Identification and functional analysis of flowering related microRNAs in common wild rice (Oryza rufipogon Griff.).
Identification and functional analysis of flowering related microRNAs in common wild rice (Oryza rufipogon Griff.).
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DOI：
10.1371/journal.pone.0082844
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Pei X
中科院分区：
文献类型：
--
作者：
Chen Z;Li F;Yang S;Dong Y;Yuan Q;Wang F;Li W;Jiang Y;Jia S;Pei X
MicroRNA (miRNA) 是一类非编码 RNA，通过降解和/或翻译抑制参与基因表达的转录后控制。已知有 661 种水稻 miRNA 对植物发育很重要。然而，野生稻中与开花相关的 miRNA 尚未得到表征。经广东省野生稻保护监督部门批准。我们使用高通量测序（深度测序）分析了普通野生稻中与开花相关的 miRNA，以了解水稻驯化过程中发生的变化，并阐明它们在开花中的功能。使用 Illumina 深度测序对三个野生野生稻 sRNA 文库、两个营养阶段（CWR-V1 和 CWR-V2）和一个开花阶段（CWR-F2）进行测序。从CWR-V1、CWR-V2和CWR-F2中分别获得了总共20,156,098、21,531,511和20,995,942个高质量的sRNA读数，其中3,448,185、4,265,048和2,833,527个读数与已知miRNA匹配。我们鉴定了 214 个 miRNA 家族中的 512 个已知的水稻 miRNA，并预测了 290 个新的 miRNA。靶向功能注释、GO 和 KEGG 通路分析预测 187 个 miRNA 调节开花相关基因的表达。开花相关miRNA的差异表达分析表明：95个miRNA在文库之间表达差异显着，其中66个为开花相关miRNA，如oru-miR97、oru-miR117、oru-miR135、oru-miR137等。 17个是早期开花相关的miRNA，包括在花转变期间诱导的osa-miR160f、osa-miR164d、osa-miR167d、osa-miR169a、osa-miR172b、oru-miR4等。实时 PCR 揭示了与深度测序相同的表达模式。 miRNA 靶点已被证实可在体内被 5'-RACE 切割，并受到 miRNA 的负调控。这是对野生稻开花 miRNA 的首次研究。该结果表明水稻驯化过程中发生了miRNA的变异，为进一步研究普通野生稻的相变和开花奠定了基础。由多个 miRNA 介导的复杂调控网络调节开花基因的表达，从而控制开花的诱导。
MicroRNAs (miRNAs) is a class of non-coding RNAs involved in post- transcriptional control of gene expression, via degradation and/or translational inhibition. Six-hundred sixty-one rice miRNAs are known that are important in plant development. However, flowering-related miRNAs have not been characterized in Oryza rufipogon Griff. It was approved by supervision department of Guangdong wild rice protection. We analyzed flowering-related miRNAs in O. rufipogon using high-throughput sequencing (deep sequencing) to understand the changes that occurred during rice domestication, and to elucidate their functions in flowering. Three O. rufipogon sRNA libraries, two vegetative stage (CWR-V1 and CWR-V2) and one flowering stage (CWR-F2) were sequenced using Illumina deep sequencing. A total of 20,156,098, 21,531,511 and 20,995,942 high quality sRNA reads were obtained from CWR-V1, CWR-V2 and CWR-F2, respectively, of which 3,448,185, 4,265,048 and 2,833,527 reads matched known miRNAs. We identified 512 known rice miRNAs in 214 miRNA families and predicted 290 new miRNAs. Targeted functional annotation, GO and KEGG pathway analyses predicted that 187 miRNAs regulate expression of flowering-related genes. Differential expression analysis of flowering-related miRNAs showed that: expression of 95 miRNAs varied significantly between the libraries, 66 are flowering-related miRNAs, such as oru-miR97, oru-miR117, oru-miR135, oru-miR137, et al. 17 are early-flowering -related miRNAs, including osa-miR160f, osa-miR164d, osa-miR167d, osa-miR169a, osa-miR172b, oru-miR4, et al., induced during the floral transition. Real-time PCR revealed the same expression patterns as deep sequencing. miRNAs targets were confirmed for cleavage by 5′-RACE in vivo, and were negatively regulated by miRNAs. This is the first investigation of flowering miRNAs in wild rice. The result indicates that variation in miRNAs occurred during rice domestication and lays a foundation for further study of phase change and flowering in O. rufipogon. Complicated regulatory networks mediated by multiple miRNAs regulate the expression of flowering genes that control the induction of flowering.
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影响因子：
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作者：
Dai X;Zhao PX
通讯作者：
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作者：
Chen C;Ridzon DA;Broomer AJ;Zhou Z;Lee DH;Nguyen JT;Barbisin M;Xu NL;Mahuvakar VR;Andersen MR;Lao KQ;Livak KJ;Guegler KJ
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