Many or most genes in Arabidopsis transposed after the origin of the order Brassicales

  1. Michael Freeling1,4,
  2. Eric Lyons1,
  3. Brent Pedersen1,
  4. Maqsudul Alam2,
  5. Ray Ming3, and
  6. Damon Lisch1
  1. 1 Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California 94720, USA;
  2. 2 Advanced Studies in Genomics, Proteomics and Bioinformatics and Department of Microbiology, University of Hawaii, Honolulu, Hawaii 96822, USA;
  3. 3 Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA

Abstract

Previous to this work, typical genes were thought to move from one position to another infrequently. On the contrary, we now estimate that between one-fourth and three-fourths of the genes in Arabidopsis transposed in the Brassicales. We used the CoGe comparative genomics system to perform and visualize multiple orthologous chromosomal alignments. Using this tool, we found large differences between different categories of genes. Ten of the gene families examined, including genes in most transcription factor families, exhibited a median frequency of 5% transposed genes. In contrast, other gene families were composed largely of transposed genes: NB-LRR disease-resistance genes, genes encoding MADS-box and B3 transcription factors, and genes encoding F-box proteins. A unique method involving transposition-rich regions of genome allowed us to obtain an indirect estimate of the positional stability of the average gene. The observed differences between gene families raise important questions concerning the causes and consequences of gene transposition.

Footnotes

  • 4 Corresponding author.

    4 E-mail freeling{at}nature.berkeley.edu; fax (510) 642-4995.

  • [Supplemental material is available online at www.genome.org.]

  • Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.081026.108.

    • Received May 18, 2008.
    • Accepted September 29, 2008.

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