Sequencing and analysis of common bean ESTs. Building a foundation for functional genomics

Plant Physiology

Volumn 137, Issue 4, 2005, Pages 1211-1227

  Ramírez, Mario ^a,b   Graham, Michelle A ^b   Blanco López, Lourdes ^a   Silvente, Sonia ^a   Medrano Soto, Arturo ^a   Blair, Matthew W ^d   Hernández, Georgina ^a   Vance, Carroll P ^b,c   Lara, Miguel ^a  

^a INSTITUTO DE CIENCIAS FÍSICAS   (Mexico)

^b UNIVERSITY OF MINNESOTA   (United States)

^c U S DEPARTMENT OF AGRICULTURE   (United States)

^d INTERNATIONAL CENTER FOR TROPICAL AGRICULTURE CIAT   (Colombia)

Author keywords

[No Author keywords available]

Indexed keywords

ARRAYS; DNA; GENES; METABOLISM; RNA;

EXPRESSED SEQUENCE TAG (EST); GENOMIC RESOURCES;

PLANTS (BOTANY);

GENES; METABOLISM; NUCLEIC ACIDS; PLANTS;

PHASEOLUS (ANGIOSPERM); PHASEOLUS VULGARIS;

CARBON; COMPLEMENTARY DNA; NITROGEN; PLANT DNA; PLANT RNA;

ARTICLE; BEAN; COMPARATIVE STUDY; DNA MICROARRAY; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENE LIBRARY; GENETICS; GENOMICS; METABOLISM; MOLECULAR GENETICS; MULTIGENE FAMILY; NITROGEN FIXATION; PLANT ROOT; SINGLE NUCLEOTIDE POLYMORPHISM;

CARBON; DNA, COMPLEMENTARY; DNA, PLANT; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE LIBRARY; GENOMICS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; NITROGEN; NITROGEN FIXATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHASEOLUS; PLANT ROOTS; POLYMORPHISM, SINGLE NUCLEOTIDE; RNA, PLANT;

EID: 20444490755     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: 10.1104/pp.104.054999     Document Type: Conference Paper

References (34)

1. 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
2. Appels MA, Haaker H (1991) Glutamate oxalacetate transaminase in pea root nodules. Plant Physiol 95: 740-747
3. Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, et al (2004) UniProt: the universal protein knowledgebase. Nucleic Acids Res 32: D115-D119
4. Blair MW, Pedraza F, Buendia HF, Gaitán-Solís E, Beebe SE, Gepts P, Tohme J (2003) Development of a genome-wide anchored microsatellite map for common bean (Phaseolus vulgaris L.). Theor Appl Genet 107: 1362-1374
5. Broughton WJ, Hernández G, Blair M, Beebe S, Gepts P, Vanderleyden J (2003) Beans (Phaseolus spp.) - model food legume. Plant Soil 252: 55-128
6. Colebatch G, Desbrosses G, Ott T, Krusell L, Montanari O, Kloska S, Kopka J, Udvardi MK (2004) Global changes in transcription orchestrate metabolic differentiation during symbiotic nitrogen fixation in Lotus japonicus. Plant J 39: 487-512
7. Colebatch G, Sebastian K, Ben T, Susanne F, Thomas A, Udvardi MK (2002) Novel aspects of symbiotic nitrogen fixation uncovered by transcript profiling with cDNA arrays. Mol Plant Microbe Interact 15: 411-420
8. Cook DR (1999) Medicago truncatula a model in the making. Curr Opin Plant Biol 2: 301-304
9. Deroche ME, Carrayol E (1988) Nodule phosphoenolpyruvate carboxylase: a review. Physiol Plant 74: 775-782
10. 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
11. Fedorova M, Van De Mortel J, Matsumoto PA, Cho J, Town CD, Vanden-Bosch KA, Gantt JS, Vance CP (2002) Genome-wide identification of nodule-specific transcripts in the model legume Medicago truncatula. Plant Physiol 130: 519-537
12. Food and Agriculture Organization of the United Nations (2001) FAOSTAT Agriculture Data. http://www.fao.org/Statistics
13. Gantt JS, Larson RJ, Farnham MW, Pathirana SM, Miller SS, Vance CP (1992) Aspartate aminotransferase in effective and ineffective alfalfa nodules. Plant Physiol 98: 868-878
14. Gepts P (1998) Origin and evolution of common bean: past events and recent trends. Hort Sci 33: 1124-1130
15. Graham MA, Silverstein KAT, Cannon SB, VandenBosch KA (2004) Computational identification and characterization of novel genes from legumes. Plant Physiol 135: 1179-1197
16. Graham PH, Vance CP (2003) Legumes: importance and constraints to greater use. Plant Physiol 131: 872-877
17. Györgyey J, Vaubert D, Jimenez-Zurdo JI, Charon C, Troussard L, Kondorosi A, Kondorosi E (2000) Analysis of Medicago truncatula nodule expressed sequence tags. Mol Plant Microbe Interact 13: 62-71
18. Handberg K, Stougaard J (1992) Lotus japonicus, an autogamous, diploid legume species for classical and molecular genetics. Plant J 2: 487-496
19. Journet EP, van Tuinen D, Gouzy J, Crespeau H, Carreau V, Farmer MJ, Niebel A, Schiex T, Jaillon O, Chatagnier O, et al (2002) Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis. Nucleic Acids Res 30: 5579-5592
20. Lamblin AF, Crow JA, Johnson JE, Silverstein KA, Kunau TM, Kilian A, Benz D, Stromvik M, Endre G, VandenBosch KA, et al (2003) MtDB: a database for personalized data mining of the model legume Medicago truncatula transcriptome. Nucleic Acids Res 31: 196-201
21. Lara M, Porta H, Padilla J, Folch J, Sánchez F (1984) Heterogeneity of glutamine synthetase polypeptides in Phaseolus vulgaris L. Plant Physiol 76: 1019-1023
22. Lee HL, Hur CG, Oh CJ, Kim HB, Park SY, An CS (2004) Analysis of the root nodule-enhanced transcriptome in soybean. Mol Cells 18: 53-62
23. Liao H, Van X, Rubio G, Beebe SE, Blair MW, Lynch JP (2004) Basal root gravitropism and phosphorus acquisition efficiency in common bean. Funct Plant Biol 31: 959-970
24. McClean P, Kami J, Gepts P (2004) Genomic and genetic diversity in common bean. In RF Wilson, HT Stalker, EC Brummer, eds, Legume Crop Genomics. AOCS Press, Champaign, IL, pp 60-82
25. Morales M, Roig E, Monforte AJ, Arús P, Garcia-Mas J (2004) Single-nucleotide polymorphisms detected in expressed sequence tags of melon (Cucumis melo L.). Genome 47: 352-360
26. 2 levels in bean (Phaseolus vulgaris L.). Plant Physiol 98: 584-587
27. Quackenbush J, Cho J, Lee D, Liang F, Holt I, Karamycheva S, Parvizi B, Pertea G, Sultana R, White J (2001) The TIGR gene indices: analysis of gene transcript sequence in highly sampled eukaryotic species. Nucleic Acids Res 29: 159-164
28. Russell J, Booth A, Fuller J, Harrower B, Hedley P, Machray G, Powell W (2004) A comparison of sequence-based polymorphism and haplotype content in transcribed and anonymous regions of the barley genome. Genome 47: 389-398
29. Silvente S, Camas A, Lara M (2003) Molecular cloning of the cDNA encoding aspartate aminotransferase from bean root nodules and determination of its role in nodule nitrogen metabolism. J Exp Bot 54: 1545-1551
30. Temple SJ, Vance CP, Gantt JS (1998) Glutamate synthase and nitrogen assimilation. Trends Plant Sci 3: 51-56
31. Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc Natl Acad Sci USA 98: 9161-9166
32. Uhde-Stone C, Zinn KE, Ramírez-Yañez M, Li A, Vance CP, Allan DL (2003) Nylon filters array reveal different gene expression in proteoid roots of white lupin in response to phosphorus deficiency. Plant Physiol 131: 1064-1079
33. Yan X, Liao H, Beebe SE, Blair MW, Lynch JP (2005) Molecular mapping of QTLs associated with root hairs and acid exudation as related to phosphorus uptake in common bean. Plant Soil (in press)
34. Zhu YL, Song QJ, Hyten DL, Tassell CP, van Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB (2003) Single-nucleotide polymorphisms in soybean. Genetics 163: 1123-1134