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Chromosomal distribution of soybean retrotransposon SORE-1 suggests its recent preferential insertion into euchromatic regions

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Abstract

Retrotransposons constitute a large portion of plant genomes. The chromosomal distribution of a wide variety of retrotransposons has been analyzed using genome sequencing data in several plants, but the evolutionary profile of transposition has been characterized for a limited number of retrotransposon families. Here, we characterized 96 elements of the SORE-1 family of soybean retrotransposons using genome sequencing data. Insertion time of each SORE-1 element into the genome was estimated on the basis of sequence differences between the 5′ and 3′ long terminal repeats (LTRs). Combining this estimation with information on the chromosomal location of these elements, we found that the insertion of the existing SORE-1 into gene-rich chromosome arms occurred on average more recently than that into gene-poor pericentromeric regions. In addition, both the number of insertions and the proportion of insertions into chromosome arms profoundly increased after 1 million years ago. Solo LTRs were detected in these regions at a similar frequency, suggesting that elimination of SORE-1 via unequal homologous recombination was unbiased. Taken together, these results suggest the preference of a recent insertion of SORE-1 into chromosome arms comprising euchromatic regions. This notion is contrary to an earlier view deduced from an overall profiling of soybean retrotransposons and suggests that the pattern of chromosomal distribution can be more diverse than previously thought between different families of retrotransposons.

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Abbreviations

LTR:

Long terminal repeat

mya:

Million years ago

Wm82:

Williams 82

SORE-1 :

SOybean RetroElement 1

ORF:

Open reading frame

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Funding

This work is supported in part by JSPS KAKENHI Grant Number JP17H03743.

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Authors and Affiliations

  1. Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, 060-8589, Japan

    Kenta Nakashima, Jun Abe & Akira Kanazawa

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  1. Kenta Nakashima
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  2. Jun Abe
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  3. Akira Kanazawa
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Correspondence to Akira Kanazawa.

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Responsible Editor:Hans de Jong

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Nakashima, K., Abe, J. & Kanazawa, A. Chromosomal distribution of soybean retrotransposon SORE-1 suggests its recent preferential insertion into euchromatic regions. Chromosome Res 26, 199–210 (2018). https://doi.org/10.1007/s10577-018-9579-y

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  • DOI: https://doi.org/10.1007/s10577-018-9579-y

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