Root architecture varies widely between species; it even varies between ecotypes of the same species, despite strong conservation of the coding portion of their genomes. By contrast, noncoding RNAs evolve rapidly between ecotypes and may control their differential responses to the environment, since several long noncoding RNAs (lncRNAs) are known to quantitatively regulate gene expression. Roots from ecotypes Columbia and Landsberg erecta of Arabidopsis (Arabidopsis thaliana) respond differently to phosphate starvation. Here, we compared transcriptomes (mRNAs, lncRNAs, and small RNAs) of root tips from these two ecotypes during early phosphate starvation. We identified thousands of lncRNAs that were largely conserved at the DNA level in these ecotypes. In contrast to coding genes, many lncRNAs were specifically transcribed in one ecotype and/or differentially expressed between ecotypes independent of phosphate availability. We further characterized these ecotype-related lncRNAs and studied their link with small interfering RNAs. Our analysis identified 675 lncRNAs differentially expressed between the two ecotypes, including antisense RNAs targeting key regulators of root-growth responses. Misregulation of several lincRNAs showed that at least two ecotype-related lncRNAs regulate primary root growth in ecotype Columbia. RNA-sequencing analysis following deregulation of lncRNA NPC48 revealed a potential link with root growth and transport functions. This exploration of the noncoding transcriptome identified ecotype-specific lncRNA-mediated regulation in root apexes. The noncoding genome may harbor further mechanisms involved in ecotype adaptation of roots to different soil environments.

物种之间的根系结构差异很大。尽管它们基因组的编码部分有很强的保守性，但即使在同一物种的生态型之间它也有所不同。相比之下，非编码RNA在生态型之间迅速发展，并可以控制它们对环境的差异反应，因为已知几种长的非编码RNA（lncRNA）可以定量调节基因表达。拟南芥（Arabidopsis thaliana）的生态型哥伦比亚和兰斯伯格直立植物的根）对磷酸盐饥饿的反应不同。在这里，我们比较了早期磷酸盐饥饿期间这两种生态型的根尖的转录组（mRNA，lncRNA和小RNA）。我们鉴定了数千种在这些生态型中在DNA水平上基本保守的lncRNA。与编码基因相反，许多lncRNA在一种生态型中特异性转录和/或在生态型之间差异表达，而与磷酸盐的可利用性无关。我们进一步表征了这些与生态型相关的lncRNA，并研究了它们与小干扰RNA的联系。我们的分析鉴定了两种生态型之间差异表达的675个lncRNA，包括靶向根生长反应关键调控因子的反义RNA。几种lincRNA的调控异常表明，至少有两种与生态型相关的lncRNA调节着哥伦比亚生态型的原根生长。lncRNA NPC48失控后的RNA测序分析显示与根生长和转运功能的潜在联系。对非编码转录组的这种探索确定了根尖中生态型特异性lncRNA介导的调控。非编码基因组可能包含与根生态型适应不同土壤环境有关的其他机制。