Durán-Fuentes Jeferson A, Maronna Maximiliano M, Palacios-Gimenez Octavio M, Castillo Elio R, Ryan Joseph F, Daly Marymegan, Stampar Sérgio N
Laboratory of Evolution and Aquatic Diversity (LEDALab), São Paulo State University (UNESP), São Paulo, Bauru, Brazil.
Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA.
BMC Genomics. 2025 May 13;26(1):473. doi: 10.1186/s12864-025-11591-0.
Genomic repetitive DNA sequences (Repeatomes, REPs) are widespread in eukaryotes, influencing biological form and function. In Cnidaria, an early-diverging animal lineage, these sequences remain largely uncharacterized. This study investigates sea anemone REPs (Cnidaria: Actiniaria) in a phylogenetic context. We sequenced and assembled de novo the genome of Actinostella flosculifera and analyzed a total of 38 nuclear genomes to create the first ActiniariaREP library (Actiniaria-REPlib). We compared Actiniaria-REPlib with Repbase and RepeatModeler2 libraries, and used dnaPipeTE to annotate REPs from genomic short-read datasets of 36 species for divergence landscapes.
Our study assembled and annotated the mitochondrial genomes, including 27 newly assembled ones. We re-annotated ~92% of the unknown sequences from the initial nuclear genome library, finding that 6.4-30.6% were DNA transposons, 2.1-11.6% retrotransposons, 1-28.4% tandem repeat sequences, and 1.2-7% unclassifiable sequences. Actiniaria-REPlib recovered 9.4x more REP sequences from actiniarian genomes than Dfam and 10.4x more than Repbase. It yielded 79,903 annotated TE consensus sequences (74,643 known, 5,260 unknown), compared to Dfam with 7,697 (3,742 known, 3,944 unknown) and Repbae (763 known).
Our study significantly enhances the characterization of sea anemone repetitive DNA, assembling mitochondrial genomes, re-annotating nuclear sequences, and identifying diverse repeat elements. Actiniaria-REPlib vastly outperforms existing databases, recovering significantly more REP sequences and providing a comprehensive resource for future genomic and evolutionary studies in Actiniaria.
基因组重复DNA序列（重复组，REPs）在真核生物中广泛存在，影响着生物的形态和功能。在刺胞动物门（一种早期分化的动物谱系）中，这些序列在很大程度上仍未得到充分表征。本研究在系统发育背景下研究海葵重复组（刺胞动物门：海葵目）。我们对花形星螅（Actinostella flosculifera）的基因组进行了测序和从头组装，并分析了总共38个核基因组，以创建首个海葵目重复组文库（Actiniaria-REPlib）。我们将Actiniaria-REPlib与Repbase和RepeatModeler2文库进行了比较，并使用dnaPipeTE从36个物种的基因组短读数据集注释重复组，以绘制分歧图谱。
我们的研究组装并注释了线粒体基因组，包括27个新组装的基因组。我们对初始核基因组文库中约92%的未知序列进行了重新注释，发现6.4 - 30.6%是DNA转座子，2.1 - 11.6%是逆转座子，1 - 28.4%是串联重复序列，1.2 - 7%是无法分类的序列。Actiniaria-REPlib从海葵目基因组中获得的重复组序列比Dfam多9.4倍，比Repbase多10.4倍。它产生了79,903个注释的转座元件共有序列（74,643个已知，5,260个未知），相比之下，Dfam有7,697个（3,742个已知，3,944个未知），Repbae有763个已知。
我们的研究显著增强了对海葵重复DNA的表征，组装了线粒体基因组，重新注释了核序列，并鉴定了多种重复元件。Actiniaria-REPlib大大优于现有数据库，获得了更多的重复组序列，并为海葵目未来的基因组和进化研究提供了全面的资源。
