Genome‐wide analysis of short interspersed nuclear elements SINES revealed high sequence conservation, gene association and retrotranspositional activity in wheat. (13th August 2013)

• Record Type: Journal Article
• Authors: Ben‐David, Smadar; Yaakov, Beery; Kashkush, Khalil
• Is Part Of: Plant journal. Volume 76:Number 2(2013:Oct.)
• Page Start: 201
• Page End: 210
• Publication Date: 2013-08-13
• Subjects: Plant molecular biology -- Periodicals; Plant cells and tissues -- Periodicals; Botany -- Periodicals; 580
• DOI: 10.1111/tpj.12285
• Languages: English
• ISSNs: 0960-7412

Abstract

<abstract abstract-type="main" id="tpj12285-abs-0001"> <title>Summary</title> <p>Short interspersed nuclear elements (SINEs) are non‐autonomous non‐LTR retroelements that are present in most eukaryotic species. While SINEs have been intensively investigated in humans and other animal systems, they are poorly studied in plants, especially in wheat (<italic>Triticum aestivum</italic>). We used quantitative PCR of various wheat species to determine the copy number of a wheat SINE family, termed <italic>Au</italic> SINE, combined with computer‐assisted analyses of the publicly available 454 pyrosequencing database of <italic>T. aestivum</italic>. In addition, we utilized site‐specific PCR on 57 <italic>Au</italic> SINE insertions, transposon methylation display and transposon display on newly formed wheat polyploids to assess retrotranspositional activity, epigenetic status and genetic rearrangements in <italic>Au</italic> SINE, respectively. We retrieved 3706 different insertions of <italic>Au</italic> SINE from the 454 pyrosequencing database of <italic>T. aestivum</italic>, and found that most of the elements are inserted in A/T‐rich regions, while approximately 38% of the insertions are associated with transcribed regions, including known wheat genes. We observed typical retrotransposition of <italic>Au</italic> SINE in the second generation of a newly formed wheat allohexaploid, and massive hypermethylation in CCGG sites surrounding <italic>Au</italic> SINE in the third generation. Finally, we observed huge differences in the copy numbers in diploid <italic>Triticum</italic> and <italic>Aegilops</italic> species, and a significant increase in the copy numbers in natural wheat polyploids, but no significant increase in the copy number of <italic>Au</italic> SINE in the first four generations for two of three newly formed allopolyploid species used in this study. Our data indicate that SINEs may play a prominent role in the genomic evolution of wheat through stress‐induced activation.</p> </abstract>