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Analysis of Expressed Sequence Tags (ESTs) from Agrostis Species Obtained Using Sequence Related Amplified Polymorphism

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Abstract

Bentgrass (Agrostis spp.), a genus of the Poaceae family, consists of more than 200 species and is mainly used in athletic fields and golf courses. Creeping bentgrass (A. stolonifera L.) is the most commonly used species in maintaining golf courses, followed by colonial bentgrass (A. capillaris L.) and velvet bentgrass (A. canina L.). The presence and nature of sequence related amplified polymorphism (SRAP) at the cDNA level were investigated. We isolated 80 unique cDNA fragment bands from these species using 56 SRAP primer combinations. Sequence analysis of cDNA clones and analysis of putative translation products revealed that some encoded amino acid sequences were similar to proteins involved in DNA synthesis, transcription, and signal transduction. The cytosolic glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene (GenBank accession no. EB812822) was also identified from velvet bentgrass, and the corresponding protein sequence is further analyzed due to its critical role in many cellular processes. The partial peptide sequence obtained was 112 amino acids long, presenting a high degree of homology to parts of the N-terminal and C-terminal regions of cytosolic phosphorylating GAPDH (GapC). The existence of common expressed sequence tags (ESTs) revealed by a minimum evolutionary dendrogram among the Agrostis ESTs indicated the usefulness of SRAP for comparative genome analysis of transcribed genes in the grass species.

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References

  • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped Blast and PSI-Blast: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  PubMed  CAS  Google Scholar 

  • Branlant G, Branlant C (1985) Nucleotide sequence of the Escherichia coligap gene. Different evolutionary behavior of the NAD+-binding domain and of the catalytic domain of glyceraldehyde-3-phosphate dehydrogenase. Eur J Biochem 150:61–66

    Article  PubMed  CAS  Google Scholar 

  • Brilman L (2003) Velvet bentgrass. In: Casler M, Duncan RR (eds) Turfgrass biology, genetics and breeding. Wiley, Hoboken, NJ, pp 201–205

    Google Scholar 

  • Budak H, Shearman RC, Gaussoin RE, Dweikat I (2004a) Application of sequence-related amplified polymorphism (SRAP) markers for characterization of turfgrass species. HortScience 39:955–958

    CAS  Google Scholar 

  • Budak H, Shearman RC, Parmaksiz I, Gaussoin RE, Riordan TP, Dweikat I (2004b) Molecular characterization of buffalograss germplasm using sequence related amplified polymorphism markers. Theor Appl Genet 108:328–334

    Article  PubMed  CAS  Google Scholar 

  • Budak H, Shearman RC, Parmaksiz I, Dweikat I (2004c) Comparative analysis of seeded and vegetative biotype buffalograsses based on phylogenetic relationship using ISSRs, SSRs, RAPDs, SRAPs. Theor Appl Genet 109:280–288

    Article  PubMed  CAS  Google Scholar 

  • Budak H, Shearman RC, Gulsen O, Dweikat I (2005a) Understanding ploidy complex and geographic origin of Buchloe dactyloides genome using cytoplasmic and nuclear marker systems. Theor Appl Genet 111:1545–1552

    Article  PubMed  CAS  Google Scholar 

  • Budak H, Shearman RC, Dweikat I (2005b) Evolution of Buchloe dactyloides based on cloning and sequencing of matK, rbcL, and cob genes from plastid and mitochondrial genomes. Genome 48:411–416

    Article  PubMed  CAS  Google Scholar 

  • Budak H, Su S, Ergen N (2006) Revealing constitutively-expressed resistance genes in Agrostis species using PCR-based motif directed RNA fingerprinting. Genet Res 88:165–175

    Article  PubMed  CAS  Google Scholar 

  • Chakraborty N, Bae J, Warnke S, Chang T, Jung G (2005) Linkage map construction in allotetraploid creeping bentgrass (Agrostis stolonifera L). Theor Appl Genet 111:795–803

    Article  PubMed  CAS  Google Scholar 

  • DeLano WL (2002) The PyMOL molecular graphics system. DeLano Scientific, San Carlos, CA, USA. Available from: http://www.pymol.org

  • Felsenstein J (1993) Phylip—phylogeny inference package (Version 3.5). University of Washington, Seattle

  • Ferriol M, Pico B, Nuez F (2003) Genetic diversity of a germplasm collection of Cucurbita pepo using SRAP and AFLP markers. Theor Appl Genet 107:271–282

    Article  PubMed  CAS  Google Scholar 

  • Fothergill-Gilmore LA, Michels PA (1993) Evolution of glycolysis. Prog Biophys Mol Biol 59(2):105–235

    Article  PubMed  CAS  Google Scholar 

  • Hitchcock AS (1971) Manual of the grasses of the United States, 2nd edn. Dover Publications, New York

    Google Scholar 

  • Jones K (1956) Species differentiation in Agrostis. I. Cytological relationships in Agrostis canina. J Genet 54:370–376

    Article  Google Scholar 

  • Kim H, Hol WG (1998) Crystal structure of Leishmania mexicana glycosomal glyceraldehyde-3-phosphate dehydrogenase in a new crystal form confirms the putative physiological active site structure. J Mol Biol 278:5–11

    Article  PubMed  CAS  Google Scholar 

  • Laxalt AM, Cassia RO, Sanllorenti PM, Madrid EA, Andreu AB, Daleo GR, Conde RD, Lamattina L (1996) Accumulation of cytosolic glyceraldehyde-3-phosphate dehydrogenase RNA under biological stress conditions and elicitor treatments in potato. Plant Mol Biol 30:961–972

    Article  PubMed  CAS  Google Scholar 

  • Li G, Quiros CF (2001) Sequence-related amplified polymorphism (SRAP) a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor Appl Genet 103:455–461

    Article  CAS  Google Scholar 

  • Macbryde B (2005) White paper: perspective on creeping bentgrass, Agrostis stolonifera L. Available from: http://www.aphis.usda.gov/about_aphis/creeping_bentgrass.shtml

  • Moras D, Olsen KW, Sabesan MN, Buehner M, Ford GC, Rossman MG (1975) Studies of asymmetry in the three-dimensional structure of lobster d-glyceraldehyde-3-phosphate dehydrogenase. J Biol Chem 250:9137–9162

    PubMed  CAS  Google Scholar 

  • Nelson EK (1985) Breeding and selection for rhizomatous colonial bentgrasses, Agrostis tenuis Sibth. PhD. thesis, Pennsylvania State University, University Park, PA

  • Ruiz JJ, Garcia-Martinez S, Pico B, Gao MQ, Quiros CF (2005) Genetic variability and relationship of closely related Spanish traditional cultivars of tomato as detected by SRAP and SSR markers. J Am Soc for Hortic Sci 130:88–94

    CAS  Google Scholar 

  • Rummele BA (2003) Colonial bentgrass. In: Casler M, Duncan RR (eds) Turfgrass biology, genetics and breeding. Wiley, Hoboken, NJ, pp 187–200

    Google Scholar 

  • Russell DA, Sachs MM (1989) Differential expression and sequence analysis of the maize glyceraldehyde-3-phosphate dehydrogenase gene family. Plant Cell 1:793–803

    Article  PubMed  CAS  Google Scholar 

  • Schwarz R, Dayhoff M (1979) Matrices for detecting distant relationships. In: Dayhoff M (ed) Atlas of protein sequences. National Biomedical Research Foundation, Washington, DC, pp 353–358

  • Skarzynski T, Moody PCE, Wonacott AJ (1987) Structure of the holo-glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus at 1.8 Å of resolution. J Mol Biol 193:171–187

    Article  PubMed  CAS  Google Scholar 

  • Velasco R, Salamini F, Bartels D (1994) Dehydration and ABA increase mRNA levels and enzyme activity of cytosolic GAPDH in the resurrection plant Craterostigma plantagineum. Plant Mol Biol 26:541–546

    Article  PubMed  CAS  Google Scholar 

  • Warnke SE (2003) Creeping bentgrass (Agrostis stolonifera L.). In: Casler M, Duncan RR (eds) Turfgrass biology, genetics and breeding. Wiley, Hoboken, NJ, pp 75–185

    Google Scholar 

  • Yang Y, Kwon HB, Peng H-P, Shih M-C (1993) Stress responses and metabolic regulation of glyceraldehyde-3-phosphate dehydrogenase genes in Arabidopsis. Plant Physiol 101:209–216

    Article  PubMed  CAS  Google Scholar 

  • Yun M, Park CG, Kim JY, Park HW (2000) Structural analysis of glyceraldehyde-3-phosphate dehydrogenase from Escherichia coli: direct evidence of substrate binding and cofactor-induced conformational changes. Biochemistry 39:10702–10710

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

The authors wish to thank Dr. Stacy Bonos for providing Agrostis species. This research was supported in part by Sabanci University Research Funding and Turkish National Academy of Science (TUBA-GEBIP).

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  1. Faculty of Engineering and Natural Sciences, Biological Science and Bioengineering Program, Sabanci University, Orhanli, Tuzla-Istanbul, 34956, Turkey

    Gizem Dinler & Hikmet Budak

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  1. Gizem Dinler
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  2. Hikmet Budak
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Correspondence to Hikmet Budak.

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Dinler, G., Budak, H. Analysis of Expressed Sequence Tags (ESTs) from Agrostis Species Obtained Using Sequence Related Amplified Polymorphism. Biochem Genet 46, 663–676 (2008). https://doi.org/10.1007/s10528-008-9181-7

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  • DOI: https://doi.org/10.1007/s10528-008-9181-7

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