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PMID: 18836034 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

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

Genome research ·Vol. 18 ·No. 12 ·2008-12-00 ·Pages 1924-37

Freeling M, Lyons E, Pedersen B, Alam M, Ming R, Lisch D

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.

MeSH Terms
Arabidopsis/genetics Brassicaceae/genetics Chromosomes, Plant Evolution, Molecular Gene Order Genes, Plant Synteny
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Freeling Michael
Department of Plant and Microbial Biology, University of California at Berkeley, California 94720, USA. [email protected]
Lyons Eric
Pedersen Brent
Alam Maqsudul
Ming Ray
Lisch Damon
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.081026.108
Email
[email protected]
Published
2008-12-00
Epub
2008-00-03
Pages
1924-37
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC2593585
Subset
IM
External Links
PubMed source DOI: 10.1101/gr.081026.108 PMC Full Text View journal details
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