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Comparative genomic paleontology across plant kingdom reveals the dynamics of TE-driven genome evolution.
Genome Biol Evol. 2013; 5(5):954-65.GB

Abstract

Long terminal repeat-retrotransposons (LTR-RTs) are the most abundant class of transposable elements (TEs) in plants. They strongly impact the structure, function, and evolution of their host genome, and, in particular, their role in genome size variation has been clearly established. However, the dynamics of the process through which LTR-RTs have differentially shaped plant genomes is still poorly understood because of a lack of comparative studies. Using a new robust and automated family classification procedure, we exhaustively characterized the LTR-RTs in eight plant genomes for which a high-quality sequence is available (i.e., Arabidopsis thaliana, A. lyrata, grapevine, soybean, rice, Brachypodium dystachion, sorghum, and maize). This allowed us to perform a comparative genome-wide study of the retrotranspositional landscape in these eight plant lineages from both monocots and dicots. We show that retrotransposition has recurrently occurred in all plant genomes investigated, regardless their size, and through bursts, rather than a continuous process. Moreover, in each genome, only one or few LTR-RT families have been active in the recent past, and the difference in genome size among the species studied could thus mostly be accounted for by the extent of the latest transpositional burst(s). Following these bursts, LTR-RTs are efficiently eliminated from their host genomes through recombination and deletion, but we show that the removal rate is not lineage specific. These new findings lead us to propose a new model of TE-driven genome evolution in plants.

Authors+Show Affiliations

Université de Perpignan Via Domitia, Laboratoire Génome et développement des plantes, UMR UPVD/CNRS 5096, 66860 Perpignan, France.No affiliation info available

Pub Type(s)

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

Language

eng

PubMed ID

23426643

Citation

El Baidouri, Moaine, and Olivier Panaud. "Comparative Genomic Paleontology Across Plant Kingdom Reveals the Dynamics of TE-driven Genome Evolution." Genome Biology and Evolution, vol. 5, no. 5, 2013, pp. 954-65.
El Baidouri M, Panaud O. Comparative genomic paleontology across plant kingdom reveals the dynamics of TE-driven genome evolution. Genome Biol Evol. 2013;5(5):954-65.
El Baidouri, M., & Panaud, O. (2013). Comparative genomic paleontology across plant kingdom reveals the dynamics of TE-driven genome evolution. Genome Biology and Evolution, 5(5), 954-65. https://doi.org/10.1093/gbe/evt025
El Baidouri M, Panaud O. Comparative Genomic Paleontology Across Plant Kingdom Reveals the Dynamics of TE-driven Genome Evolution. Genome Biol Evol. 2013;5(5):954-65. PubMed PMID: 23426643.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Comparative genomic paleontology across plant kingdom reveals the dynamics of TE-driven genome evolution. AU - El Baidouri,Moaine, AU - Panaud,Olivier, PY - 2013/2/22/entrez PY - 2013/2/22/pubmed PY - 2013/12/16/medline KW - LTR-retrotransposons KW - comparative genomics KW - deletion KW - genome dynamics KW - plants KW - solo-LTR KW - transposable elements KW - transpositional burst SP - 954 EP - 65 JF - Genome biology and evolution JO - Genome Biol Evol VL - 5 IS - 5 N2 - Long terminal repeat-retrotransposons (LTR-RTs) are the most abundant class of transposable elements (TEs) in plants. They strongly impact the structure, function, and evolution of their host genome, and, in particular, their role in genome size variation has been clearly established. However, the dynamics of the process through which LTR-RTs have differentially shaped plant genomes is still poorly understood because of a lack of comparative studies. Using a new robust and automated family classification procedure, we exhaustively characterized the LTR-RTs in eight plant genomes for which a high-quality sequence is available (i.e., Arabidopsis thaliana, A. lyrata, grapevine, soybean, rice, Brachypodium dystachion, sorghum, and maize). This allowed us to perform a comparative genome-wide study of the retrotranspositional landscape in these eight plant lineages from both monocots and dicots. We show that retrotransposition has recurrently occurred in all plant genomes investigated, regardless their size, and through bursts, rather than a continuous process. Moreover, in each genome, only one or few LTR-RT families have been active in the recent past, and the difference in genome size among the species studied could thus mostly be accounted for by the extent of the latest transpositional burst(s). Following these bursts, LTR-RTs are efficiently eliminated from their host genomes through recombination and deletion, but we show that the removal rate is not lineage specific. These new findings lead us to propose a new model of TE-driven genome evolution in plants. SN - 1759-6653 UR - https://www.unboundmedicine.com/medline/citation/23426643/Comparative_genomic_paleontology_across_plant_kingdom_reveals_the_dynamics_of_TE_driven_genome_evolution_ L2 - https://academic.oup.com/gbe/article-lookup/doi/10.1093/gbe/evt025 DB - PRIME DP - Unbound Medicine ER -