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The subtelomeric region of the Arabidopsis thaliana chromosome IIIR contains potential genes and duplicated fragments from other chromosomes

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Abstract

The subtelomere and a portion of the associated telomeric region (together named 3RTAS) of chromosome IIIR from the Arabidopsis thaliana ecotypes Columbia (Col) and Wassilewskija (Ws) were specifically amplified by polymerase chain reaction and subsequently cloned and sequenced. The centromere-proximal portion of 3RTAS from both ecotypes contained two newly identified potential genes, one encoding the chloroplast luminal 19-kDa protein precursor and the other encoding three potential alternatively spliced CCCH-type zinc finger proteins. The telomere-proximal portion of 3RTAS from the Col ecotype contained short duplicated fragments derived from chromosomes I, II, and III, and that from the Ws ecotype contained a duplicated fragment derived from chromosome V. Each duplicated fragment has diverged somewhat in sequence from that of the ectopic template. Small patches of homologous nucleotides were found within the flanking sequences of both the duplicated fragments and the corresponding ectopic template sequences. The structural characteristics of these duplicated fragments suggest that they are filler DNAs captured by non-homologous end joining during double-strand break repair. Our characterization of 3RTAS not only filled up a gap in the chromosome IIIR sequence of A. thaliana but also identified new genes with unknown functions.

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Abbreviations

DIG:

Digoxigenin

DSB:

Double-strand break

NCBI:

National Center for Biotechnology Information

NHEJ:

Non-homologous end joining

PCR:

Polymerase chain reaction

STELA:

Single-telomere length analysis

TAIR:

The Arabidopsis Information Resources

TAS:

Telomere-associated sequence

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Acknowledgment

We thank the transgenic plant core laboratory at Academia Sinica for providing the picture of Arabidopsis plant shown in the cover page.

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Authors and Affiliations

  1. Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115, Taiwan, Republic of China

    Chi-Ting Wang & Chung-Mong Chen

  2. Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, 106, Taiwan, Republic of China

    Chia-Hsing Ho

  3. Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan, Republic of China

    Ming-Jhy Hseu

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  1. Chi-Ting Wang
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Correspondence to Chung-Mong Chen.

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Wang, CT., Ho, CH., Hseu, MJ. et al. The subtelomeric region of the Arabidopsis thaliana chromosome IIIR contains potential genes and duplicated fragments from other chromosomes. Plant Mol Biol 74, 155–166 (2010). https://doi.org/10.1007/s11103-010-9664-x

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  • DOI: https://doi.org/10.1007/s11103-010-9664-x

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