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LTR Retrotransposon Dynamics and Specificity in Setaria italica

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Genetics and Genomics of Setaria

Part of the book series: Plant Genetics and Genomics: Crops and Models ((PGG,volume 19))

Abstract

The distributions of different LTR retrotransposon families and structures were analyzed across the ~400 Mb assembly for the ~500 Mb genome of Setaria italica. The results indicated different genomic distributions for all five of the highly abundant LTR retrotransposon families that were investigated. Unequal recombination and illegitimate recombination appeared to be more active in LTR retrotransposon removal in the gene-rich regions towards the ends of all chromosomes. In striking contrast to this result, LTR retrotransposon ages did not differ dramatically across the assembled genome, suggesting that LTR retrotransposon removal rates are not dramatically influenced by genomic location. These two, largely incompatible, observations indicate that the dynamics of LTR retrotransposon activation, insertion, and removal all need a great deal of additional investigation, including highly detailed intraspecies analyses and interspecies comparisons.

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Acknowledgements

These analyses and the writing of this manuscript were supported by funding from the Giles Professorship to J. L. B. We thank Aye Htun for assistance with manuscript production.

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Authors and Affiliations

  1. Department of Genetics, University of Georgia, Athens, GA, 30677, USA

    Jeffrey L. Bennetzen, Minkyu Park, Hao Wang & Hongye Zhou

Authors
  1. Jeffrey L. Bennetzen
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  2. Minkyu Park
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  3. Hao Wang
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  4. Hongye Zhou
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Correspondence to Jeffrey L. Bennetzen .

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Editors and Affiliations

  1. Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, Oklahoma, USA

    Andrew Doust

  2. Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China

    Xianmin Diao

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Bennetzen, J.L., Park, M., Wang, H., Zhou, H. (2017). LTR Retrotransposon Dynamics and Specificity in Setaria italica . In: Doust, A., Diao, X. (eds) Genetics and Genomics of Setaria. Plant Genetics and Genomics: Crops and Models, vol 19. Springer, Cham. https://doi.org/10.1007/978-3-319-45105-3_9

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