Elimination of a Retrotransposon for Quenching Genome Instability in Modern Rice
Elimination of a Retrotransposon for Quenching Genome Instability in Modern Rice
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消除现代水稻基因组不稳定性的逆转录转座子
DOI：
10.1016/j.molp.2019.06.004
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发表时间：
2019
期刊：
影响因子：
27.5
通讯作者：
He Zuhua
中科院分区：
文献类型：
--
作者：
Peng Yu;Zhang Yingying;Gui Yijie;An Dong;Liu Junzhong;Xu Xun;Li Qun;Wang Junmin;Wang Wen;Shi Chunhai;Fan Longjiang;Lu Baorong;Deng Yiwen;Teng Sheng;He Zuhua
转座因子是植物基因组中含量最丰富的部分，在植物进化过程中对宿主基因组的形成起着重要的作用。它们在作物驯化中也发挥着重要作用。然而，在作物驯化过程中是否也选择了TE本身仍然未知。在此，我们鉴定了一个活性长末端重复序列（LTR）反转录转座子HUO，它是一个低拷贝数的LTR反转录转座子，在自然生长条件下具有活性，并通过雄性配子发生传递，HUO基因在所有野生稻和近半数的考古稻中都存在（1200-7000年前）和调查的地方品种，但在几乎所有现代品种中都不存在，表明它在水稻驯化和育种过程中逐渐消失。进一步的分析表明HUO通过RNA指导的DNA甲基化途径受到严格的基因沉默。我们的研究结果还表明，多个HUO拷贝可能通过改变全基因组DNA甲基化和小RNA生物合成以及改变整体基因表达来触发基因组不稳定性，从而导致抗病性和产量下降，与其在水稻育种中的消除相一致。总之，我们的研究表明，在作物驯化和育种过程中，活性反转录转座子的负选择可能对基因组稳定性很重要。
Transposable elements (TEs) constitute the most abundant portions of plant genomes and can dramatically shape host genomes during plant evolution. They also play important roles in crop domestication. However, whether TEs themselves are also selected during crop domestication has remained unknown. Here, we identify an active long terminal repeat (LTR) retrotransposon,HUO, as a potential target of selection during rice domestication and breeding.HUOis a low-copy-number LTR retrotransposon, and is active under natural growth conditions and transmitted through male gametogenesis, preferentially inserting into genomic regions capable of transcription.HUOexists in all wild rice accessions and about half of the archaeological rice grains (1200–7000 years ago) and landraces surveyed, but is absent in almost all modern varieties, indicating its gradual elimination during rice domestication and breeding. Further analyses showed thatHUOis subjected to strict gene silencing through the RNA-directed DNA methylation pathway. Our results also suggest that multipleHUOcopies may trigger genomic instability through altering genome-wide DNA methylation and small RNA biogenesis and changing global gene expression, resulting in decreased disease resistance and yield, coinciding with its elimination during rice breeding. Together, our study suggests that negative selection of an active retrotransposon might be important for genome stability during crop domestication and breeding.