Hostname: page-component-cd9895bd7-gxg78 Total loading time: 0 Render date: 2024-12-22T19:38:16.327Z Has data issue: false hasContentIssue false
  • English
  • Français

Random sequencing of cDNAs and identification of mRNAs

Published online by Cambridge University Press:  20 January 2017

James V. Anderson  and
David P. Horvath
David P. Horvath
Affiliation:
U.S. Department of Agriculture, Agricultural Research Service, Biosciences Research Laboratory, Plant Science Research, 1605 Albrecht Boulevard, P.O. Box 5674, Fargo, ND 58105
Get access Rights & Permissions [Opens in a new window]

Abstract

As a first step toward developing a genomics-based research program to study growth and development of underground adventitious shoot buds of leafy spurge, we initiated a leafy spurge expressed sequence tag (EST) database. From the approximately 2,000 clones randomly isolated from a cDNA library made from a population containing growth-induced underground adventitious shoot buds, we have obtained ESTs for 1,105 cDNAs. Approximately 29% of the leafy spurge EST database consists of expressed genes of unknown identity (hypothetical proteins), and 10% represents ribosomal proteins. The remaining 60% of the database is composed of expressed genes that show BLASTX sequence identity scores of ≥ 80 with known GenBank accessions. Clones showing sequence identity to a Histone H3, a gibberellic acid-responsive gene, Tubulin, and a light-harvesting chlorophyll a/b-binding protein were shown to be differentially expressed in underground adventitious shoot buds of leafy spurge after breaking of dormancy. RNA encoding a putative cyclin-dependent protein kinase (CDK)-activating kinase, a gene associated with cell division, and Scarecrow-like 7, a gene involved in GA signaling, were present at similar levels in dormant and growth-induced underground adventitious shoot buds. These data show how even a small EST database can be used to develop a genomics-based research program that will help us identify genes responsive to or involved in the mechanisms controlling underground adventitious shoot bud growth and development.

Keywords

Amp, ampicillinCAK, CDK-activating protein kinaseCDK, cyclin-dependent protein kinaseEST, expressed sequence tagLB, Luria–Bertani brothLhcb, light-harvesting chlorophyll a/b-binding proteinNCBI, National Center for Biotechnology InformationSSC, sodium chloride sodium citrate solutionCell cycledormancygenomicsperennial weedssignal transduction
Type
Research Article
Information
Weed Science , Volume 49 , Issue 5 , October 2001 , pp. 590 - 597
Copyright
Copyright © Weed Science Society of America 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Literature Cited

Aharoni, A. L., Keizer, C. P., Bouwmeester, H. J., et al. 2000. Identification of the SAAT gene involved in strawberry flavor biogenesis by use of DNA microarrays. Plant Cell 12:647–662.CrossRefGoogle ScholarPubMed
Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389–3402.CrossRefGoogle ScholarPubMed
Anderson, J.V. and Horvath, D. P. 2000. Isolation of a cDNA clone (Accession No. AF220527) encoding a light-harvesting chlorophyll a/b-binding protein (Lhcb1) in underground adventitious buds of leafy spurge (Euphorbia esula L.). PGR00-052. Plant Physiol. 122:1457.Google Scholar
The Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana . Nature 408:796–815.CrossRefGoogle Scholar
Aubert, D., Chevillard, M., Dorne, A. M., Arlaud, G., and Herzog, M. 1998. Expression patterns of GASA genes in Arabidopsis thaliana: the GASA4 gene is up-regulated by gibberellins in meristematic regions. Plant Mol. Biol. 36:871–883.CrossRefGoogle ScholarPubMed
Bangsund, D. A., Leistritz, F. L., and Leitch, J. A. 1999. Assessing economic impacts of biological control of weeds: the case of leafy spurge in the northern great plains of the United States. J. Environ. Manag. 56:35–43.CrossRefGoogle Scholar
Biesboer, D. D. and Eckardt, N. 1996. Euphorbia esula Element Stewardship Abstract. Arlington, VA: The Nature Conservancy. pp. 1–17.Google Scholar
Boguski, M. S., Lowe, T. M., and Tolstoshev, C. M. 1993. dbEST database for “expressed sequence tags.” Nat. Genet. 4:332–333.Google Scholar
Chang, S., Puryear, J., and Cairney, J. 1993. A simple and efficient method for isolating RNA from pine trees. Plant Mol. Biol. Rep. 11:113–116.CrossRefGoogle Scholar
Chao, W. S., Anderson, J. V., and Horvath, D. P. 2000. Sugar Plays a Role in Inhibition of Underground Adventitious Bud Growth in Leafy Spurge (Euphorbia esula L.). Page 46 In Plant Biology 2000 Final Program and Abstract Supplement. Rockville, MD: American Society of Plant Biologists.Google Scholar
Coupland, R. T., Selleck, G. W., and Alex, J. F. 1955. Distribution of vegetative buds on the underground parts of leafy spurge (Euphorbia esula L.). Can. J. Agric. Sci. 35:161–167.Google Scholar
Horvath, D. P. 1999. Role of mature leaves in inhibition of root bud growth in Euphorbia esula . Weed Sci. 47:544–550.CrossRefGoogle Scholar
Horvath, D. P. and Anderson, J. V. 2000. The effect of photosynthesis on underground adventitious shoot bud dormancy/quiescence in leafy spurge (Euphorbia esula L.). Pages 30–34 in Viemont, J.-D. and Crabbe, J. J., eds. 2nd International Symposium on Plant Dormancy: Short Communications. Presses de L’Universite d’Angers and CAB International.Google Scholar
Horvath, D. P. and Olson, P. A. 1998. Cloning and characterization of cold-regulated glycine-rich RNA-binding protein genes from leafy spurge (Euphorbia esula L.) and comparison to heterologous genomic clones. Plant Mol. Biol. 38:531–538.CrossRefGoogle ScholarPubMed
Kamalay, J. C. and Goldberg, R. B. 1980. Regulation of structural gene expression in tobacco. Cell 19:935–946.CrossRefGoogle ScholarPubMed
Kato, J.-Y., Matsuoka, M., Strom, D. K., and Sherr, C. J. 1994. Regulation of cyclin D-dependent kinase 4 (cdk4) by cdk4-activating kinase. Mol. Cell. Biol. 14:2713–2721.Google ScholarPubMed
Keith, C. S., Hoang, D. O., Barrett, B. M., Feigelman, B., Nelson, M. C., Thai, H., and Baysdorfer, C. 1993. Partial sequence analysis of 130 randomly selected maize cDNA clones. Plant Physiol. 101:329–332.CrossRefGoogle ScholarPubMed
Kirby, D. R., Carlson, R. B., Krabbenhoft, K. D., Mundal, D., and Kirby, M. M. 2000. Biological control of leafy spurge with introduced flea beetles (Aphthona spp.). J. Range Manag. 53:305–308.CrossRefGoogle Scholar
Leitch, J. A., Leistritz, F. L., and Bangsund, D. A. 1996. Economic effect of leafy spurge in the upper great plains: methods, models, and results. Impact Assessment 14:419–433.CrossRefGoogle Scholar
Newman, T., de Bruijn, F. J., Green, P., et al. 1994. Genes galore: a summary of methods for accessing results from large-scale partial sequencing of anonymous Arabidopsis cDNA clones. Plant Physiol. 106:1241–1255.CrossRefGoogle ScholarPubMed
Park, Y. S., Kwak, J. M., Kwon, O.-Y., Kim, Y. S., Lee, D. S., Cho, M. J., Lee, H. H., and Nam, H. G. 1993. Generation of expressed sequence tags of random root cDNA clones of Brassica napus by single-run partial sequencing. Plant Physiol. 103:359–370.CrossRefGoogle ScholarPubMed
Pennisi, E. 2001. The human genome. Science 291:1177–1180.CrossRefGoogle ScholarPubMed
Sambrook, J., Fritsch, E. F., and Maniatis, T. 1989. Molecular Cloning, A Laboratory Manual. 2nd ed. New York: Cold Spring Harbor Laboratory Press. pp. New York.37-7.52.Google Scholar
Sauter, M. and Kende, H. 1992. Gibberellin-induced growth and regulation of the cell division cycle in deepwater rice. Planta 188:362–368.CrossRefGoogle ScholarPubMed
Sell, R. S., Bangsund, D. A., Leistritz, L. F., and Nudell, D. 1998. Perceptions of Leafy Spurge by Public Land Managers, Local Decision Makers, and Ranch Operators. Fargo, ND: North Dakota State University, Dept. of Ag. Sci. Agricultural Economic Rep. 406-S. 8 p.Google Scholar
Stein, B. A. and Flack, S. R., eds. 1996. The Dirty Dozen. America's Least Wanted: Alien Species Invasions of U.S. Ecosystems. Arlington, VA: The Nature Conservancy. Available online at http://www.consci.org/library/pubs/dd/toc.html. Last accessed July 5, 2001.Google Scholar
Uchimiya, H., Kidou, S., Shimazaki, T., et al. 1992. Random sequencing of cDNA libraries reveals a variety of expressed genes in cultured cells of rice (Oryza sativa L.). Plant J. 2:1005–1009.CrossRefGoogle Scholar
Umeda, M., Bhalerao, R. P., Schell, J., Uchimiya, H., and Koncz, C. 1998. A distinct cyclin-dependent kinase-activating kinase of Arabidopsis thaliana . Proc. Natl. Acad. Sci. USA 95:5021–5026.CrossRefGoogle ScholarPubMed