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An EST survey of the sugarcane transcriptome

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Abstract

Its large genome and high polyploidy makes sugarcane (Saccharum spp.) a singularly challenging crop to study and improve using genetic approaches. To provide large numbers of functionally characterized candidate genes that might be tested for direct association (rather than distant linkage) with economically important traits, we sequenced the 5′ ends of 9,216 clones from three cDNA libraries (apex, leaf and mature internode), representing 3,401 non-redundant sequences. About 57% of these sequences could be assigned a tentative function based on statistically significant similarity to previously characterized proteins or DNA sequences. Another 28% corresponded to previously identified, but uncharacterized, sequences. Some of the remaining unidentified sequences were predicted to be genes which could potentially be new to plants or unique to sugarcane. Comparisons of the sugarcane ESTs to a large sorghum EST database revealed similar compositions of expressed genes between some different tissues. Comparison to a detailed Arabidopsis protein database showed some highly conserved sequences, which might be useful DNA markers for pan-angiosperm comparative mapping. These EST sequences provide a foundation for many new studies to accelerate isolation of agronomically important genes from the cumbersome sugarcane genome.

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References

  • Al-Janabi SM, McClelland M, Peterson C, Sobral BWS (1994) Phylogenetic analysis of organellar DNA sequences in the Andropogoneae: Saccharinae. Theor Appl Genet 88:933–944

    CAS  Google Scholar 

  • Baulcombe DC (1999) Fast forward genetics based on virus-induced gene silencing. Curr Opin Plant Biol 2:109–113

    CAS  PubMed  Google Scholar 

  • Benda, GTA (1969) Numbering sugarcane leaves and shoots. Sugarcane Pathol Newsl 3:16–18

    Google Scholar 

  • Berding N, Roach BT (1987) Germplasm collection, maintenance, and use. In: Heinz DJ (ed) Sugarcane improvement through breeding. Elsevier, Amsterdam, pp 143–210

  • Cai WW, Reneker J, Chow CW, Vaishnav M, Bradley A (1998) An anchored framework BAC map of mouse chromosome 11 assembled using multiplex oligonucleotide hybridization. Genomics 54:387–397

    Article  PubMed  Google Scholar 

  • Carson DL, Botha FC (2000) Preliminary analysis of expressed sequence tags for sugarcane. Crop Sci 40:1769–1779

    CAS  Google Scholar 

  • Carson DL, Botha FC (2002) Genes expressed in sugarcane maturing internodal tissue. Plant Cell Rep 20:1075–1081

    Article  Google Scholar 

  • Carson DL, Huckett BI, Botha FC (2002) Sugarcane ESTs differentially expressed in immature and maturing internodal tissue. Plant Sci 162:289–300

    Article  Google Scholar 

  • Cashmore AR, Broadhurst MK, Gray RE (1978) Cell-free synthesis of leaf protein: Identification of an apparent precursor of the small subunit of ribulose-1, 5-bisphosphate carboxylase. Proc Natl Acad Sci USA 75:655–659

    CAS  Google Scholar 

  • Church GM, Gilbert W (1984) Genomic sequencing. Proc Natl Acad Sci USA 81:1991–1995

    CAS  PubMed  Google Scholar 

  • Daugrois JH, Grivet L, Roques D, Hoarau JY, Lombard H, Glaszmann JC, D’Hont A (1996) A putative major gene for rust resistance linked with a RFLP marker in sugarane cultivar ‘R5 70’. Theor Appl Genet 92:1059–1064

    Article  CAS  Google Scholar 

  • Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred II Error probabilities. Genome Res 8:186–194

    CAS  PubMed  Google Scholar 

  • Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred I Accuracy assessment. Genome Res 8:175–185

    CAS  PubMed  Google Scholar 

  • Ewing RM, Kahla AB, Poirot O, Lopez F, Audic S, Claverie J-M (1999) Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression. Genome Res 9:950–959

    CAS  PubMed  Google Scholar 

  • Gordon D, Abajian C, Green P (1998) Consed: a graphical toll for sequence finishing. Genome Res 8:195–202

    CAS  PubMed  Google Scholar 

  • Hawker, JS (1985) Sucrose. In: Dey PM, Dixon RA (eds) Biochemistry of storage carbohydrates in green plants. Academic Press, New York, pp 1–51

  • Koch KE (1996) Carbohydrate-modulated gene expression in plants. Annu Rev Plant Physiol Plant Mol Biol 47:509–540

    CAS  Google Scholar 

  • Kohom BD (2000) Plasma membrane-cell wall contacts. Plant Physiol 124:31–38

    Article  PubMed  Google Scholar 

  • Krakowski K, Bunville J, Seto J, Baskin D, Seto, D (1995) Rapid purification of fluorescent dyelabeled products in a 96-well format for high-throughput automated DNA sequencing. Nucleic Acids Res 23:4930–4931

    PubMed  Google Scholar 

  • Marra MA, Hillier L, Waterston RH (1998) Expressed sequence tags - ESTablishing bridges between genomes. Trends Genet 14:4–7

    Article  PubMed  Google Scholar 

  • Ming R, Liu S-C, Lin Y-R, da Silva J, Wilson W, Braga D, van Deynze A, Wenslaff TE, Wu KK, Moore PH, Burnquist W, Sorrells ME, Irvine JE, Paterson AH (1998) Detailed alignment of the saccharum and sorghum chromosomes: comparative organization of closely related diploid and polyploid genomes. Genetics 150:1663–1682

    CAS  PubMed  Google Scholar 

  • Ming R, Liu S-C, Moore PH, Irvine JE, Paterson AH (2001) QTL analysis in a complex autopolyploid: genetic control of sucrose content in suarcane. Genome Res 11:2075–2084

    CAS  PubMed  Google Scholar 

  • Mullikin J, McMurray A (1999) Sequencing the Genome, Fast. Science 283:1867–1868

    Article  PubMed  Google Scholar 

  • Nielsen R, Yang Z (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929–936.

    CAS  PubMed  Google Scholar 

  • Nizetic D, Drmanac R, Lehrach H (1991) An improved bacterial colony lysis procedure enables direct DNA hybridisation using short (10, 11 bases) oligonucleotides to cosmids. Nucleic Acids Res 19:182

    PubMed  Google Scholar 

  • Peterson DG, Schulze SR, Sciara EB, Lee SA, Bowers JE, Nagel A, Jiang N, Tibbitts DC, Wessler SR, Paterson AH (2002a) Integration of cot analysis, DNA cloning, and high throughput sequencing facilitates genome characterization and gene discovery. Genome Res 12:795–807

    Article  PubMed  Google Scholar 

  • Peterson DG, Wessler SR, Paterson AH (2002b) Efficient capture of sequence complexity using Cot-based cloning and sequencing. Trends Genet 18:547–550

    Article  PubMed  Google Scholar 

  • Schmid KJ, Nigro L, Aquadro CF, Tautz D (1999) Large number of replacement polymorphisms in rapidly evolving genes of Drosophila: implications for genome-wide surveys of DNA polymorphism. Genetics 153:1717–1729

    PubMed  Google Scholar 

  • Shaw A (2000) The 14–3-3 proteins. Curr Biol 10:R400

    Article  PubMed  Google Scholar 

  • Swanson WJ, Clark AG, Waldrip-Dail HM, Wolfner MT, Aquadro CF (2001a) Evolutionary EST analysis identifies rapidly evolving male reproductive proteins in Drosophila. Proc Natl Acad Sci USA 98:7375–7379

    Article  PubMed  Google Scholar 

  • Swanson WJ, Yang Z, Wolfner MF, Aquadro CF (2001b) Positive Darwinian selection drives the evolution of several reproductive proteins in mammals. Proc Natl Acad Sci USA, 98:2509–2514

    Google Scholar 

  • Wang M-B, Waterhouse PM (2001) Application of gene silencing in plants. Curr Opin Plant Biol 5:146–150

    Article  Google Scholar 

  • Wu KK, Burnquist W, Sorrells ME, Tew TL, Moore PH, Tanksley SD (1992) The detection and estimation of linkage in polyploids using single-dose restriction fragments. Theor Appl Genet 83:294–300

    Google Scholar 

  • Yang Z (1998) Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol 15:568–573

    PubMed  Google Scholar 

  • Yang Z, Nielsen R, Goldman N, Krabbe Pedersen AM (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431–449

    Google Scholar 

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Acknowledgements

This work was funded by the International Consortium for Sugarcane Biotechnology. We thank Meizhu Yang and Dr. Yang Si for making the sugarcane leaf and internode libraries and Dr Veera Padmanabhan for the apex library. We also thank Dr. John Bowers and Dr. Alan Gingle for assistance in data processing.

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Author notes

  1. H.-M. Ma

    Present address: USDA/ARS, US National Arboretum, 3501 New York Ave. NE, Washington, DC 20002, USA

Authors and Affiliations

  1. Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Rd., Athens, GA 30602, USA

    H.-M. Ma, S. Schulze, S. Lee & A. Paterson

  2. Department of Plant Pathology and Microbiology, Texas A&M Agricultural Experiment Station, 2415 East Hwy. 83, Weslaco, TX 78596, USA

    M. Yang & E. Mirkov

  3. Department of Soil and Crop Sciences, Texas A&M Agricultural Experiment Station, 241 Hwy. 83, Weslaco, TX 78596, USA

    J. Irvine

  4. USDA-ARS at Hawaii Agriculture Research Center, 99-193 Aiea Heights Dr, Aiea, HI 9, USA

    P. Moore

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  1. H.-M. Ma
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  2. S. Schulze
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  3. S. Lee
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  4. M. Yang
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  7. P. Moore
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  8. A. Paterson
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Corresponding author

Correspondence to A. Paterson.

Additional information

Communicated by D.A. Hoisington

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Ma, HM., Schulze, S., Lee, S. et al. An EST survey of the sugarcane transcriptome. Theor Appl Genet 108, 851–863 (2004). https://doi.org/10.1007/s00122-003-1510-y

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  • DOI: https://doi.org/10.1007/s00122-003-1510-y

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