, Crow JA, Tuteja R, Shah T, Dutta S, Gupta DK, Singh A, Gaikwad K, Sharma TR, May GD, Singh NK, Varshney RK (2012) A comprehensive transcriptome assembly of pigeonpea (Cajanus cajan L.) using sanger and second-generation sequencing platforms. Mol Plant 5:1020–1028
20. Kumar A, Mirza N, Charan T, Sharma N, Gaur VS (2014) Isolation, characterization and immunolocalization of a seed dominant Cam from finger millet (Eleusine coracana L. Gartn.) for studying its functional role in differential accumulation of calcium in developing grains. Appl Biochem Biotechnol. doi:10.1007/s12010-013-0714-0
21. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10(3):R25
22. Lawson MJ, Zhang L (2006) Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes. Genome Biol 7:R14
23. Li B, Dewey C (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinforma 12:323
24. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup (2009) The sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25:2078–2079
25. Lin H, Moghe G, Ouyang S et al (2010) Comparative analyses reveal distinct sets of lineage-specific genes within Arabidopsis thaliana. BMC Evol Biol 10:41
26. Lisso J, Altmann T, Mussig C (2006) The AtNFXL1 gene encodes a NF-X1 type zinc finger protein required for growth under salt stress. FEBS Lett 580(20):4851–4856
27. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25:402–408
28. Lulin H, Xiao Y, Pei S, Wen T, Shangqin H (2012) The first Illumina-based de novo transcriptome sequencing and analysis of safflower flowers. PLoS One 7(6):e38653
29. Maher CA, Palanisamy N, Brenner JC, Cao XH, Kalyana-Sundaram S, Luo SJ, Khrebtukova I, Barrette TR, Grasso C, Yu JD et al (2009) Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Natl Acad Sci U S A 106:12353–12358
30. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8(19):4321–4325
31. Nath M, Goel A, Taj G, Kumar A (2010) Molecular cloning and comparative in silico analysis of calmodulin genes from cereals and millets for understanding the mechanism of differential calcium accumulation. J Proteom Bioinforma 3:294–301
32. Nath M, Roy P, Shukla A, Kumar A (2013) Spatial distribution and accumulation of calcium in different tissues, developing spikes and seeds of finger millet genotypes. J Plant Nutr 36(4):539–550
33. National Research Council (1996) Lost crops of Africa, vol I, Grains. National Academy Press, Washington
34. Oono Y, Kobayashi F, Kawahara Y, Yazawa T, Handa H, Itoh T, Matsumoto T (2013) Characterisation of the wheat (Triticum aestivum L.) transcriptome by de novo assembly for the discovery of phosphate starvation-responsive genes: gene expression in Pi-stressed wheat. BMC Genomics 14:77
35. Panwar P, Nath M, Yadav VK, Kumar A (2010) Comparative evaluation of genetic diversity using RAPD, SSR and cytochome P450 gene based markers with respect to calcium content in finger millet (Eleusine coracana L. Gaertn.). J Genet 89:121–133
36. Park CY, Lee JH, Yoo JH, Moon BC, Choi MS, Kang YH, Lee SM, Kim HS, Kang KY, Chung WS (2005) WRKY group II transcription factors interact with calmodulin. FEBS Lett 579:1545–1550
37. Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1:215–222
38. Raventos D, Skriver K, Schlein M, Karnahl K, Rogers SW, Rogers JC, Mundy J (1998) HRT, a novel zinc finger, transcriptional repressor from barley. J Biol Chem 273(36):23313–23320
39. Shobana S, Krishnaswamy K, Sudha V, Malleshi NG, Anjana RM, Palaniappan L, Mohan V (2013) Nutritional properties, processing, and plausible health benefits. Adv Food Nutr Res 69:1–39
40. Srinivasachary, Dida MM, Gale MD, Devos KM (2007) Comparative analyses reveal high levels of conserved colinearity between the finger millet and rice genomes. Theor Appl Genet 115:489–499
41. Subrahmanyan V, Narayana Rao M, Rama Rao G, Swaminathan M (1955) The metabolism of nitrogen, calcium and phosphorus in human adults on a poor vegetarian diet containing ragi (Eleusine coracana). Br J Nutr 9:350–357
42. Vega-Arreguin JC, Ibarra-Laclette E, Jimenez-Moraila B, Martinez O, Vielle-Calzada JP, Herrera-Estrella L, Herrera-Estrella A (2009) Deep sampling of the Palomero maize transcriptome by a high throughput strategy of pyrosequencing. BMC Genomics 10:299
43. Virupaksha TK, Ramachandra G, Nagaraju D (1975) Seed proteins of finger millet and their amino acid composition. J Sci Food Agric 26:1237–1246
44. Wang Z, Fang B, Chen J, Zhang X, Luo Z, Huang L, Chen X, Li Y (2010) De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas). BMC Genomics 11:726
45. Wei W, Qi X, Wang L, Zhang Y, Hua W, Li D, Lv H, Zhang X (2011) Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics 12:451
46. Yadav S, Singh UM, Gaur VS, Jaiswal JP, Kumar A (2014) Simple sequence repeat (SSR) analysis in relation to calcium transport and signaling genes reveals transferability amongst grasses and a conserved behavior within finger millet genotypes. Plant Syst Evol. doi:10.1007/s00606-014-0982-3
47. Zhang GJ, Guo GW, Hu XD et al (2010) Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res 20:646–654
48. +-ATPase activity. Planta 227:659–669