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. 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). 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. We found that 86% of CNSs were comprised of annotated features, including introns, UTRs, putative cis-regulatory elements, chromatin loop anchors, noncoding RNA (ncRNA) genes, and several transposable element superfamilies. 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. More than half of putative cis-regulatory sequences (identified via other methods) overlapped with CNSs detected in this study. Variants in CNSs were associated with gene expression levels, and CNS absence contributed to loss of gene expression. Furthermore, the evolution of CNSs was associated with the functional diversification of duplicated genes in the context of maize subgenomes. Our results provide a quantitative understanding of the molecular processes governing the evolution of CNSs in maize.

中文翻译：

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保守的非编码序列提供了对玉米调控序列和基因表达缺失的见解

未来几年将对数千个物种进行测序；然而，在没有无限预算的情况下，了解它们的基因组是如何工作的，需要分子和新颖的进化方法。我们开发了一个敏感的序列比对管道来识别 Androgogonae 部落（多种作物物种源自约 1800 万年前的共同祖先）中的保守非编码序列 (CNS)。穿心莲亚科具有相似的生理学特征，同时具有巨大的基因组多样性，具有广泛的倍性水平、结构变异和转座子。这些有助于发挥 Andropogonae 作为研究 CNS 的强大系统的潜力，也是我们用来了解玉米 CNS 功能的因素。我们发现 86% 的 CNS 由注释特征组成，包括内含子、UTR、推定的顺式调控元件、染色质环锚、非编码 RNA (ncRNA) 基因和几个转座元件超家族。CNS 在有丝分裂细胞周期早期 S 期的 DNA 复制活跃区域富集，并且与全基因组背景相比表现出不同的 DNA 甲基化比率。超过一半的推定顺式调控序列（通过其他方法鉴定）与本研究中检测到的 CNS 重叠。CNS 的变异与基因表达水平相关，CNS 的缺失会导致基因表达的丧失。此外，中枢神经系统的进化与玉米亚基因组中重复基因的功能多样化有关。我们的结果提供了对控制玉米中枢神经系统进化的分子过程的定量理解。