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Sequence organization and evolutionary dynamics of Brachypodium-specific centromere retrotransposons

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Abstract

Brachypodium distachyon is a wild annual grass belonging to the Pooideae, more closely related to wheat, barley, and forage grasses than rice and maize. As an experimental model, the completed genome sequence of B. distachyon provides a unique opportunity to study centromere evolution during the speciation of grasses. Centromeric satellite sequences have been identified in B. distachyon, but little is known about centromeric retrotransposons in this species. In the present study, bacterial artificial chromosome (BAC)-fluorescence in situ hybridization was conducted in maize, rice, barley, wheat, and rye using B. distachyon (Bd) centromere-specific BAC clones. Eight Bd centromeric BAC clones gave no detectable fluorescence in situ hybridization (FISH) signals on the chromosomes of rice and maize, and three of them also did not yield any FISH signals in barley, wheat, and rye. In addition, four of five Triticeae centromeric BAC clones did not hybridize to the B. distachyon centromeres, implying certain unique features of Brachypodium centromeres. Analysis of Brachypodium centromeric BAC sequences identified a long terminal repeat (LTR)-centromere retrotransposon of B. distachyon (CRBd1). This element was found in high copy number accounting for 1.6 % of the B. distachyon genome, and is enriched in Brachypodium centromeric regions. CRBd1 accumulated in active centromeres, but was lost from inactive ones. The LTR of CRBd1 appears to be specific to B. distachyon centromeres. These results reveal different evolutionary events of this retrotransposon family across grass species.

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Abbreviations

BAC:

Bacterial artificial chromosome

Bd_CENT:

Brachypodium distachyon centromeric repeat

CCD:

Charge-coupled device

CENH3:

Centromere-specific histone H3

CR:

Centromeric retrotransposon

CRBd:

Centromeric retrotransposon of B. distachyon

CRM:

Centromeric retrotransposon of maize

CRR:

Centromeric retrotransposon of rice

CRW:

Centromeric retrotransposon of wheat

EST:

Expressed sequence tag

FISH:

Fluorescence in situ hybridization

LTR:

Long terminal repeat

MYA:

Million years ago

PBS:

Primer-binding site

PPT:

Polypurine tract

REBd:

Retrotransposon element of B. distachyon

TSD:

Target site duplication

TREP:

Triticeae Repeat Sequence Database

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Acknowledgments

We thank Drs Zhao Liu and Gerald Seiler for critical review of the manuscript. This research was supported by a special USDA-NIFA grant to the Wheat Genetic Resources Center, Kansas State University, USA, and fund for excellent young scholar of Shandong Province of China (BS2011SW027).

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Authors and Affiliations

  1. Northern Crop Science Laboratory, USDA-ARS, 1605 Albrecht Blvd N, Fargo, ND, 58102-2765, USA

    L. L. Qi

  2. State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, 61 Daizong Street, Taian, Shandong, 271018, People’s Republic of China

    J. J. Wu & D. L. Fu

  3. Department of Plant Pathology, Wheat Genetic Resources Center, Kansas State University, Manhattan, KS, 66506-5502, USA

    B. Friebe, C. Qian & B. S. Gill

  4. Genomics and Gene Discovery Research Unit, Western Regional Research Center, USDA-ARS, 800 Buchanan Street, Albany, CA, 94710, USA

    Y. Q. Gu

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  1. L. L. Qi
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  4. C. Qian
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Correspondence to L. L. Qi.

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Responsible Editor: Hans de Jong

L.L. Qi and J.J Wu contributed equally to this work

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Fig. S1

The dot matrix view of self-alignment of the BAC DB069J23. (PPT 189 kb)

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Qi, L.L., Wu, J.J., Friebe, B. et al. Sequence organization and evolutionary dynamics of Brachypodium-specific centromere retrotransposons. Chromosome Res 21, 507–521 (2013). https://doi.org/10.1007/s10577-013-9378-4

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  • DOI: https://doi.org/10.1007/s10577-013-9378-4

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