Plant Physiology 135:1179-1197 (2004)
© 2004 American Society of Plant Biologists
GENOME ANALYSIS
Computational Identification and Characterization of Novel Genes from Legumes1,[w]
Michelle A. Graham2,
Kevin A.T. Silverstein2,
Steven B. Cannon and
Kathryn A. VandenBosch*
Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108
The Fabaceae, the third largest family of plants and the source of many crops, has been the target of many genomic studies. Currently, only the grasses surpass the legumes for the number of publicly available expressed sequence tags (ESTs). The quantity of sequences from diverse plants enables the use of computational approaches to identify novel genes in specific taxa. We used BLAST algorithms to compare unigene sets from Medicago truncatula, Lotus japonicus, and soybean (Glycine max and Glycine soja) to nonlegume unigene sets, to GenBank's nonredundant and EST databases, and to the genomic sequences of rice (Oryza sativa) and Arabidopsis. As a working definition, putatively legume-specific genes had no sequence homology, below a specified threshold, to publicly available sequences of nonlegumes. Using this approach, 2,525 legume-specific EST contigs were identified, of which less than three percent had clear homology to previously characterized legume genes. As a first step toward predicting function, related sequences were clustered to build motifs that could be searched against protein databases. Three families of interest were more deeply characterized: F-box related proteins, Pro-rich proteins, and Cys cluster proteins (CCPs). Of particular interest were the >300 CCPs, primarily from nodules or seeds, with predicted similarity to defensins. Motif searching also identified several previously unknown CCP-like open reading frames in Arabidopsis. Evolutionary analyses of the genomic sequences of several CCPs in M. truncatula suggest that this family has evolved by local duplications and divergent selection.
1 This work was supported by the National Science Foundation Plant Genome Research Program (award on Medicago truncatula genomics; grant no. 0110206 to D.R.C.) and by the University of Minnesota College of Biological Sciences.
2 These authors contributed equally to the paper.
[w] The online version of this article contains Web-only data.
www.plantphysiol.org/cgi/doi/10.1104/pp.104.037531.
* Corresponding author; e-mail kvandenb{at}cbs.umn.edu; fax 612–625–1738.
Received December 10, 2003;
returned for revision April 1, 2004;
accepted April 3, 2004.
This article has been cited by other articles:
|
|
|
|
 
H. C. Pelissier, W. S. Peters, R. Collier, A. J. E. v. Bel, and M. Knoblauch
GFP Tagging of Sieve Element Occlusion (SEO) Proteins Results in Green Fluorescent Forisomes
Plant Cell Physiol.,
November 1, 2008;
49(11):
1699 - 1710.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
T. Vernie, S. Moreau, F. de Billy, J. Plet, J.-P. Combier, C. Rogers, G. Oldroyd, F. Frugier, A. Niebel, and P. Gamas
EFD Is an ERF Transcription Factor Involved in the Control of Nodule Number and Differentiation in Medicago truncatula
PLANT CELL,
October 1, 2008;
20(10):
2696 - 2713.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
M. A. Campbell, W. Zhu, N. Jiang, H. Lin, S. Ouyang, K. L. Childs, B. J. Haas, J. P. Hamilton, and C. R. Buell
Identification and Characterization of Lineage-Specific Genes within the Poaceae
Plant Physiology,
December 1, 2007;
145(4):
1311 - 1322.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
B. H. Le, J. A. Wagmaister, T. Kawashima, A. Q. Bui, J. J. Harada, and R. B. Goldberg
Using Genomics to Study Legume Seed Development
Plant Physiology,
June 1, 2007;
144(2):
562 - 574.
[Full Text]
[PDF]
|
|
|
|
|
|
|
D. A. Samac and M. A. Graham
Recent Advances in Legume-Microbe Interactions: Recognition, Defense Response, and Symbiosis from a Genomic Perspective
Plant Physiology,
June 1, 2007;
144(2):
582 - 587.
[Full Text]
[PDF]
|
|
|
|
|
|
|
M.-X. Chou, X.-Y. Wei, D.-S. Chen, and J.-C. Zhou
Thirteen nodule-specific or nodule-enhanced genes encoding products homologous to cysteine cluster proteins or plant lipid transfer proteins are identified in Astragalus sinicus L. by suppressive subtractive hybridization
J. Exp. Bot.,
August 1, 2006;
57(11):
2673 - 2685.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
F. Goes da Silva, A. Iandolino, F. Al-Kayal, M. C. Bohlmann, M. A. Cushman, H. Lim, A. Ergul, R. Figueroa, E. K. Kabuloglu, C. Osborne, et al.
Characterizing the Grape Transcriptome. Analysis of Expressed Sequence Tags from Multiple Vitis Species and Development of a Compendium of Gene Expression during Berry Development
Plant Physiology,
October 1, 2005;
139(2):
574 - 597.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
L. Sauviac, A. Niebel, A. Boisson-Dernier, D. G. Barker, and F. de Carvalho-Niebel
Transcript enrichment of Nod factor-elicited early nodulin genes in purified root hair fractions of the model legume Medicago truncatula
J. Exp. Bot.,
September 1, 2005;
56(419):
2507 - 2513.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
K. A.T. Silverstein, M. A. Graham, T. D. Paape, and K. A. VandenBosch
Genome Organization of More Than 300 Defensin-Like Genes in Arabidopsis
Plant Physiology,
June 1, 2005;
138(2):
600 - 610.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
H. Zhu, H.-K. Choi, D. R. Cook, and R. C. Shoemaker
Bridging Model and Crop Legumes through Comparative Genomics
Plant Physiology,
April 1, 2005;
137(4):
1189 - 1196.
[Full Text]
[PDF]
|
|
|
|
|
|
|
M. Ramirez, M. A. Graham, L. Blanco-Lopez, S. Silvente, A. Medrano-Soto, M. W. Blair, G. Hernandez, C. P. Vance, and M. Lara
Sequencing and Analysis of Common Bean ESTs. Building a Foundation for Functional Genomics
Plant Physiology,
April 1, 2005;
137(4):
1211 - 1227.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
