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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
MeSH Review

Genome, Plant

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Disease relevance of Genome, Plant


High impact information on Genome, Plant


Chemical compound and disease context of Genome, Plant

  • Plant signal molecules such as acetosyringone and certain monosaccharides induce the expression of Agrobacterium tumefaciens virulence (vir) genes, which are required for the processing, transfer, and possibly integration of a piece of the bacterial plasmid DNA (T-DNA) into the plant genome [9].

Biological context of Genome, Plant

  • The octopine tumor-inducing (Ti) plasmid pTiA66 has an insertion mutation in its T region (the DNA region incorporated into the plant genome) that results in the slow growth of crown gall tumors [10].
  • DNA sequence analysis of 29 cloned PCR products and of a maize retrotransposon cDNA confirmed the identity of these sequences as copia-like reverse transcriptase sequences, thereby demonstrating that this class of retrotransposons is a ubiquitous component of plant genomes [11].
  • This can be interpreted as a consequence of a difference in mutation pressure related to spontaneous deamination of 5mC to thymine between the different compartments of plant genomes [12].
  • Moreover, this elevated expansion rate of plant TF is not simply due to higher duplication rates of plant genomes but also to a higher degree of expansion compared to other plant genes [13].
  • This paper describes expression profiles of the Arabidopsis HSP18.2 heat-shock gene promoter by using three different reporter genes, and the application of this promoter to a method we have developed to drive heat-shock-dependent transcription of plant genome DNA flanked by T-DNA insertions [14].

Anatomical context of Genome, Plant

  • Based on the definition of these major and minor PTS and on the recognition of additional conserved properties, the accuracy of predicting peroxisomal proteins can be raised and plant genomes can be screened for novel proteins of peroxisomes more successfully [15].

Associations of Genome, Plant with chemical compounds


Gene context of Genome, Plant

  • Only unique homologs of SPO11 are found in animals and fungi whereas three distantly related SPO11 copies are present in plant genomes [21].
  • To help resolve this conflict, we used parsimony and likelihood methods to analyze a 6, 095-character data set composed of four genes (chloroplast rbcL and small-subunit rDNA from all three plant genomes) from all major land plant lineages [22].
  • This fusion has not been retained in plant genomes, which solely express unfused SCP-2 domains [23].
  • Gene for proliferating-cell nuclear antigen (DNA polymerase delta auxiliary protein) is present in both mammalian and higher plant genomes [24].
  • The virulence protein VirD2 of A. tumefaciens is tightly linked to the T-DNA and is thought to direct it to the plant genome [25].

Analytical, diagnostic and therapeutic context of Genome, Plant


  1. Right 25 bp terminus sequence of the nopaline T-DNA is essential for and determines direction of DNA transfer from agrobacterium to the plant genome. Wang, K., Herrera-Estrella, L., Van Montagu, M., Zambryski, P. Cell (1984) [Pubmed]
  2. Gene transfer with subsequent removal of the selection gene from the host genome. Dale, E.C., Ow, D.W. Proc. Natl. Acad. Sci. U.S.A. (1991) [Pubmed]
  3. Identification of cyanobacterial cell division genes by comparative and mutational analyses. Miyagishima, S.Y., Wolk, C.P., Osteryoung, K.W. Mol. Microbiol. (2005) [Pubmed]
  4. NIPBL, encoding a homolog of fungal Scc2-type sister chromatid cohesion proteins and fly Nipped-B, is mutated in Cornelia de Lange syndrome. Tonkin, E.T., Wang, T.J., Lisgo, S., Bamshad, M.J., Strachan, T. Nat. Genet. (2004) [Pubmed]
  5. NSF urged to increase plant genome sequencing effort. Macilwain, C. Nature (1997) [Pubmed]
  6. Receptor kinase signalling in plants and animals: distinct molecular systems with mechanistic similarities. Cock, J.M., Vanoosthuyse, V., Gaude, T. Curr. Opin. Cell Biol. (2002) [Pubmed]
  7. DNA methylation is critical for Arabidopsis embryogenesis and seed viability. Xiao, W., Custard, K.D., Brown, R.C., Lemmon, B.E., Harada, J.J., Goldberg, R.B., Fischer, R.L. Plant Cell (2006) [Pubmed]
  8. Severe acute respiratory syndrome (SARS) S protein production in plants: development of recombinant vaccine. Pogrebnyak, N., Golovkin, M., Andrianov, V., Spitsin, S., Smirnov, Y., Egolf, R., Koprowski, H. Proc. Natl. Acad. Sci. U.S.A. (2005) [Pubmed]
  9. Preformed dimeric state of the sensor protein VirA is involved in plant--Agrobacterium signal transduction. Pan, S.Q., Charles, T., Jin, S., Wu, Z.L., Nester, E.W. Proc. Natl. Acad. Sci. U.S.A. (1993) [Pubmed]
  10. Nucleotide sequence of the insertion sequence found in the T-DNA region of mutant Ti plasmid pTiA66 and distribution of its homologues in octopine Ti plasmid. Machida, Y., Sakurai, M., Kiyokawa, S., Ubasawa, A., Suzuki, Y., Ikeda, J.E. Proc. Natl. Acad. Sci. U.S.A. (1984) [Pubmed]
  11. copia-like retrotransposons are ubiquitous among plants. Voytas, D.F., Cummings, M.P., Koniczny, A., Ausubel, F.M., Rodermel, S.R. Proc. Natl. Acad. Sci. U.S.A. (1992) [Pubmed]
  12. The distribution of 5-methylcytosine in the nuclear genome of plants. Montero, L.M., Filipski, J., Gil, P., Capel, J., Martínez-Zapater, J.M., Salinas, J. Nucleic Acids Res. (1992) [Pubmed]
  13. Transcription factor families have much higher expansion rates in plants than in animals. Shiu, S.H., Shih, M.C., Li, W.H. Plant Physiol. (2005) [Pubmed]
  14. Heat-shock tagging: a simple method for expression and isolation of plant genome DNA flanked by T-DNA insertions. Matsuhara, S., Jingu, F., Takahashi, T., Komeda, Y. Plant J. (2000) [Pubmed]
  15. Specification of the peroxisome targeting signals type 1 and type 2 of plant peroxisomes by bioinformatics analyses. Reumann, S. Plant Physiol. (2004) [Pubmed]
  16. Higher plant plastids and cyanobacteria have folate carriers related to those of trypanosomatids. Klaus, S.M., Kunji, E.R., Bozzo, G.G., Noiriel, A., de la Garza, R.D., Basset, G.J., Ravanel, S., Rébeillé, F., Gregory, J.F., Hanson, A.D. J. Biol. Chem. (2005) [Pubmed]
  17. Gene organization features in A/T-rich organisms. Szafranski, K., Lehmann, R., Parra, G., Guigo, R., Glöckner, G. J. Mol. Evol. (2005) [Pubmed]
  18. Splicing of arabidopsis tRNA(Met) precursors in tobacco cell and wheat germ extracts. Akama, K., Junker, V., Yukawa, Y., Sugiura, M., Beier, H. Plant Mol. Biol. (2000) [Pubmed]
  19. Stable transformation and long-term expression of the gusA reporter gene in callus lines of perennial ryegrass (Lolium perenne L.). van der Maas, H.M., de Jong, E.R., Rueb, S., Hensgens, L.A., Krens, F.A. Plant Mol. Biol. (1994) [Pubmed]
  20. Variability in CpNpG methylation in higher plant genomes. Kovarík, A., Matyásek, R., Leitch, A., Gazdová, B., Fulnecek, J., Bezdek, M. Gene (1997) [Pubmed]
  21. Intron gain and loss in the evolution of the conserved eukaryotic recombination machinery. Hartung, F., Blattner, F.R., Puchta, H. Nucleic Acids Res. (2002) [Pubmed]
  22. Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants. Nickrent, D.L., Parkinson, C.L., Palmer, J.D., Duff, R.J. Mol. Biol. Evol. (2000) [Pubmed]
  23. Fusion and fission, the evolution of sterol carrier protein-2. Edqvist, J., Blomqvist, K. J. Mol. Evol. (2006) [Pubmed]
  24. Gene for proliferating-cell nuclear antigen (DNA polymerase delta auxiliary protein) is present in both mammalian and higher plant genomes. Suzuka, I., Daidoji, H., Matsuoka, M., Kadowaki, K., Takasaki, Y., Nakane, P.K., Moriuchi, T. Proc. Natl. Acad. Sci. U.S.A. (1989) [Pubmed]
  25. The T-DNA-linked VirD2 protein contains two distinct functional nuclear localization signals. Tinland, B., Koukolíková-Nicola, Z., Hall, M.N., Hohn, B. Proc. Natl. Acad. Sci. U.S.A. (1992) [Pubmed]
  26. Further insight on the transferred-DNA of octopine crown gall. De Beuckeleer, M., Lemmers, M., De Vos, G., Willmitzer, L., Van Montagu, M., Schell, J. Mol. Gen. Genet. (1981) [Pubmed]
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