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Genome-wide analysis of Stowaway-like MITEs in wheat reveals high sequence conservation, gene association, and genomic diversification.
Plant Physiol. 2013 Jan; 161(1):486-96.PP

Abstract

The diversity and evolution of wheat (Triticum-Aegilops group) genomes is determined, in part, by the activity of transposable elements that constitute a large fraction of the genome (up to 90%). In this study, we retrieved sequences from publicly available wheat databases, including a 454-pyrosequencing database, and analyzed 18,217 insertions of 18 Stowaway-like miniature inverted-repeat transposable element (MITE) families previously characterized in wheat that together account for approximately 1.3 Mb of sequence. All 18 families showed high conservation in length, sequence, and target site preference. Furthermore, approximately 55% of the elements were inserted in transcribed regions, into or near known wheat genes. Notably, we observed significant correlation between the mean length of the MITEs and their copy number. In addition, the genomic composition of nine MITE families was studied by real-time quantitative polymerase chain reaction analysis in 40 accessions of Triticum spp. and Aegilops spp., including diploids, tetraploids, and hexaploids. The quantitative polymerase chain reaction data showed massive and significant intraspecific and interspecific variation as well as genome-specific proliferation and nonadditive quantities in the polyploids. We also observed significant differences in the methylation status of the insertion sites among MITE families. Our data thus suggest a possible role for MITEs in generating genome diversification and in the establishment of nascent polyploid species in wheat.

Authors+Show Affiliations

Department of Life Sciences, Ben-Gurion University, Beer-Sheva 84105, Israel.No affiliation info availableNo affiliation info available

Pub Type(s)

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

Language

eng

PubMed ID

23104862

Citation

Yaakov, Beery, et al. "Genome-wide Analysis of Stowaway-like MITEs in Wheat Reveals High Sequence Conservation, Gene Association, and Genomic Diversification." Plant Physiology, vol. 161, no. 1, 2013, pp. 486-96.
Yaakov B, Ben-David S, Kashkush K. Genome-wide analysis of Stowaway-like MITEs in wheat reveals high sequence conservation, gene association, and genomic diversification. Plant Physiol. 2013;161(1):486-96.
Yaakov, B., Ben-David, S., & Kashkush, K. (2013). Genome-wide analysis of Stowaway-like MITEs in wheat reveals high sequence conservation, gene association, and genomic diversification. Plant Physiology, 161(1), 486-96. https://doi.org/10.1104/pp.112.204404
Yaakov B, Ben-David S, Kashkush K. Genome-wide Analysis of Stowaway-like MITEs in Wheat Reveals High Sequence Conservation, Gene Association, and Genomic Diversification. Plant Physiol. 2013;161(1):486-96. PubMed PMID: 23104862.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide analysis of Stowaway-like MITEs in wheat reveals high sequence conservation, gene association, and genomic diversification. AU - Yaakov,Beery, AU - Ben-David,Smadar, AU - Kashkush,Khalil, Y1 - 2012/10/26/ PY - 2012/10/30/entrez PY - 2012/10/30/pubmed PY - 2013/6/19/medline SP - 486 EP - 96 JF - Plant physiology JO - Plant Physiol. VL - 161 IS - 1 N2 - The diversity and evolution of wheat (Triticum-Aegilops group) genomes is determined, in part, by the activity of transposable elements that constitute a large fraction of the genome (up to 90%). In this study, we retrieved sequences from publicly available wheat databases, including a 454-pyrosequencing database, and analyzed 18,217 insertions of 18 Stowaway-like miniature inverted-repeat transposable element (MITE) families previously characterized in wheat that together account for approximately 1.3 Mb of sequence. All 18 families showed high conservation in length, sequence, and target site preference. Furthermore, approximately 55% of the elements were inserted in transcribed regions, into or near known wheat genes. Notably, we observed significant correlation between the mean length of the MITEs and their copy number. In addition, the genomic composition of nine MITE families was studied by real-time quantitative polymerase chain reaction analysis in 40 accessions of Triticum spp. and Aegilops spp., including diploids, tetraploids, and hexaploids. The quantitative polymerase chain reaction data showed massive and significant intraspecific and interspecific variation as well as genome-specific proliferation and nonadditive quantities in the polyploids. We also observed significant differences in the methylation status of the insertion sites among MITE families. Our data thus suggest a possible role for MITEs in generating genome diversification and in the establishment of nascent polyploid species in wheat. SN - 1532-2548 UR - https://www.unboundmedicine.com/medline/citation/23104862/Genome_wide_analysis_of_Stowaway_like_MITEs_in_wheat_reveals_high_sequence_conservation_gene_association_and_genomic_diversification_ L2 - http://www.plantphysiol.org/cgi/pmidlookup?view=long&pmid=23104862 DB - PRIME DP - Unbound Medicine ER -