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Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families.
Genome Res 2007; 17(7):1072-81GR

Abstract

Although copia retrotransposons are major components of all plant genomes, the evolutionary relationships between individual copia families and between elements from different plant species are only poorly studied. We used 20 copia families from the large-genome plants barley and wheat to identify 46 families of homologous copia elements from rice and 22 from Arabidopsis, two plant species with much smaller genomes. In total, 599 copia elements were analyzed. Phylogenetic analysis showed that copia elements from the four species can be classified into six ancient lineages that existed before the divergence of monocots and dicots. The six lineages show a surprising degree of conservation in sequence organization and other characteristics across species. Additionally, the phylogenetic data suggest at least one case of horizontal gene transfer between the Arabidopsis and rice lineages. Insertion time estimates for 522 high-copy elements showed that retrotransposons from rice were active at different times in waves of activity lasting 0.5-2 million years, depending on the family, whereas elements from wheat and barley had longer periods of activity. We estimated that half of the rice copia elements are truncated or otherwise rearranged after approximately 790,000 yr, which is almost twice the half-life of Arabidopsis elements. In contrast, wheat and barley copia elements appear to have a massively longer half-life, beyond our ability to estimate from the available data. These findings suggest that genome size can be explained by the specific rate of DNA removal from the genome and the length of active periods of retrotransposon families.

Authors+Show Affiliations

Institute of Plant Biology, University of Zürich, Zürich, Switzerland. wicker@botinst.unizh.chNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

17556529

Citation

Wicker, Thomas, and Beat Keller. "Genome-wide Comparative Analysis of Copia Retrotransposons in Triticeae, Rice, and Arabidopsis Reveals Conserved Ancient Evolutionary Lineages and Distinct Dynamics of Individual Copia Families." Genome Research, vol. 17, no. 7, 2007, pp. 1072-81.
Wicker T, Keller B. Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families. Genome Res. 2007;17(7):1072-81.
Wicker, T., & Keller, B. (2007). Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families. Genome Research, 17(7), pp. 1072-81.
Wicker T, Keller B. Genome-wide Comparative Analysis of Copia Retrotransposons in Triticeae, Rice, and Arabidopsis Reveals Conserved Ancient Evolutionary Lineages and Distinct Dynamics of Individual Copia Families. Genome Res. 2007;17(7):1072-81. PubMed PMID: 17556529.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families. AU - Wicker,Thomas, AU - Keller,Beat, Y1 - 2007/06/07/ PY - 2007/6/9/pubmed PY - 2007/9/19/medline PY - 2007/6/9/entrez SP - 1072 EP - 81 JF - Genome research JO - Genome Res. VL - 17 IS - 7 N2 - Although copia retrotransposons are major components of all plant genomes, the evolutionary relationships between individual copia families and between elements from different plant species are only poorly studied. We used 20 copia families from the large-genome plants barley and wheat to identify 46 families of homologous copia elements from rice and 22 from Arabidopsis, two plant species with much smaller genomes. In total, 599 copia elements were analyzed. Phylogenetic analysis showed that copia elements from the four species can be classified into six ancient lineages that existed before the divergence of monocots and dicots. The six lineages show a surprising degree of conservation in sequence organization and other characteristics across species. Additionally, the phylogenetic data suggest at least one case of horizontal gene transfer between the Arabidopsis and rice lineages. Insertion time estimates for 522 high-copy elements showed that retrotransposons from rice were active at different times in waves of activity lasting 0.5-2 million years, depending on the family, whereas elements from wheat and barley had longer periods of activity. We estimated that half of the rice copia elements are truncated or otherwise rearranged after approximately 790,000 yr, which is almost twice the half-life of Arabidopsis elements. In contrast, wheat and barley copia elements appear to have a massively longer half-life, beyond our ability to estimate from the available data. These findings suggest that genome size can be explained by the specific rate of DNA removal from the genome and the length of active periods of retrotransposon families. SN - 1088-9051 UR - https://www.unboundmedicine.com/medline/citation/17556529/Genome_wide_comparative_analysis_of_copia_retrotransposons_in_Triticeae_rice_and_Arabidopsis_reveals_conserved_ancient_evolutionary_lineages_and_distinct_dynamics_of_individual_copia_families_ L2 - http://genome.cshlp.org/cgi/pmidlookup?view=long&pmid=17556529 DB - PRIME DP - Unbound Medicine ER -