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Nested Ty3-gypsy retrotransposons of a single Beta procumbens centromere contain a putative chromodomain

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Abstract

LTR retrotransposons belong to a major group of DNA sequences that are often localized in plant centromeres. Using BAC inserts originating from the centromere of a monosomic wild beet (Beta procumbens) chromosome fragment in Beta vulgaris, two complete LTR retrotransposons were identified. Both elements, designated Beetle1 and Beetle2, possess a coding region with genes in the order characteristic for Ty3-gypsy retrotransposons. Beetle1 and Beetle2 have a chromodomain in the C-terminus of the integrase gene and are highly similar to the centromeric retrotransposons (CRs) of rice, maize, and barley. Both retroelements were localized in the centromeric region of B. procumbens chromosomes by fluorescence in-situ hybridization. They can therefore be classified as centromere-specific chromoviruses. PCR analysis using RNA as template indicated that Beetle1 and Beetle2 are transcriptionally active. On the basis of the sequence diversity between the LTR sequences, it was estimated that Beetle1 and Beetle2 transposed within the last 60 000 years and 130 000 years, respectively. The centromeric localization of Beetle1 and Beetle2 and their transcriptional activity combined with high sequence conservation within each family play an important structural role in the centromeres of B. procumbens chromosomes.

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Abbreviations

BAC:

bacterial artificial chromosome

CR:

centromeric retrotransposon

DAPI:

4′,6′-diamidino-2-phenylindole

FISH:

fluorescence in-situ hybridization

FITC:

fluorescein isothiocyanate

IPCR:

inverse PCR

LTR:

long terminal repeat

ORF:

open reading frame

PBS:

primer binding site

PPT:

polypurine tract

RT-PCR:

reverse-transcription PCR

SDS:

sodium dodecyl sulfate

SSC:

standard saline citrate (1× SSC = 0.15 M NaCl, 0.015 M Na3-citrate)

TAE:

standard Tris acetate buffer (1× TAE = 40 mM Tris-HCl pH 8, 0.114% acetic acid, 1 mM EDTA)

UTR:

untranslated region

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Acknowledgements

This research was funded by grants from the BMBF (BioFuture grant 0311860) to Thomas Schmidt. Beatrice Weber acknowledges a FAZIT fellowship.

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  1. Institute of Botany, Dresden University of Technology, 01062, Dresden, Germany

    Beatrice Weber & Thomas Schmidt

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  1. Beatrice Weber
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Correspondence to Thomas Schmidt.

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Supplementary Figure S1

Plant centromeric retrotransposons contain different chromointegrases. This alignment was constructed with the program MEGA 4 using a ClustalW alignment of the integrase gene (Tamura et al. 2007). The shading marks a 50% consensus, with the black boxes indicating identical amino acids and the grey boxes representing amino acids with a similar residue group. All sequences have been obtained from the GenBank; for the annotated sequences, the name of the retroelement is added, for retroelements not described, the initials of the species and the accession numbers are given. The sequences are: Beetle1 (AJ539424) and Beetle2 (FM242082) from B. procumbens; Mt_AC131249 from Medicago truncatula; Lj_AP004525 from Lotus japonicus; At_A1161506 from Arabidopsis thaliana; CRM (AY129008) from Zea mays; CRR (AB033235) from Oryza sativa; cereba (AY040382) from Hordeum vulgare; Galadriel (AF119040) from Lycopersicon esculentum; monkey (AF143332) from Musa sp.; Tekay (AF448416) from Zea mays; del1 (X13886) from Lilium henryi; Reina (U69258) from Zea mays; Gimli (AL049655) from Arabidopsis thaliana; Maggy (L35035) from Magnaportha grisea; and sushi (AF030881) from Takifugu rubripes (DOC 187 KB)

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Weber, B., Schmidt, T. Nested Ty3-gypsy retrotransposons of a single Beta procumbens centromere contain a putative chromodomain. Chromosome Res 17, 379–396 (2009). https://doi.org/10.1007/s10577-009-9029-y

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