Extensive Families of miRNAs and PHAS Loci in Norway Spruce Demonstrate the Origins of Complex phasiRNA Networks in Seed Plants.
Extensive Families of miRNAs and PHAS Loci in Norway Spruce Demonstrate the Origins of Complex phasiRNA Networks in Seed Plants.
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DOI：
10.1093/molbev/msv164
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发表时间：
2015-11
影响因子：
10.7
通讯作者：
Meyers BC
中科院分区：
文献类型：
--
作者：
Xia R;Xu J;Arikit S;Meyers BC
在真双子叶植物中，miR 482/miR 2118超家族调控并促使编码抗病蛋白的NB-LRR（核苷酸结合富含亮氨酸重复序列）基因产生阶段性次级小干扰RNA（siRNA）。在禾本科植物中，该miRNA家族触发长非编码RNA在生殖组织中特异性地产生siRNA。为了了解这种功能的分歧，我们研究了小RNA人口在古代裸子植物挪威云杉（云杉）。云杉中有多达41个miRNA家族被发现可以触发不同PHAS基因座产生phasiRNA（阶段性二级siRNA），其中有19个miRNA家族能够靶向超过750个NB-LRR基因以产生phasiRNA。miR 482/miR 2118在云杉中由至少24个前体基因座编码，不仅靶向NB-LRR基因以触发phasiRNA产生（如在真双子叶植物中），而且靶向非编码PHAS基因座，优先在雄性或雌性球果中产生phasiRNA，这让人想起其在禾本科植物中的作用。这些数据表明，存在于裸子植物中的miR 482/miR 2118的双重功能选择性地但分歧地保留在开花植物中。一些MIR 482/MIR 2118前体具有极长的茎环结构，其中一个臂显示出与云杉NB-LRR基因的显著序列相似性，表明通过基因复制从NB-LRR基因进化起源。我们还表征了扩展的miR 390-TAS 3（TRANS-ACTING siRNA GENE 3）-ARF（AUXIN responsible FACTOR）途径，其包含18个具有不同特征的TAS 3基因。最后，我们对云杉miRNAs及其靶基因进行了注释。总之，这些数据扩展了我们对植物中phasiRNA网络和植物miRNAs进化的理解，特别是miR 482/miR 2118及其功能多样性。
In eudicot plants, the miR482/miR2118 superfamily regulates and instigates the production of phased secondary small interfering RNAs (siRNAs) from NB-LRR (nucleotide binding leucine-rich repeat) genes that encode disease resistance proteins. In grasses, this miRNA family triggers siRNA production specifically in reproductive tissues from long noncoding RNAs. To understand this functional divergence, we examined the small RNA population in the ancient gymnosperm Norway spruce (Picea abies). As many as 41 miRNA families in spruce were found to trigger phasiRNA (phased, secondary siRNAs) production from diverse PHAS loci, with a remarkable 19 miRNA families capable of targeting over 750 NB-LRR genes to generate phasiRNAs. miR482/miR2118, encoded in spruce by at least 24 precursor loci, targets not only NB-LRR genes to trigger phasiRNA production (as in eudicots) but also noncoding PHAS loci, generating phasiRNAs preferentially in male or female cones, reminiscent of its role in the grasses. These data suggest a dual function of miR482/miR2118 present in gymnosperms that was selectively yet divergently retained in flowering plants. A few MIR482/MIR2118 precursors possess an extremely long stem-loop structure, one arm of which shows significant sequence similarity to spruce NB-LRR genes, suggestive of an evolutionary origin from NB-LRR genes through gene duplication. We also characterized an expanded miR390-TAS3 (TRANS-ACTING SIRNA GENE 3)-ARF (AUXIN RESPONSIVE FACTOR) pathway, comprising 18 TAS3 genes of diverse features. Finally, we annotated spruce miRNAs and their targets. Taken together, these data expand our understanding of phasiRNA network in plants and the evolution of plant miRNAs, particularly miR482/miR2118 and its functional diversification.