Evolution of lmiRNAs and their targets from MITEs for rice adaptation. Evolution of lmiRNAs and their targets from MITEs for rice adaptation

Twenty-four nucleotide long miRNAs (lmiRNAs) direct DNA methylation at target genes and regulate their transcription. The evolutionary origin of lmiRNAs and the range of lmiRNA-mediated regulation remain obscure. Here, we reannotated lmiRNAs and their targets in rice by applying stringent criteria. We found that the majority of lmiRNAs are derived from MITEs and most sites targeted by MITE-derived lmiRNAs reside within MITEs, suggesting co-evolution of lmiRNAs and their targets through MITE amplification. lmiRNAs undergo dynamically changes under stressed conditions and the genes targeted by lmiRNAs show an enrichment for stress responsive genes, suggesting that lmiRNAs are widely involved in plant response to stresses. We constructed the evolutionary histories of lmiRNAs and their targets. lmiRNAs emerged before or when the AA genome was diverged, while the emergence of lmiRNA targets coincided with or followed the emergence of lmiRNAs. Furthermore, we found that the sequences of a lmiRNA target site underwent variations, coincident with the divergence of rice accessions and the distribution of rice accessions in different geographical locations and climatic conditions. Our findings highlight MITEs as an important origin of lmiRNAs and suggest that the evolution of lmiRNA-target regulatory modules may contribute to rice adaptation to environmental changes. Overall design: sRNA-seq and WGBS-seq of 4-week-old seedling of NIP, dcl3a-17, osnrpd1-1. sRNA-seq line has three replication.

24核苷酸长度的微小RNA（lmiRNAs）可靶向调控靶基因的DNA甲基化，并进而调控其转录过程。目前，lmiRNAs的进化起源以及其介导的调控范围仍不明确。本研究通过严格的筛选标准，对水稻中的lmiRNAs及其靶标进行了重新注释。研究发现，绝大多数lmiRNAs源自微型反向重复转座子（MITEs），且由MITE来源的lmiRNAs所靶向的位点大多位于MITE内部，这表明lmiRNAs与其靶标可通过MITE的扩增实现协同进化。lmiRNAs在胁迫条件下会发生动态表达变化，且lmiRNAs所靶向的基因显著富集于胁迫响应基因集合中，这提示lmiRNAs广泛参与植物对胁迫的应答过程。本研究还构建了lmiRNAs及其靶标的进化历史。lmiRNAs的出现时间早于或与AA基因组分化时期同步，而lmiRNA靶标的出现则与lmiRNAs的出现时间一致或稍晚。此外，本研究发现，lmiRNA靶位点的序列会发生变异，且该变异与水稻种质的分化以及水稻种质在不同地理区位和气候条件下的分布特征相契合。本研究结果表明，MITEs是lmiRNAs的重要起源之一，且lmiRNA-靶标调控模块的进化可能有助于水稻适应环境变化。实验整体设计：对4周龄的日本晴（NIP）、dcl3a-17及osnrpd1-1突变体幼苗进行小RNA测序（sRNA-seq）与全基因组亚硫酸氢盐测序（WGBS-seq），其中sRNA-seq设置3次生物学重复。