Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza

Jetty S S Ammiraju, Andrea Zuccolo, Yeisoo Yu, Xiang Song, Benoit Piegu, Frederic Chevalier, Jason G. Walling, Jianxin Ma, Jayson Talag, Darshan S. Brar, Phillip J. SanMiguel, Ning Jiang, Scott A. Jackson, Olivier Panaud, Rod A Wing

Research output: Contribution to journalArticle

66 Citations (Scopus)

Abstract

Long terminal repeat (LTR) retrotransposons constitute a significant portion of most eukaryote genomes and can dramatically change genome size and organization. Although LTR retrotransposon content variation is well documented, the dynamics of genomic flux caused by their activity are poorly understood on an evolutionary time scale. This is primarily because of the lack of an experimental system composed of closely related species whose divergence times are within the limits of the ability to detect ancestrally related retrotransposons. The genus Oryza, with 24 species, ten genome types, different ploidy levels and over threefold genome size variation, constitutes an ideal experimental system to explore genus-level transposon dynamics. Here we present data on the discovery and characterization of an LTR retrotransposon family named RWG in the genus Oryza. Comparative analysis of transposon content (approximately 20 to 27 000 copies) and transpositional history of this family across the genus revealed a broad spectrum of independent and lineage-specific changes that have implications for the evolution of genome size and organization. In particular, we provide evidence that the basal GG genome of Oryza (O. granulata) has expanded by nearly 25% by a burst of the RWG lineage Gran3 subsequent to speciation. Finally we describe the recent evolutionary origin of Dasheng, a large retrotransposon derivative of the RWG family, specifically found in the A, B and C genome lineages of Oryza.

Original languageEnglish (US)
Pages (from-to)342-351
Number of pages10
JournalPlant Journal
Volume52
Issue number2
DOIs
StatePublished - Oct 2007

Fingerprint

Genome Size
Retroelements
Oryza
retrotransposons
Terminal Repeat Sequences
genome
Genome
terminal repeat sequences
transposons
Ploidies
Eukaryota
ploidy
eukaryotic cells
genomics

Keywords

  • Genome size
  • Large retrotransposon derivative
  • Long terminal repeat (LTR) retrotransposon
  • Oryza
  • RWG family

ASJC Scopus subject areas

  • Plant Science

Cite this

Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza. / Ammiraju, Jetty S S; Zuccolo, Andrea; Yu, Yeisoo; Song, Xiang; Piegu, Benoit; Chevalier, Frederic; Walling, Jason G.; Ma, Jianxin; Talag, Jayson; Brar, Darshan S.; SanMiguel, Phillip J.; Jiang, Ning; Jackson, Scott A.; Panaud, Olivier; Wing, Rod A.

In: Plant Journal, Vol. 52, No. 2, 10.2007, p. 342-351.

Research output: Contribution to journalArticle

Ammiraju, JSS, Zuccolo, A, Yu, Y, Song, X, Piegu, B, Chevalier, F, Walling, JG, Ma, J, Talag, J, Brar, DS, SanMiguel, PJ, Jiang, N, Jackson, SA, Panaud, O & Wing, RA 2007, 'Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza', Plant Journal, vol. 52, no. 2, pp. 342-351. https://doi.org/10.1111/j.1365-313X.2007.03242.x
Ammiraju, Jetty S S ; Zuccolo, Andrea ; Yu, Yeisoo ; Song, Xiang ; Piegu, Benoit ; Chevalier, Frederic ; Walling, Jason G. ; Ma, Jianxin ; Talag, Jayson ; Brar, Darshan S. ; SanMiguel, Phillip J. ; Jiang, Ning ; Jackson, Scott A. ; Panaud, Olivier ; Wing, Rod A. / Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza. In: Plant Journal. 2007 ; Vol. 52, No. 2. pp. 342-351.
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AU - Song, Xiang

AU - Piegu, Benoit

AU - Chevalier, Frederic

AU - Walling, Jason G.

AU - Ma, Jianxin

AU - Talag, Jayson

AU - Brar, Darshan S.

AU - SanMiguel, Phillip J.

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AB - Long terminal repeat (LTR) retrotransposons constitute a significant portion of most eukaryote genomes and can dramatically change genome size and organization. Although LTR retrotransposon content variation is well documented, the dynamics of genomic flux caused by their activity are poorly understood on an evolutionary time scale. This is primarily because of the lack of an experimental system composed of closely related species whose divergence times are within the limits of the ability to detect ancestrally related retrotransposons. The genus Oryza, with 24 species, ten genome types, different ploidy levels and over threefold genome size variation, constitutes an ideal experimental system to explore genus-level transposon dynamics. Here we present data on the discovery and characterization of an LTR retrotransposon family named RWG in the genus Oryza. Comparative analysis of transposon content (approximately 20 to 27 000 copies) and transpositional history of this family across the genus revealed a broad spectrum of independent and lineage-specific changes that have implications for the evolution of genome size and organization. In particular, we provide evidence that the basal GG genome of Oryza (O. granulata) has expanded by nearly 25% by a burst of the RWG lineage Gran3 subsequent to speciation. Finally we describe the recent evolutionary origin of Dasheng, a large retrotransposon derivative of the RWG family, specifically found in the A, B and C genome lineages of Oryza.

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