New Insights into Nested Long Terminal Repeat Retrotransposons in Brassica Species
New Insights into Nested Long Terminal Repeat Retrotransposons in Brassica Species
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DOI：
10.1093/mp/sss081
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发表时间：
2013-03-01
期刊：
影响因子：
27.5
通讯作者：
Fu, Donghui
中科院分区：
文献类型：
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作者：
Wei, Lijuan;Xiao, Meili;Fu, Donghui
长末端重复（LTR）反转录转座子是最重要的转座子类型之一，它不断改变或修改基因功能，并通过急剧增殖来重组基因组。许多 LTR-TE 优先插入其他 LTR-TE 中，但这些嵌套 LTR-TE 的原因和进化意义尚不清楚。本研究扫描了总共1.52Gb的含有2020个细菌人工染色体（BAC）的Brassica序列，并选择了6个具有极其嵌套的LTR-TE（LTR-TE密度：7.24/kb）的细菌人工染色体（BAC）克隆进行进一步分析。发现6个BAC中的4个中的大多数LTR-TE源自BAC区域内的逆转录转座子的快速增殖，只有少数LTR-TE源自BAC区域外的逆转录转座子的增殖和插入，大约523Mya。 LTR-TE 也优选插入富含 TA 的重复区域。 Genescan 进行基因预测，在 0.84Mb 的 BAC 总序列中识别出 207 个基因。只有少数基因（3/207）可以与芸苔表达序列标签（EST）数据库匹配，表明大多数基因在逆转录转座子插入后处于失活状态。六个 BAC 中的五个被认为是着丝粒。因此，着丝粒区域中的嵌套LTR-TE会快速复制、重复插入，并起到抑制基因活性和重新洗牌着丝粒序列结构的作用。我们的结果表明，LTR-TE 在局部范围内爆发和增殖，以创建嵌套的 LTR-TE 区域，并且这些嵌套的 LTR-TE 在着丝粒的形成中发挥作用。
Long terminal repeat (LTR) retrotransposons, one of the foremost types of transposons, continually change or modify gene function and reorganize the genome through bursts of dramatic proliferation. Many LTR-TEs preferentially insert within other LTR-TEs, but the cause and evolutionary significance of these nested LTR-TEs are not well understood. In this study, a total of 1.52Gb of Brassica sequence containing 2020 bacterial artificial chromosomes (BACs) was scanned, and six bacterial artificial chromosome (BAC) clones with extremely nested LTR-TEs (LTR-TEs density: 7.24/kb) were selected for further analysis. The majority of the LTR-TEs in four of the six BACs were found to be derived from the rapid proliferation of retrotransposons originating within the BAC regions, with only a few LTR-TEs originating from the proliferation and insertion of retrotransposons from outside the BAC regions approximately 523Mya. LTR-TEs also preferably inserted into TA-rich repeat regions. Gene prediction by Genescan identified 207 genes in the 0.84Mb of total BAC sequences. Only a few genes (3/207) could be matched to the Brassica expressed sequence tag (EST) database, indicating that most genes were inactive after retrotransposon insertion. Five of the six BACs were putatively centromeric. Hence, nested LTR-TEs in centromere regions are rapidly duplicated, repeatedly inserted, and act to suppress activity of genes and to reshuffle the structure of the centromeric sequences. Our results suggest that LTR-TEs burst and proliferate on a local scale to create nested LTR-TE regions, and that these nested LTR-TEs play a role in the formation of centromeres.