背景回顾：Thousands of species will be sequenced in the next few years; however, understanding how their genomes work without an unlimited budget requires both molecular and novel evolutionary approaches. 

主要研究：We developed a sensitive sequence alignment pipeline to identify conserved noncoding sequences (CNSs) in the Andropogoneae tribe(multiple crop species descended from a common ancestor ~18 million years ago). 

研究对象：The Andropogoneae share similar physiology while being tremendously genomically diverse, harboring a broad range of ploidy levels, structural variation, and transposons. These contribute to the potential of Andropogoneae as a powerful system for studying CNSs and are factors we leverage to understand the function of maize CNSs. 

结果1-CNS分布模式：We found that 86% of CNSs were comprised of annotated features, including introns, UTRs, putative cis-regulatory elements, chromatin loop anchors, noncoding RNA genes, and several transposable element superfamilies. 

结果2-CNS富集区域：CNSs were enriched in active regions of DNA replication in the early S phase of the mitotic cell cycle and showed different DNA methylation ratios compared to the genome-wide background. 

结果3-CNS与顺式调控序列：More than half of putative cis-regulatory sequences (identified via other methods) overlapped with CNSs detected in this study. 

结果4-CNS与基因表达：Variants in CNSs were associated with gene expression levels, and CNS absence contributed to loss of gene expression. 

结果5-CNS与复制基因功能分化：Furthermore, the evolution of CNSs was associated with the functional diversification of duplicated genes in the context of maize subgenomes. 

结论：Our results provide a quantitative understanding of the molecular processes governing the evolution of CNSs in maize.

 摘 要 

在接下来的几年里，会有成千上万的物种将被测序；然而，让这些基因组如何在预算有限的情况下仍然发挥作用需要分子和新的进化研究方法。本文中，作者开发了一个敏感的序列比对流程，以鉴定蜀黍族（Andropogoneae tribe）中保守的非编码序列（CNS）。蜀黍族是包含玉米、高粱等多个作物在内的，起源于1800万年前共同祖先的一个分类单元。蜀黍族的植物虽然基因组多样性巨大，并具有广泛的倍性水平、结构变异和转座子，但是仍然具有相似的植物生理。这些特征使得蜀黍族成为了研究保守非编码序列的理想系统，同时也是用来理解玉米中保守非编码序列功能的绝佳途径。作者发现，86%的保守非编码序列由能够注释的序列组成，包括内含子、UTRs、假定的顺式调控元件、染色质环锚点（chromatin loop anchors）、非编码RNA基因以及一些转座子亚家族。在细胞有丝分裂S期早期，保守非编码序列主要富集于DNA复制的活跃区域，并且与全基因组背景相比，具有不同的DNA甲基化比率。作者发现，超过一半的预测顺式调控序列和本文所鉴定的保守非编码序列存在重叠。保守非编码序列的变异与基因的表达水平相关联，并且保守非编码序列的存在会导致基因表达的丢失。此外，玉米亚基因组中的研究显示，保守非编码序列的演化与复制基因的功能分化相关。本文的研究结果为玉米中保守非编码序列的演化提供了一个定量化的分子进程。