De novo assembly of the pennycress (Thlaspi arvense) transcriptome provides tools for the development of a winter cover crop and biodiesel feedstock

Plant Journal

Volumn 75, Issue 6, 2013, Pages 1028-1038

  Dorn, Kevin M ^a   Fankhauser, Johnathon D ^a   Wyse, Donald L ^a   Marks, M David ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

comparative transcriptomics; de novo assembly; pennycress; RNA seq; Thlaspi arvense; translational research

Indexed keywords

DE NOVO ASSEMBLIES; PENNYCRESS; RNA-SEQ; THLASPI; TRANSCRIPTOMICS; TRANSLATIONAL RESEARCH;

AGRONOMY; BIODIESEL; CONSERVATION; CROPS; FEEDSTOCKS; RATIONAL FUNCTIONS; RNA; TOOLS;

GENES;

ARABIDOPSIS; BRASSICACEAE; THLASPI; THLASPI ARVENSE;

BIOFUEL; GLUCOSINOLATE; TRANSCRIPTOME;

ARTICLE; COMPARATIVE STUDY; COMPARATIVE TRANSCRIPTOMICS; DE NOVO ASSEMBLY; FLOWER; METABOLISM; MOLECULAR GENETICS; PENNYCRESS; PHYSIOLOGY; RNA-SEQ; SEQUENCE ANALYSIS; THLASPI; THLASPI ARVENSE; TRANSLATIONAL RESEARCH;

COMPARATIVE TRANSCRIPTOMICS; DE NOVO ASSEMBLY; PENNYCRESS; RNA-SEQ; THLASPI ARVENSE; TRANSLATIONAL RESEARCH;

BIOFUELS; FLOWERS; GLUCOSINOLATES; MOLECULAR SEQUENCE ANNOTATION; SEQUENCE ANALYSIS, RNA; THLASPI; TRANSCRIPTOME;

EID: 84883826615     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/tpj.12267     Document Type: Article

References (58)

1. Amasino, R.M., (2005) Vernalization and flowering time. Curr. Opin. Biotechnol. 16, 154-158.
2. Beilstein, M.A., Nagalingum, N.S., Clements, M.D., et al. (2010) Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana. Proc. Natl Acad. Sci. USA, 107, 18724-18728.
3. Best, K.F., and, Mcintyre, G.I., (1975) Biology of Canadian weeds, 9. Thlaspi arvense L. Can. J. Plant Sci. 55, 279-292.
4. Best, K.F., and, Mcintyre, G.I., (1976) Studies on flowering of Thlaspi arvense L. 3. Influence of vernalization under natural and controlled conditions. Bot. Gaz. 137, 121-127.
5. Boateng, A.A., Mullen, C.A., and, Goldberg, N.M., (2010) Producing stable pyrolysis liquids from the oil-seed presscakes of mustard family plants: pennycress (Thlaspi arvense L.) and camelina (Camelina sativa). Energy Fuels, 24, 6624-6632.
6. Bones, A.M., and, Rossiter, J.T., (1996) The myrosinase-glucosinolate system, its organisation and biochemistry. Physiol. Plant. 97, 194-208.
7. Choi, K., Kim, J., Hwang, H.J., et al. (2011) The FRIGIDA complex activates transcription of FLC, a strong flowering repressor in Arabidopsis, by recruiting chromatin modification factors. Plant Cell, 23, 289-303.
8. Conesa, A., Gotz, S., Garcia-Gomez, J.M., et al. (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21, 3674-3676.
9. Dabney, S.M., Delgado, J.A., and, Reeves, D.W., (2001) Using winter cover crops to improve soil and water quality. Commun. Soil Sci. Plant Anal. 32, 1221-1250.
10. Fan, J., Shonnard, D., Kalnes, T., Johnsen, P., and, Rao, S., (2013) A life cycle assessment of pennycress (Thlaspi arvense L.)-derived jet fuel and diesel. Biomass Bioenergy, 55, 87-100.
11. Fargione, J., Hill, J., Tilman, D., et al. (2008) Land clearing and the biofuel carbon debt. Science, 319, 1235-1238.
12. Franzke, A., Lysak, M.A., Al-Shehbaz, I.A., et al. (2011) Cabbage family affairs: the evolutionary history of Brassicaceae. Trends Plant Sci. 16, 108-116.
13. Gazzani, S., (2003) Analysis of the molecular basis of flowering time variation in Arabidopsis accessions. Plant Physiol. 132, 1107-1114.
14. Gongora-Castillo, E., and, Buell, C.R., (2013) Bioinformatics challenges in de novo transcriptome assembly using short read sequences in the absence of a reference genome sequence. Nat. Prod. Rep. 30, 490-500.
15. Gruenheit, N., Deusch, O., Esser, C., et al. (2012) Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants. BMC Genomics, 13, 92.
16. Hammond, J.P., Bowen, H.C., White, P.J., et al. (2006) A comparison of the Thlaspi caerulescens and Thlaspi arvense shoot transcriptomes. New Phytol. 170, 239-260.
17. Hill, J., Nelson, E., Tilman, D., et al. (2006) Environmental, economic, and energetic costs and benefits of biodiesel and ethanol biofuels. Proc. Natl Acad. Sci. USA, 103, 11206-11210.
18. Hojilla-Evangelista, M.P., Evangelista, R.L., Isbell, T.A., and, Selling, G.W., (2013) Effects of cold-pressing and seed cooking on functional properties of protein in pennycress (Thlaspi arvense L.) seed and press cakes. Ind. Crops Prod. 45, 223-229.
19. Hu, T.T., Pattyn, P., Bakker, E.G., et al. (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat. Genet. 43, 476-481.
20. Hume, L., Devine, M.D., and, Shirriff, S., (1995) The influence of temperature upon physiological processes in early-flowering and late-flowering strains of Thlaspi arvense L. Int. J. Plant Sci. 156, 445-449.
21. Irwin, J.A., Lister, C., Soumpourou, E., et al. (2012) Functional alleles of the flowering time regulator FRIGIDA in the Brassica oleracea genome. BMC Plant Biol. 12, 21.
22. Isbell, T.A., and, Cermak, S.C., (2012) Extraction of pennycress (Thlaspi arvense L.) seed oil by full pressing. Ind. Crops Prod. 37, 76-81.
23. Johanson, U., West, J., Lister, C., et al. (2000) Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time. Science, 290, 344-347.
24. Johnston, J.S., (2005) Evolution of genome size in Brassicaceae. Ann. Bot. 95, 229-235.
25. Jung, C., and, Müller, A.E., (2009) Flowering time control and applications in plant breeding. Trends Plant Sci. 14, 563-573.
26. Kaul, S., Koo, H.L., Jenkins, J., et al. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
27. Kim, D.-H., Doyle, M.R., Sung, S., et al. (2009) Vernalization: winter and the timing of flowering in plants. Annu. Rev. Cell Dev. Biol. 25, 277-299.
28. Kuchernig, J.C., Backenkohler, A., Lubbecke, M., et al. (2011) A thiocyanate-forming protein generates multiple products upon allylglucosinolate breakdown in Thlaspi arvense. Phytochemistry, 72, 1699-1709.
29. Kurowska, M., Daszkowska-Golec, A., Gruszka, D., et al. (2011) TILLING-a shortcut in functional genomics. J. Appl. Genet. 52, 371-390.
30. Lamesch, P., Berardini, T.Z., Li, D.H., et al. (2012) The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res. 40, D1202-D1210.
31. McCallum, C.M., Comai, L., Greene, E.A., et al. (2000) Targeting induced local lesions in genomes (TILLING) for plant functional genomics. Plant Physiol. 123, 439-442.
32. Mcintyre, G.I., and, Best, K.F., (1978) Studies on flowering of Thlaspi arvense L. 4. Genetic and ecological differences between early-flowering and late-flowering strains. Bot. Gaz. 139, 190-195.
33. Michaels, S.D., and, Amasino, R.M., (2001) Loss of FLOWERING LOCUS C activity eliminates the late-flowering phenotype of FRIGIDA and autonomous pathway mutations but not responsiveness to vernalization. Plant Cell, 13, 935-941.
34. Milner, M.J., and, Kochian, L.V., (2008) Investigating heavy-metal hyperaccumulation using Thlaspi caerulescens as a model system. Ann. Bot. 102, 3-13.
35. Mitich, L.W., (1996) Field pennycress (Thlaspi arvense L.)-the stinkweed. Weed Technol. 10, 675-678.
36. Moser, B.R., Knothe, G., Vaughn, S.F., et al. (2009a) Production and evaluation of biodiesel from field pennycress (Thlaspi arvense L.) oil. Energy Fuels, 23, 4149-4155.
37. Moser, B.R., Shah, S.N., Winkler-Moser, J.K., et al. (2009b) Composition and physical properties of cress (Lepidium sativum L.) and field pennycress (Thlaspi arvense L.) oils. Ind. Crops Prod. 30, 199-205.
38. Nour-Eldin, H.H., Andersen, T.G., Burow, M., et al. (2012) NRT/PTR transporters are essential for translocation of glucosinolate defence compounds to seeds. Nature, 488, 531-534.
39. Phippen, W.B., and, Phippen, M.E., (2012) Soybean seed yield and quality as a response to field pennycress residue. Crop Sci. 52, 2767-2773.
40. R Development Core Team (2008) R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing.
41. Schranz, M.E., Quijada, P., Sung, S.B., et al. (2002) Characterization and effects of the replicated flowering time gene FLC in Brassica rapa. Genetics, 162, 1457-1468.
42. Selling, G.W., Hojilla-Evangelista, M.P., Evangelista, R.L., et al. (2013) Extraction of proteins from pennycress seeds and press cake. Ind. Crops Prod. 41, 113-119.
43. Sharma, N., Cram, D., Huebert, T., et al. (2007) Exploiting the wild crucifer Thlaspi arvense to identify conserved and novel genes expressed during a plant's response to cold stress. Plant Mol. Biol. 63, 171-184.
44. Sheldon, C.C., Rouse, D.T., Finnegan, E.J., et al. (2000) The molecular basis of vernalization: the central role of FLOWERING LOCUS C (FLC). Proc. Natl Acad. Sci. USA, 97, 3753-3758.
45. Simpson, G.G., (2002) Arabidopsis, the Rosetta stone of flowering time? Science, 296, 285-289.
46. Slotte, T., Hazzouri, K.M., Ågren, J.A., et al. (2013) The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat. Genet., 45, 831-835.
47. Snapp, S.S., Swinton, S.M., Labarta, R., et al. (2005) Evaluating cover crops for benefits, costs and performance within cropping system niches. Agron. J. 97, 322-332.
48. Tadege, M., Sheldon, C.C., Helliwell, C.A., et al. (2001) Control of flowering time by FLC orthologues in Brassica napus. Plant J. 28, 545-553.
49. Tilman, D., Socolow, R., Foley, J.A., et al. (2009) Beneficial biofuels-the food, energy, and environment trilemma. Science, 325, 270-271.
50. Varshney, R.K., Nayak, S.N., May, G.D., et al. (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol. 27, 522-530.
51. Vaughn, S.F., Isbell, T.A., Weisleder, D., et al. (2005) Biofumigant compounds released by field pennycress (Thlaspi arvense) seedmeal. J. Chem. Ecol. 31 167-177.
52. Wang, N.A., Qian, W., Suppanz, I., et al. (2011a) Flowering time variation in oilseed rape (Brassica napus L.) is associated with allelic variation in the FRIGIDA homologue BnaA.FRI.a. J. Exp. Bot. 62, 5641-5658.
53. Wang, X.W., Wang, H.Z., Wang, J., et al. (2011b) The genome of the mesopolyploid crop species Brassica rapa. Nat. Genet. 43, 1035-1039.
54. Warwick, S.I., Francis, A., and, Susko, D.J., (2002) The biology of Canadian weeds. 9. Thlaspi arvense L. (updated). Can. J. Plant Sci. 82, 803-823.
55. Winchester, N., McConnachie, D., Wollersheim, C., and, Waitz, I., (2013) Market cost of renewable jet fuel adoption in the United States Massachusetts Institute of Technology. http://globalchange.mit.edu/files/document/MITJPSPGC- Rpt238.pdf
56. Wittstock, U., and, Burow, M., (2010) Glucosinolate breakdown in Arabidopsis: mechanism, regulation and biological significance. Arabidopsis Book, 8, e0134.
57. Yuan, Y.X., Wu, J., Sun, R.F., et al. (2009) A naturally occurring splicing site mutation in the Brassica rapa FLC1 gene is associated with variation in flowering time. J. Exp. Bot. 60, 1299-1308.
58. Zhao, Q.Y., Wang, Y., Kong, Y.M., et al. (2011) Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinformatics, 12 (Suppl. 14), S2.