Molecular Biology and Evolution 18:882-892 (2001)
© 2001 Society for Molecular Biology and Evolution
ARTICLE |
Structural and Evolutionary Analysis of the copia-like Elements in the Arabidopsis thaliana Genome
Departamento de Genética, Facultad de Ciencias Biológicas, Universitat de València, Valencia, Spain
The analysis of 460 kb of genomic sequence of Arabidopsis thaliana chromosome III allowed us to identify two new transposable elements named AtC1 and AtC2. AtC1 shows identical long terminal repeats (LTRs) and all the structural features characteristic of the copia-like active elements. AtC2 is also a full copia-like element, but a putative stop codon in the open reading frame (ORF) would produce a truncated protein. In order to identify the copia-like fraction of the A. thaliana genome, a careful computer-based analysis of the available sequences (which correspond to 92% of the genome) was performed. Approximately 300 nonredundant copia-like sequences homologous to AtC1 and AtC2 were detected, which showed an extreme heterogeneity in size and degree of conservation. This number of copies would correspond to approximately 1% of the A. thaliana genome. Seventy-one sequences were selected for further analysis, with 23 of them being full complete elements. Five corresponded to previously described ones, and the remaining ones, named AtC3 to AtC18 are new elements described in this work. Most of these elements presented a putative functional ORF, nearly identical LTRs, and the other elements necessary for retrotransposon activity. Phylogenetic trees, supported by high bootstrap values, indicated that these 23 elements could be considered separate families. In turn, these 23 families could be clustered into six major lineages, named copia I–VI. Most of the 71 analyzed sequences clustered into these six main clades. The widespread presence of these copia-like superfamilies throughout plant genomes is discussed.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  H. Ner-Gaon, N. Leviatan, E. Rubin, and R. Fluhr Comparative Cross-Species Alternative Splicing in Plants Plant Physiology, July 1, 2007; 144(3): 1632 - 1641. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Zhang and S. R. Wessler Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea PNAS, April 13, 2004; 101(15): 5589 - 5594. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. D. Peterson-Burch and D. F. Voytas Genes of the Pseudoviridae (Ty1/copia Retrotransposons) Mol. Biol. Evol., November 1, 2002; 19(11): 1832 - 1845. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. M. Devos, J. K.M. Brown, and J. L. Bennetzen Genome Size Reduction through Illegitimate Recombination Counteracts Genome Expansion in Arabidopsis Genome Res., July 1, 2002; 12(7): 1075 - 1079. [Abstract] [Full Text] [PDF]
|
|