Files for viewing multiple genome alignment of marine invertebrates from "Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes"

<b>In Brief</b><br>This dataset contains the files needed to view a multiple genome alignment created for the publication "Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes", by Magri, Voronov, and Foley et al., 2025 (Nature Ecology &amp; Evolution).<br><b>Manuscript Abstract</b><br>Despite the growing abundance of sequenced animal genomes, we only have detailed knowledge of regulatory organization for a handful of lineages, particularly flies and vertebrates. These two taxa show contrasting trends in the molecular mechanisms of 3D chromatin organization and long-term evolutionary dynamics of cis-regulatory element (CREs) conservation. Here, we studyi the evolution and organization of the regulatory genome of echinoderms, a lineage whose phylogenetic position and relatively slow molecular evolution has proven particularly useful for evolutionary studies. We generated new reference genome assemblies for two species belonging to two different echinoderm classes: the purple sea urchin Strongylocentrotus purpuratus and the bat sea star Patiria miniata using PacBio and HiC data and characterize their 3D chromatin architecture. We show that these echinoderms have TAD-like domains that, like in flies, do not seem to be associated with CTCF motif orientation. We systematically profiled CREs during sea star and sea urchin development using ATAC-seq, comparing their regulatory logic and dynamics over multiple developmental stages. Finally, our analysis of sea urchin and sea star CRE evolution across multiple evolutionary distances and timescales showed several thousand elements conserved for hundreds of millions of years, revealing a vertebrate-like pattern of CRE evolution that probably constitutes an ancestral property of the regulatory evolution of animals.

**简要说明**
本数据集包含用于查看Magri、Voronov与Foley等人2025年发表于《自然·生态与演化》（*Nature Ecology & Evolution*）的论文《棘皮动物顺式调控元件与染色质组织的深度保守性揭示动物基因组的祖先调控特征》所构建的多基因组比对所需的全部文件。

**论文摘要**
尽管已测序的动物基因组数量与日俱增，但目前我们仅对少数几个类群的调控组组织模式具备详细认知，尤以果蝇与脊椎动物为甚。这两类群在三维染色质组织的分子机制以及顺式调控元件（cis-regulatory element, CRE）保守性的长期演化动力学上呈现出截然不同的趋势。本研究聚焦棘皮动物的调控基因组演化与组织模式——该类群的系统发育位置与相对缓慢的分子演化速率已被证实对演化研究极具价值。我们利用PacBio与Hi-C测序数据，为隶属于两个不同棘皮动物纲的两个物种构建了全新的参考基因组组装结果：紫球海胆（*Strongylocentrotus purpuratus*）与蝙蝠海星（*Patiria miniata*），并对二者的三维染色质结构进行了表征。研究发现，这类棘皮动物拥有类TAD结构域，与果蝇中的情况类似，这类结构域似乎并不与CTCF基序的取向相关联。我们通过ATAC-seq技术，对海星与海胆发育过程中的CRE进行了系统性表征，并比较了二者在多个发育阶段的调控逻辑与动态变化。最后，我们对海胆与海星在不同演化距离与时间尺度下的CRE演化进行分析，结果显示存在数千个保守了数亿年的调控元件，揭示出一类类似脊椎动物的CRE演化模式，这大概率代表了动物调控演化的祖先特征。