Abstract
A large collection of expressed sequence tags (ESTs) have been generated for Medicago truncatula. With the progress of genome sequencing, M. truncatula has become a model legume for genomics. However, the sequence and related information is distributed across several sites, and thus not organized in an optimal way for genomic studies. We developed computational methods to transform, clean and load the sequence data into a local warehouse, and to integrate the data with other information from major public databases (e.g. GenBank, Pfam and PDB). The integrated database system allows us to build web-based tools for genomics target selection. For our own research, the system permits a genome-wide search for genes that may be involved in legume-specific biological processes. The database and related bioinformatic tools are available at http://bioinfo.noble.org/.
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References
Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL (2002) The Pfam protein families database. Nucleic Acids Res. 30: 276–280.
Boisson-Dernier A, Chabaud M, Garcia F, Becard G, Rosenberg C, Barker DG (2001) Agrobacterium rhizogenes-transformed roots of Medicago truncatula for the study of nitrogen-fixing and endomycorrhizal symbiotic associations. Mol. Plant Microbe Interact. 14: 695–700.
Cook DR (1999) Medicago truncatula– a model in the making. Curr. Opin. Plant Biol. 2: 301–304.
Dixon RA, Steele CL (1999) Flavonoids and isoflavonoids–a gold mine for metabolic engineering. Trends Plant Sci. 4: 394–400.
Dixon RA, Sumner LW (2003) Legume natural products: understanding and manipulating complex pathways for human and animal health. Plant Physiol. 131: 878–885.
Ewing RM, Kahla AB, Poirot O, Lopez F, Audic S, Claverie JM (1999) Large-scale statistical analysis of rice ESTs reveal correlated patterns of gene expression. Genome Res. 9: 950–959.
Fedorova M, Van De Mortel J, Matsumoto P, Cho J, Town C, VandenBosch K, Gantt J, Vance C (2002) Genome-wide identification of nodule-specific transcripts in the model legume Medicago truncatula. Plant Physiol. 130: 519–537.
Frugoli J, Harris J (2001) Medicago truncatula on the move! Plant Cell 13: 458–463.
Harrison MJ (1999) Molecular and cellular aspects of arbuscular mycorrhizal symbiosis. Annu. Rev. Plant Physiol. Plant Mol. Biol. 50: 361–389.
Journet E, van Tuinen D, Gouzy J, Crespeau H, Carreau V, Farmer M, Niebel A, Schiex T, Jaillon O, Chatagnier O, Godiard L, Micheli F, Kahn D, Gianinazzi-Pearson V, Gamas P (2002) Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis. Nucleic Acids Res. 30: 5579–5592.
Leser U, Lehrach H, Roest-Crollius H (1998) Issues in developing integrated genomic databases and application to the human X chromosome. Bioinformatics 14: 583–590.
Paton NW, Khan SA, Hayes A, Moussouni F, Brass A, Eilbeck K, Goble CA, Hubbard SJ, Oliver SG (2000) Conceptual modeling of genomic information. Bioinformatics 16: 548–557.
Quackenbush J, Liang F, Holt I, Pertea G, Upton J (2000) The TIGR Gene Indices: reconstruction and representation of expressed gene sequences. Nucleic Acids Res. 28: 141–145.
Rabinowicz PD, Braun EL, Wolfe AD, Bowen B, Grotewold E (1999) Maize R2R3 Myb genes: Sequence analysis reveals amplification in the higher plants. Genetics 153: 427–444.
Riechmann JL, Heard J, Martin G, Reuber L, Jiang C, Keddie J, Adam L, Pineda O, Ratcliffe OJ, Samaha RR, Creelman R, Pilgrim M, Broun P, Zhang JZ, Ghandehari D, Sherman BK, Yu G (2000) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290: 2105–2110.
Shepherd AJ, Martin NJ, Johnson RG, Kellam P, Orengo CA (2002) PFDB: a generic protein family database integrating the CATH domain structure database with sequence based protein family resources. Bioinformatics 18: 1666–1672.
Shoop E, Silverstein KA, Johnson JE, Retzel EF (2001) MetaFam: a unified classification of protein families. II. Schema and query capabilities. Bioinformatics 17: 262–271.
Somers DA, Samac DA, Olhoft PM (2003) Recent advances in Legume transformation. Plant Physiol. 131: 892–899.
Stougaard J (2000) Regulators and regulation of legume root nodule development. Plant Physiol. 124: 531–540.
Stougaard J (2001) Genetics and genomics of root symbiosis. Curr. Opin. Plant Biol. 4: 328–335.
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Wang, L., Zhang, Y. (2004). Data Integration and Target Selection for Medicago Genomics. In: Hopkins, A., Wang, ZY., Mian, R., Sledge, M., Barker, R.E. (eds) Molecular Breeding of Forage and Turf. Developments in Plant Breeding, vol 11. Springer, Dordrecht. https://doi.org/10.1007/1-4020-2591-2_23
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DOI: https://doi.org/10.1007/1-4020-2591-2_23
Publisher Name: Springer, Dordrecht
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