Tags

Type your tag names separated by a space and hit enter

Effective isolation of retrotransposons and repetitive DNA families from the wheat genome.
J Integr Plant Biol 2010; 52(7):679-91JI

Abstract

New classes of repetitive DNA elements were effectively identified by isolating small fragments of the elements from the wheat genome. A wheat A genome library was constructed from Triticum monococcum by degenerate cleavage with EcoO109I, the recognition sites of which consisted of 5'-PuGGNCCPy-3' multi-sequences. Three novel repetitive sequences pTm6, pTm69 and pTm58 derived from the A genome were screened and tested for high copy number using a blotting approach. pTm6 showed identity with integrase domains of the barley Ty1-Copia-retrotransposon BARE-1 and pTm58 showed similarity to the barley Ty3-gypsy-like retrotransposon Romani. pTm69, however, constituted a tandem array with useful genomic specificities, but did not share any identity with known repetitive elements. This study also sought to isolate wheat D-genome-specific repetitive elements regardless of the level of methylation, by genomic subtraction. Total genomic DNA of Aegilops tauschii was cleaved into short fragments with a methylation-insensitive 4 bp cutter, MboI, and then common DNA sequences between Ae. tauschii and Triticum turgidum were subtracted by annealing with excess T. turgidum genomic DNA. The D genome repetitive sequence pAt1 was isolated and used to identify an additional novel repetitive sequence family from wheat bacterial artificial chromosomes with a size range of 1 395-1 850 bp. The methods successfully led pathfinding of two unique repetitive families.

Authors+Show Affiliations

Molecular Genetics Laboratory, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan. tomita206@gmail.comNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

20590997

Citation

Tomita, Motonori, et al. "Effective Isolation of Retrotransposons and Repetitive DNA Families From the Wheat Genome." Journal of Integrative Plant Biology, vol. 52, no. 7, 2010, pp. 679-91.
Tomita M, Asao M, Kuraki A. Effective isolation of retrotransposons and repetitive DNA families from the wheat genome. J Integr Plant Biol. 2010;52(7):679-91.
Tomita, M., Asao, M., & Kuraki, A. (2010). Effective isolation of retrotransposons and repetitive DNA families from the wheat genome. Journal of Integrative Plant Biology, 52(7), pp. 679-91. doi:10.1111/j.1744-7909.2010.00954.x.
Tomita M, Asao M, Kuraki A. Effective Isolation of Retrotransposons and Repetitive DNA Families From the Wheat Genome. J Integr Plant Biol. 2010;52(7):679-91. PubMed PMID: 20590997.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Effective isolation of retrotransposons and repetitive DNA families from the wheat genome. AU - Tomita,Motonori, AU - Asao,Munenori, AU - Kuraki,Aya, PY - 2010/7/2/entrez PY - 2010/7/2/pubmed PY - 2010/10/1/medline SP - 679 EP - 91 JF - Journal of integrative plant biology JO - J Integr Plant Biol VL - 52 IS - 7 N2 - New classes of repetitive DNA elements were effectively identified by isolating small fragments of the elements from the wheat genome. A wheat A genome library was constructed from Triticum monococcum by degenerate cleavage with EcoO109I, the recognition sites of which consisted of 5'-PuGGNCCPy-3' multi-sequences. Three novel repetitive sequences pTm6, pTm69 and pTm58 derived from the A genome were screened and tested for high copy number using a blotting approach. pTm6 showed identity with integrase domains of the barley Ty1-Copia-retrotransposon BARE-1 and pTm58 showed similarity to the barley Ty3-gypsy-like retrotransposon Romani. pTm69, however, constituted a tandem array with useful genomic specificities, but did not share any identity with known repetitive elements. This study also sought to isolate wheat D-genome-specific repetitive elements regardless of the level of methylation, by genomic subtraction. Total genomic DNA of Aegilops tauschii was cleaved into short fragments with a methylation-insensitive 4 bp cutter, MboI, and then common DNA sequences between Ae. tauschii and Triticum turgidum were subtracted by annealing with excess T. turgidum genomic DNA. The D genome repetitive sequence pAt1 was isolated and used to identify an additional novel repetitive sequence family from wheat bacterial artificial chromosomes with a size range of 1 395-1 850 bp. The methods successfully led pathfinding of two unique repetitive families. SN - 1744-7909 UR - https://www.unboundmedicine.com/medline/citation/20590997/Effective_isolation_of_retrotransposons_and_repetitive_DNA_families_from_the_wheat_genome_ L2 - https://doi.org/10.1111/j.1744-7909.2010.00954.x DB - PRIME DP - Unbound Medicine ER -