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MBE Advance Access published online on April 2, 2003
Molecular Biology and Evolution, doi:10.1093/molbev/msg095
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2003; all rights reserved
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Accepted January 20, 2003
© 2003 Society for Molecular Biology and Evolution

Original Articles

Study on the Evolution of the Grande Retrotransposon in the Zea Genus

José García-Martínez 1 José A. Martínez-Izquierdo 1*

1 Departamento de Genética Molecular, Instituto de Biología Molecular de Barcelona, (CSIC), Barcelona, Spain

* To whom correspondence should be addressed. E-mail: jamgmj{at}cid.csic.es.


  Abstract

The study of Grande retrotransposon (RTN) variation reported here comprises the intrinsic element variability and the changes that element insertion provokes in the Zea genome including its abundance among species. Sequence analysis of a defined long terminal repeat (LTR) region from Grande RTN revealed high level of sequence divergence since no identical sequences were found among the 65 clones examined which belong to different Zea species or maize inbred lines. Average diversity values within accessions ranged from 0.17 to 0.37 substitutions per nucleotide. Phylogenetic analysis revealed a lack of concordance between the phylogenetic tree obtained from LTR sequences and the conventional taxonomic tree, suggesting that different subfamilies of Grande elements existed before Zea speciation. When sequence-specific amplification polymorphism (SSAP) marker data, that combines genomic and RTN variation, are used, the derived trees reflect the established species phylogeny; and allow, as well, differentiating among some maize lines. Finally, the evaluation of Grande abundance, using different element probes, in all the Zea species, but Z. luxurians, revealed around 5700 copies per haploid genome in all the diploid species examined, indicating a similar expansion process of Grande in all the Zea genomes. This number of copies represents in all cases around a 3% of the genome, which implies that Grande RTN is an important component of the maize genome. The copy number ratio LTR/gag is around 2 in all the species analyzed, indicating that overwhelming majority of elements have internal region. Thus, mechanisms such as homologous recombination between LTRs of a single RTN, which would remove the internal region and one LTR leaving behind a single recombinant LTR, seems not to be active in maize for Grande RTN.

Key Words: Grande retrotransposon, copy number, phylogenetics, SSAP markers, maize, teosinte


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J. C. Lamb and J. A. Birchler
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[Abstract] [Full Text] [PDF]


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