Genome-wide analysis of short interspersed nuclear elements SINES revealed high sequence conservation, gene association and retrotranspositional activity in wheat.
Genome-wide analysis of short interspersed nuclear elements SINES revealed high sequence conservation, gene association and retrotranspositional activity in wheat.
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DOI：
10.1111/tpj.12285
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发表时间：
2013-10
期刊：
影响因子：
--
通讯作者：
Kashkush K
中科院分区：
文献类型：
--
作者：
Ben-David S;Yaakov B;Kashkush K
短散在核元件（西内斯）是存在于大多数真核生物中的非自主的非LTR逆转录元件。虽然西内斯在人类和其他动物系统中得到了深入研究，但在植物中，特别是在小麦（Triticum aestivum）中的研究很少。我们使用不同小麦物种的定量PCR来确定小麦SINE家族的拷贝数，称为Au SINE，结合计算机辅助分析公开可用的T.小麦此外，我们利用位点特异性PCR对57个Au SINE插入，转座子甲基化展示和转座子展示新形成的小麦多倍体，以评估反转录转座活性，表观遗传状态和遗传重排Au SINE。我们从T的454焦磷酸测序数据库中检索到3706个不同的Au SINE插入。aestivum的基因组序列，发现大多数元件插入在富含A/T的区域，而大约38%的插入与转录区域相关，包括已知的小麦基因。我们观察到Au SINE在一个新形成的小麦异源六倍体的第二代中发生了典型的反转录转座，而在第三代中Au SINE周围的CCGG位点发生了大量的超甲基化。最后，我们观察到二倍体小麦和山羊草属物种的拷贝数存在巨大差异，天然小麦多倍体的拷贝数显著增加，但本研究中使用的三个新形成的异源多倍体物种中的两个物种的Au SINE的拷贝数在前四代没有显著增加。我们的数据表明，西内斯可能通过胁迫诱导的激活在小麦基因组进化中发挥重要作用。
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 (Triticum aestivum). We used quantitative PCR of various wheat species to determine the copy number of a wheat SINE family, termed Au SINE, combined with computer-assisted analyses of the publicly available 454 pyrosequencing database of T. aestivum. In addition, we utilized site-specific PCR on 57 Au SINE insertions, transposon methylation display and transposon display on newly formed wheat polyploids to assess retrotranspositional activity, epigenetic status and genetic rearrangements in Au SINE, respectively. We retrieved 3706 different insertions of Au SINE from the 454 pyrosequencing database of T. aestivum, 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 Au SINE in the second generation of a newly formed wheat allohexaploid, and massive hypermethylation in CCGG sites surrounding Au SINE in the third generation. Finally, we observed huge differences in the copy numbers in diploid Triticum and Aegilops species, and a significant increase in the copy numbers in natural wheat polyploids, but no significant increase in the copy number of Au 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.
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影响因子：
5.1
作者：
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