Evolutionary epigenomics and, more generally, evolutionary functional-genomics, are emerging fields that study how non-DNA-encoded alterations in gene expression regulation are an important form of plasticity and adaptation. Previous evidence analysing plants’ comparative functional genomics has mostly focused on comparing same assay-matched experiments, missing the power of heterogeneous datasets for conservation inference. To fill this gap, we developed PlantFUN(ctional)CO(nservation) database, which is constituted by several tools and two main resources: inter-species chromatin states and functional genomics conservation scores, presented and analysed in this work for three well-established plant models (Arabidopsis thaliana, Oryza sativa and Zea mays). Overall, PlantFUNCO elucidated evolutionary information in terms of cross-species functional agreement. Therefore, providing a new complementary comparative-genomics source for assessing evolutionary studies. To illustrate the potential applications of this database, we replicated two previously published models predicting genetic redundancy in A. thaliana and found that chromatin states are a determinant of paralogs degree of functional divergence. These predictions were validated based on the phenotypes of mitochondrial alternative oxidase knockout mutants under two different stressors. Taking all the above into account, PlantFUNCO aim to leverage data diversity and extrapolate molecular mechanisms findings from different model organisms to determine the extent of functional conservation, thus, deepening our understanding of how plants epigenome and functional non-coding genome have evolved. PlantFUNCO is available at https://rocesv.github.io/PlantFUNCO.

中文翻译：

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PlantFUNCO：综合功能基因组数据库揭示重复分化进化的线索

进化表观基因组学，更一般地说，进化功能基因组学，是研究基因表达调控中非 DNA 编码的改变如何成为可塑性和适应的重要形式的新兴领域。先前分析植物比较功能基因组学的证据主要集中于比较相同的测定匹配实验，忽略了异质数据集用于保护推断的能力。为了填补这一空白，我们开发了 PlantFUN(ctional)CO(nservation) 数据库，该数据库由多种工具和两个主要资源组成：种间染色质状态和功能基因组学保守评分，在本工作中针对三个成熟的项目进行了介绍和分析植物模型（拟南芥、水稻和玉米）。总体而言，PlantFUNCO 阐明了跨物种功能一致性方面的进化信息。因此，为评估进化研究提供了一个新的补充比较基因组学来源。为了说明该数据库的潜在应用，我们复制了两个先前发表的预测拟南芥遗传冗余的模型，并发现染色质状态是旁系同源物功能分歧程度的决定因素。这些预测根据两种不同应激源下线粒体替代氧化酶敲除突变体的表型得到验证。考虑到上述所有因素，PlantFUNCO 旨在利用数据多样性并推断不同模式生物的分子机制发现，以确定功能保守的程度，从而加深我们对植物表观基因组和功能非编码基因组如何进化的理解。PlantFUNCO 可在 https://rocesv.github.io/PlantFUNCO 上获取。