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In-depth sequence analysis of the tomato chromosome 12 centromeric region: identification of a large CAA block and characterization of pericentromere retrotranposons

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Abstract

We sequenced a continuous 326-kb DNA stretch of a microscopically defined centromeric region of tomato chromosome 12. A total of 84% of the sequence (270 kb) was composed of a nested complex of repeat sequences including 27 retrotransposons, two transposable elements, three MITEs, two terminal repeat retrotransposons in miniature (TRIMs), ten unclassified repeats and three chloroplast DNA insertions. The retrotransposons were grouped into three families of Ty3-Gypsy type long terminal repeat (LTR) retrotransposons (PCRT1–PCRT3) and one LINE-like retrotransposon (PCRT4). High-resolution fluorescence in situ hybridization analyses on pachytene complements revealed that PCRT1a occurs on the pericentromere heterochromatin blocks. PCRT1 was the prevalent retrotransposon family occupying more than 60% of the 326-kb sequence with 19 members grouped into eight subfamilies (PCRT1a–PCRT1h) based on LTR sequence. The PCRT1a subfamily is a rapidly amplified element occupying tens of megabases. The other PCRT1 subfamilies (PCRT1b–PCRT1h) were highly degenerated and interrupted by insertions of other elements. The PCRT1 family shows identity with a previously identified tomato-specific repeat TGR2 and a CENP-B like sequence. A second previously described genomic repeat, TGR3, was identified as a part of the LTR sequence of an Athila-like PCRT2 element of which four copies were found in the 326-kb stretch. A large block of trinucleotide microsatellite (CAA)n occupies the centromere and large portions of the flanking pericentromere heterochromatin blocks of chromosome 12 and most of the other chromosomes. Five putative genes in the remaining 14% of the centromere region were identified, of which one is similar to a transcription regulator (ToCPL1) and a candidate jointless-2 gene.

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Acknowledgements

This work was supported by the NSF Plant Genome Grant # 0116076 to R.A.W.

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Authors and Affiliations

  1. Brassica Genomics Team, National Institute of Agricultural Biotechnology (NIAB), RDA, Suwon, 441-707, South Korea

    Tae-Jin Yang

  2. Arizona Genomics Institute, 303 Forbes building, University of Arizona, Tucson, AZ, 85721, USA

    Tae-Jin Yang, Seunghee Lee, Yeisoo Yu & Rod A. Wing

  3. Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands

    Song-Bin Chang & Hans de Jong

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  1. Tae-Jin Yang
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  2. Seunghee Lee
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  3. Song-Bin Chang
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  4. Yeisoo Yu
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  5. Hans de Jong
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  6. Rod A. Wing
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Correspondence to Rod A. Wing.

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Communicated by P. Shaw

The sequence data from this study have been submitted to GenBank under accession no. AY850394

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Yang, TJ., Lee, S., Chang, SB. et al. In-depth sequence analysis of the tomato chromosome 12 centromeric region: identification of a large CAA block and characterization of pericentromere retrotranposons. Chromosoma 114, 103–117 (2005). https://doi.org/10.1007/s00412-005-0342-8

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