黑海胆(Arbacialixula)是居住在地中海沿海浅水区的基石物种,这是沿海社区结构的关键驱动力。这里,我们介绍了该物种的第一个基因组组装和注释,作为第一个Arbacioida基因组,包括核基因组和线粒体基因组.为了获得染色体水平的装配,我们使用了PacBio高保真(HiFi)读取和染色质捕获读取(Omni-C)的组合。此外,我们产生了编码和非编码基因的高质量核注释,通过使用来自A.lixula的几个个体的已发表的RNA-Seq数据和来自密切相关物种的基因模型。核基因组组装的总跨度为607.91Mb,与其实验估计的基因组大小一致。组装包含22个染色体尺度的支架(总长度的96.52%),这与它已知的核型一致。从核基因组中预测了总共72,767个转录本,24,171编码,和48,596个非编码,包括lncRNA,snoRNA,和tRNA。环化的线粒体基因组有15740bp,包含13个蛋白质编码基因,2rRNA,和22tRNA。该参考基因组将增强正在进行的A.lixula研究,并使更广泛的海胆科学界受益。
The black sea urchin (Arbacia lixula) is a keystone species inhabiting the coastal shallow waters of the Mediterranean Sea, which is a key driver of littoral communities\' structure. Here, we present the first genome assembly and annotation of this species, standing as the first Arbacioida genome, including both nuclear and mitochondrial genomes. To obtain a chromosome-level assembly, we used a combination of PacBio high fidelity (HiFi) reads and chromatin capture reads (Omni-C). In addition, we generated a high-quality nuclear annotation of both coding and non-coding genes, by using published RNA-Seq data from several individuals of A. lixula and gene models from closely related species. The nuclear genome assembly has a total span of 607.91 Mb, being consistent with its experimentally estimated genome size. The assembly contains 22 chromosome-scale scaffolds (96.52% of the total length), which coincides with its known karyotype. A total of 72,767 transcripts were predicted from the nuclear genome, 24,171 coding, and 48,596 non-coding that included lncRNA, snoRNA, and tRNAs. The circularized mitochondrial genome had 15,740 bp comprising 13 protein-coding genes, 2 rRNA, and 22 tRNA. This reference genome will enhance ongoing A. lixula studies and benefit the wider sea urchin scientific community.