International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China.
Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China.
Gigascience. 2021 Apr 23;10(4). doi: 10.1093/gigascience/giab024.
The hard-shelled mussel (Mytilus coruscus) is widely distributed in the temperate seas of East Asia and is an important commercial bivalve in China. Chromosome-level genome information of this species will contribute not only to the development of hard-shelled mussel genetic breeding but also to studies on larval ecology, climate change biology, marine biology, aquaculture, biofouling, and antifouling.
We applied a combination of Illumina sequencing, Oxford Nanopore Technologies sequencing, and high-throughput chromosome conformation capture technologies to construct a chromosome-level genome of the hard-shelled mussel, with a total length of 1.57 Gb and a median contig length of 1.49 Mb. Approximately 90.9% of the assemblies were anchored to 14 linkage groups. We assayed the genome completeness using BUSCO. In the metazoan dataset, the present assemblies have 89.4% complete, 1.9% incomplete, and 8.7% missing BUSCOs. Gene modeling enabled the annotation of 37,478 protein-coding genes and 26,917 non-coding RNA loci. Phylogenetic analysis showed that M. coruscus is the sister taxon to the clade including Modiolus philippinarum and Bathymodiolus platifrons. Conserved chromosome synteny was observed between hard-shelled mussel and king scallop, suggesting that this is shared ancestrally. Transcriptomic profiling indicated that the pathways of catecholamine biosynthesis and adrenergic signaling in cardiomyocytes might be involved in metamorphosis.
The chromosome-level assembly of the hard-shelled mussel genome will provide novel insights into mussel genome evolution and serve as a fundamental platform for studies regarding the planktonic-sessile transition, genetic diversity, and genomic breeding of this bivalve.
贻贝（Mytilus coruscus）广泛分布于东亚温带海域，是中国重要的商业双壳贝类。该物种的染色体水平基因组信息不仅将有助于贻贝遗传育种的发展，还有助于幼虫生态学、气候变化生物学、海洋生物学、水产养殖、生物污损和防污研究。
我们采用 Illumina 测序、Oxford Nanopore Technologies 测序和高通量染色体构象捕获技术相结合的方法，构建了贻贝的染色体水平基因组，总长 1.57Gb，平均 Contig 长度为 1.49Mb。大约 90.9%的组装序列锚定在 14 个连锁群上。我们使用 BUSCO 评估了基因组的完整性。在后生动物数据集方面，本研究的组装体具有 89.4%完整、1.9%不完整和 8.7%缺失 BUSCO。基因建模使注释 37478 个蛋白质编码基因和 26917 个非编码 RNA 基因成为可能。系统发育分析表明，贻贝与菲律宾蛤仔和扁玉螺所在的分支是姐妹群。贻贝和扇贝之间观察到保守的染色体同线性，这表明这是共同祖先的特征。转录组分析表明，心肌细胞儿茶酚胺生物合成和肾上腺素能信号通路可能参与变态。
贻贝染色体水平基因组的组装将为贻贝基因组进化提供新的见解，并为该双壳贝类的浮游-固着过渡、遗传多样性和基因组育种研究提供基础平台。
