jarcasariego/ACER_clonal_divergence: v.1.0

This repository provides data and scripts used for the creation of the manuscript: "Multi-omic characterization of mechanisms contributing to rapid phenotypic plasticity in the coral Acropora cervicornis under divergent environments" Abstract Phenotypic plasticity is defined as a property of individual genotypes to produce different phenotypes when exposed to different environmental conditions. This ability may be expressed at behavioral, biochemical, physiological, and/or developmental levels, exerting direct influence over species' demographic performance. In reef-building corals, a group critically threatened by global change in the Anthropocene, non-genetic mechanisms (i.e., epigenetic and microbiome variation) have been shown to participate in plastic physiological responses to environmental change. Yet, the precise way in which these mechanisms interact, contribute to such responses, and their adaptive potential is still obscure. The present work aims to fill this gap by using a multi-omics approach targeting the complexity and interconnection among the components modulating phenotypic plasticity in staghorn coral (Acropora cervicornis) clones subject to different depth conditions. Results show conspicuous variation in lipidome, epigenome and transcriptome, but not in symbiotic and microbial communities. In addition, a potential shift towards a more heterotrophic feeding behavior was found in corals at higher depth. These observations are consistent with a multi-mechanism modulation of rapid acclimation in corals, underscoring the complexity of this process and the importance of a multifactorial approach to inform potential intervention to enhance coral adaptive capacity. <strong>Full Changelog</strong>: https://github.com/jarcasariego/ACER_clonal_divergence/commits/v.1.0本仓库提供了用于撰写下述手稿的数据与脚本文件：《不同环境下鹿角珊瑚（Acropora cervicornis）快速表型可塑性（phenotypic plasticity）调控机制的多组学（multi-omics）表征》。 摘要 表型可塑性（phenotypic plasticity）指单个基因型在不同环境条件下产生不同表型的特性。该能力可在行为、生化、生理及发育层面得以体现，直接影响物种的种群存续表现。造礁珊瑚（reef-building corals）是全新世（Anthropocene）全球变化下受到严重威胁的类群，已有研究表明，其非遗传调控机制（即表观遗传与微生物组（microbiome）变异）参与了对环境变化的可塑性生理响应。然而，这类机制如何相互作用、促成此类响应，以及其适应性潜力，目前仍不明确。本研究旨在填补这一研究空白：针对处于不同水深环境的鹿角珊瑚（Acropora cervicornis）克隆株，采用多组学方法解析调控表型可塑性的各组分间的复杂性与相互关联。 研究结果显示，珊瑚的脂质组（lipidome）、表观基因组（epigenome）与转录组（transcriptome）存在显著差异，但共生群落与微生物群落并未出现明显变化。此外，在水深较深的珊瑚中，发现其存在向异养（heterotrophic）摄食行为转变的潜在趋势。上述观测结果与珊瑚快速适应的多机制调控模型相符，凸显了该过程的复杂性，以及采用多因素研究方法为提升珊瑚适应性能力的潜在干预措施提供依据的重要性。 完整变更日志：https://github.com/jarcasariego/ACER_clonal_divergence/commits/v.1.0