背景回顾：DNA methylation is changed and associates with gene expression alterations in plant response to phosphate starvation (Pi-), a common stress that impacts plant growth and productivity.

提出问题：However, in the horticultural model species tomato, the dynamics of DNA methylation and its relation with the changes of gene transcription and alternative splicing (AS) under Pi- are unknown. 

主要研究：Here, we performed integrative methylome and transcriptome analyses of tomato seedlings under Pi deficient and sufficient conditions.

结果1-磷饥饿诱导的差异甲基化、基因表达和可变剪切：We found Pi- caused a slight increase in overall methylation level, with millions of differentially methylated cytosines (DmCs) and a few hundred differentially methylated regions (DMRs). We also identified thousands of differentially expressed (DE) and differential AS (DAS) genes induced by Pi-, and found DmCs were more distributed in non-expressed genes than in DE or DAS genes. 

结果2-DNA甲基化与DE和DAS之间的关联：Moreover, DNA methylation alterations weakly correlated with transcription changes but not DAS events, and hyper-CHH-DMRs overlapping with transposable elements (TEs) were enriched in a subset of PSR genes. 

结果3-DNA甲基化与TEs：We propose that DNA methylation changes may associate with differential expression of some PSR genes, but most of these changes probably control the expression of nearby TEs, rather than directly affecting transcription or AS of PSR genes. Besides, the pattern of methylation changes upon Pi- may largely be shaped by TE distributions. 

结论：Together, our study provides comprehensive insights into the association of DNA methylation with gene transcription and AS under Pi- in tomato, and may contribute to unveiling novel roles of epigenetic mechanisms in plant stress response.

 摘 要 

磷饥饿对于植物来说，是一种普遍性的植物生长和产量限制因子，而在植物响应磷饥饿时，DNA甲基化会发生改变，并且与基因表达的改变存在关联。但是，在园艺模式植物番茄中，磷饥饿条件下DNA甲基化动态及其与基因转录和可变剪切之间的关系都还不清楚。本文中，作者对磷饥饿和磷饱和条件下的番茄实生苗进行了甲基化组和转录组分析。作者发现，磷饥饿导致了整体甲基化水平的略微上调，同时在磷饥饿和磷饱和条件下，番茄基因组上存在数百万个差异甲基化的胞嘧啶（DmCs）以及数百个差异甲基化的区域（DMRs）。作者还鉴定了数千个由磷诱导的差异表达（DE）和差异可变剪切（DAS）的基因，并且发现相比于DE和DAS，DmCs更多的分布在非表达的基因中。此外，DNA甲基化的改变与转录改变呈现出弱的相关，但是与DAS则不存在相关性，并且与转座子TEs重叠的hyper-CHH-DMRs在PSR基因的一个子集中富集。作者提出DNA甲基化的改变可能与某些PSR基因的差异表达存在关联，但是大部分这些DNA甲基化的改变可能更加偏向于控制基因邻近TEs的表达，而不是直接控制PSRs基因的转录或者可变剪切。此外，磷饥饿诱导的甲基化改变模式可能受到TE分布的影响较大。综上，本文的研究为番茄在磷饥饿条件下DNA甲基化与基因表达和可变剪切的相关性提供了综合的见解，同时也揭示了表观机制作用于植物胁迫响应的新作用。