Plant Cell Hybrigenics The Protein Interactions Experts
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
QUICK SEARCH:   [advanced]


     

This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via CrossRef
Right arrow Citing Articles via ISI Web of Science (106)
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Fulton, T. M.
Right arrow Articles by Tanksley, S. D.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Fulton, T. M.
Right arrow Articles by Tanksley, S. D.
Agricola
Right arrow Articles by Fulton, T. M.
Right arrow Articles by Tanksley, S. D.
The Plant Cell, Vol. 14, 1457-1467, July 2002, Copyright © 2002,
American Society of Plant Biologists

GENOMICS ARTICLE

Identification, Analysis, and Utilization of Conserved Ortholog Set Markers for Comparative Genomics in Higher Plants

Theresa M. Fulton, Rutger Van der Hoeven, Nancy T. Eannetta and Steven D. Tanksley1

Department of Plant Breeding and Department of Plant Biology, Cornell University, Ithaca, New York 14853

1 To whom correspondence should be addressed. E-mail sdt4{at}cornell.edu; fax 607-255-6683

We have screened a large tomato EST database against the Arabidopsis genomic sequence and report here the identification of a set of 1025 genes (referred to as a conserved ortholog set, or COS markers) that are single or low copy in both genomes (as determined by computational screens and DNA gel blot hybridization) and that have remained relatively stable in sequence since the early radiation of dicotyledonous plants. These genes were annotated, and a large portion could be assigned to putative functional categories associated with basic metabolic processes, such as energy-generating processes and the biosynthesis and degradation of cellular building blocks. We further demonstrate, through computational screens (e.g., against a Medicago truncatula database) and direct hybridization on genomic DNA of diverse plant species, that these COS markers also are conserved in the genomes of other plant families. Finally, we show that this gene set can be used for comparative mapping studies between highly divergent genomes such as those of tomato and Arabidopsis. This set of COS markers, identified computationally and experimentally, may further studies on comparative genomes and phylogenetics and elucidate the nature of genes conserved throughout plant evolution.




This article has been cited by other articles:


Home page
 jashsHome page
Y. Ji, J. W. Scott, D. J. Schuster, and D. P. Maxwell
Molecular Mapping of Ty-4, a New Tomato Yellow Leaf Curl Virus Resistance Locus on Chromosome 3 of Tomato
J. Amer. Soc. Hort. Sci., March 1, 2009; 134(2): 281 - 288.
[Abstract] [Full Text] [PDF]

Home page
 The Plant GenomeHome page
K. Gasic, D. O. Gonzalez, J. Thimmapuram, L. Liu, M. Malnoy, G. Gong, Y. Han, L. O. Vodkin, H. S. Aldwinckle, N. J. Carroll, et al.
Comparative Analysis and Functional Annotation of a Large Expressed Sequence Tag Collection of Apple
The Plant Genome, March 1, 2009; 2(1): 23 - 38.
[Abstract] [Full Text] [PDF]

Home page
 The Plant GenomeHome page
L. A. Mueller, R. K. Lankhorst, S. D. Tanksley, J. J. Giovannoni, R. White, J. Vrebalov, Z. Fei, J. van Eck, R. Buels, A. A. Mills, et al.
A Snapshot of the Emerging Tomato Genome Sequence
The Plant Genome, March 1, 2009; 2(1): 78 - 92.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
X. Tang, D. Szinay, C. Lang, M. S. Ramanna, E. A. G. van der Vossen, E. Datema, R. K. Lankhorst, J. de Boer, S. A. Peters, C. Bachem, et al.
Cross-Species Bacterial Artificial Chromosome-Fluorescence in Situ Hybridization Painting of the Tomato and Potato Chromosome 6 Reveals Undescribed Chromosomal Rearrangements
Genetics, November 1, 2008; 180(3): 1319 - 1328.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Bot.Home page
Y.-W. Yuan and R. G. Olmstead
Evolution and phylogenetic utility of the PHOT gene duplicates in the Verbena complex (Verbenaceae): dramatic intron size variation and footprint of ancestral recombination
Am. J. Botany, September 1, 2008; 95(9): 1166 - 1176.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
I. J. Maureira-Butler, B. E. Pfeil, A. Muangprom, T. C. Osborn, and J. J. Doyle
The Reticulate History of Medicago (Fabaceae)
Syst Biol, June 1, 2008; 57(3): 466 - 482.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
L. A. Mueller, A. A. Mills, B. Skwarecki, R. M. Buels, N. Menda, and S. D. Tanksley
The SGN comparative map viewer
Bioinformatics, February 1, 2008; 24(3): 422 - 423.
[Abstract] [Full Text] [PDF]

Home page
 J Exp BotHome page
C Espinoza, C Medina, S Somerville, and P Arce-Johnson
Senescence-associated genes induced during compatible viral interactions with grapevine and Arabidopsis
J. Exp. Bot., September 4, 2007; (2007) erm165v2.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Bot.Home page
M. D. Pirie, M. P. B. Vargas, M. Botermans, F. T. Bakker, and L. W. Chatrou
Ancient paralogy in the cpDNA trnL-F region in Annonaceae: implications for plant molecular systematics
Am. J. Botany, June 1, 2007; 94(6): 1003 - 1016.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
R. Stevens, M. Buret, P. Duffe, C. Garchery, P. Baldet, C. Rothan, and M. Causse
Candidate Genes and Quantitative Trait Loci Affecting Fruit Ascorbic Acid Content in Three Tomato Populations
Plant Physiology, April 1, 2007; 143(4): 1943 - 1953.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
F. Wu, L. A. Mueller, D. Crouzillat, V. Petiard, and S. D. Tanksley
Combining Bioinformatics and Phylogenetics to Identify Large Sets of Single-Copy Orthologous Genes (COSII) for Comparative, Evolutionary and Systematic Studies: A Test Case in the Euasterid Plant Clade
Genetics, November 1, 2006; 174(3): 1407 - 1420.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
L. Timms, R. Jimenez, M. Chase, D. Lavelle, L. McHale, A. Kozik, Z. Lai, A. Heesacker, S. Knapp, L. Rieseberg, et al.
Analyses of Synteny Between Arabidopsis thaliana and Species in the Asteraceae Reveal a Complex Network of Small Syntenic Segments and Major Chromosomal Rearrangements
Genetics, August 1, 2006; 173(4): 2227 - 2235.
[Abstract] [Full Text] [PDF]

Home page
 J Exp BotHome page
F. Carrari and A. R. Fernie
Metabolic regulation underlying tomato fruit development
J. Exp. Bot., June 1, 2006; 57(9): 1883 - 1897.
[Abstract] [Full Text] [PDF]

Home page
 Plant Cell PhysiolHome page
T. Okada, P. L. Bhalla, and M. B. Singh
Expressed Sequence Tag Analysis of Lilium longiflorum Generative Cells
Plant Cell Physiol., June 1, 2006; 47(6): 698 - 705.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
Y. Wang, X. Tang, Z. Cheng, L. Mueller, J. Giovannoni, and S. D. Tanksley
Euchromatin and Pericentromeric Heterochromatin: Comparative Composition in the Tomato Genome
Genetics, April 1, 2006; 172(4): 2529 - 2540.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
J. A. Udall, J. M. Swanson, K. Haller, R. A. Rapp, M. E. Sparks, J. Hatfield, Y. Yu, Y. Wu, C. Dowd, A. B. Arpat, et al.
A global assembly of cotton ESTs
Genome Res., March 1, 2006; 16(3): 441 - 450.
[Abstract] [Full Text] [PDF]

Home page
 Phil Trans R Soc BHome page
C. E Hughes, R. J Eastwood, and C Donovan Bailey
From famine to feast? Selecting nuclear DNA sequence loci for plant species-level phylogeny reconstruction
Phil Trans R Soc B, January 29, 2006; 361(1465): 211 - 225.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Bot.Home page
J. Syring, A. Willyard, R. Cronn, and A. Liston
Evolutionary relationships among Pinus (Pinaceae) subsections inferred from multiple low-copy nuclear loci
Am. J. Botany, December 1, 2005; 92(12): 2086 - 2100.
[Abstract] [Full Text] [PDF]

Home page
 J Exp BotHome page
S. Moore, P. Payton, M. Wright, S. Tanksley, and J. Giovannoni
Utilization of tomato microarrays for comparative gene expression analysis in the Solanaceae
J. Exp. Bot., November 1, 2005; 56(421): 2885 - 2895.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
H. Schoof, M. Spannagl, L. Yang, R. Ernst, H. Gundlach, D. Haase, G. Haberer, and K. F.X. Mayer
Munich Information Center for Protein Sequences Plant Genome Resources. A Framework for Integrative and Comparative Analyses
Plant Physiology, July 1, 2005; 138(3): 1301 - 1309.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
L. A. Mueller, T. H. Solow, N. Taylor, B. Skwarecki, R. Buels, J. Binns, C. Lin, M. H. Wright, R. Ahrens, Y. Wang, et al.
The SOL Genomics Network. A Comparative Resource for Solanaceae Biology and Beyond
Plant Physiology, July 1, 2005; 138(3): 1310 - 1317.
[Abstract] [Full Text] [PDF]

Home page
 J HeredHome page
V. Poncet, P. Hamon, M.-B. Sauvage de Saint Marc, T. Bernard, S. Hamon, and M. Noirot
Base Composition of Coffea AFLP Sequences and Their Conservation Within the Genus
J. Hered., January 1, 2005; 96(1): 59 - 65.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Rudd, H. Schoof, and K. Mayer
PlantMarkers--a database of predicted molecular markers from plants
Nucleic Acids Res., January 1, 2005; 33(suppl_1): D628 - D632.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
P. Bauer, T. Thiel, M. Klatte, Z. Bereczky, T. Brumbarova, R. Hell, and I. Grosse
Analysis of Sequence, Map Position, and Gene Expression Reveals Conserved Essential Genes for Iron Uptake in Arabidopsis and Tomato
Plant Physiology, December 1, 2004; 136(4): 4169 - 4183.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
K.-Y. Chen and S. D. Tanksley
High-Resolution Mapping and Functional Analysis of se2.1: A Major Stigma Exsertion Quantitative Trait Locus Associated With the Evolution From Allogamy to Autogamy in the Genus Lycopersicon
Genetics, November 1, 2004; 168(3): 1563 - 1573.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Bot.Home page
M. W. Chase
Monocot relationships: an overview
Am. J. Botany, October 1, 2004; 91(10): 1645 - 1655.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Bot.Home page
C. R. Linder and L. H. Rieseberg
Reconstructing patterns of reticulate evolution in plants.
Am. J. Botany, October 1, 2004; 91: 1700 - 1708.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
K. V. Krutovsky, M. Troggio, G. R. Brown, K. D. Jermstad, and D. B. Neale
Comparative Mapping in the Pinaceae
Genetics, September 1, 2004; 168(1): 447 - 461.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
M. Vincentz, F. A.A. Cara, V. K. Okura, F. R. da Silva, G. L. Pedrosa, A. S. Hemerly, A. N. Capella, M. Marins, P. C. Ferreira, S. C. Franca, et al.
Evaluation of Monocot and Eudicot Divergence Using the Sugarcane Transcriptome
Plant Physiology, March 1, 2004; 134(3): 951 - 959.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Q. Dong, S. D. Schlueter, and V. Brendel
PlantGDB, plant genome database and analysis tools
Nucleic Acids Res., January 1, 2004; 32(90001): D354 - 359.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
S. Doganlar, A. Frary, M.-C. Daunay, R. N. Lester, and S. D. Tanksley
A Comparative Genetic Linkage Map of Eggplant (Solanum melongena) and Its Implications for Genome Evolution in the Solanaceae
Genetics, August 1, 2002; 161(4): 1697 - 1711.
[Abstract] [Full Text] [PDF]

Home page
 Plant CellHome page
R. Van der Hoeven, C. Ronning, J. Giovannoni, G. Martin, and S. Tanksley
Deductions about the Number, Organization, and Evolution of Genes in the Tomato Genome Based on Analysis of a Large Expressed Sequence Tag Collection and Selective Genomic Sequencing
PLANT CELL, July 1, 2002; 14(7): 1441 - 1456.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
ASPB Publications THE PLANT CELL PLANT PHYSIOLOGY
Copyright © 2002 by the American Society of Plant Biologists