The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK.
Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ 08349, USA.
Gigascience. 2021 Mar 25;10(3). doi: 10.1093/gigascience/giab020.
The Pacific oyster (Crassostrea gigas) is a bivalve mollusc with vital roles in coastal ecosystems and aquaculture globally. While extensive genomic tools are available for C. gigas, highly contiguous reference genomes are required to support both fundamental and applied research. Herein we report the creation and annotation of a chromosome-level assembly for C. gigas.
High-coverage long- and short-read sequence data generated on Pacific Biosciences and Illumina platforms were used to generate an initial assembly, which was then scaffolded into 10 pseudo-chromosomes using both Hi-C sequencing and a high-density linkage map. The assembly has a scaffold N50 of 58.4 Mb and a contig N50 of 1.8 Mb, representing a step advance on the previously published C. gigas assembly. Annotation based on Pacific Biosciences Iso-Seq and Illumina RNA-Seq resulted in identification of ∼30,000 putative protein-coding genes. Annotation of putative repeat elements highlighted an enrichment of Helitron rolling-circle transposable elements, suggesting their potential role in shaping the evolution of the C. gigas genome.
This new chromosome-level assembly will be an enabling resource for genetics and genomics studies to support fundamental insight into bivalve biology, as well as for selective breeding of C. gigas in aquaculture.
太平洋牡蛎（Crassostrea gigas）是一种双壳贝类软体动物，在全球沿海生态系统和水产养殖中具有重要作用。虽然有广泛的基因组工具可用于 C. gigas，但需要高度连续的参考基因组来支持基础研究和应用研究。本文报告了为 C. gigas 创建和注释染色体水平组装的情况。
在 Pacific Biosciences 和 Illumina 平台上生成的高覆盖度长读长和短读长序列数据用于生成初始组装，然后使用 Hi-C 测序和高密度连锁图谱将其支架构建成 10 个假染色体。该组装的支架 N50 为 58.4 Mb，串联 N50 为 1.8 Mb，代表了之前发表的 C. gigas 组装的一个进步。基于 Pacific Biosciences Iso-Seq 和 Illumina RNA-Seq 的注释导致鉴定了约 30,000 个推定的蛋白质编码基因。推定重复元件的注释突出了 Helitron 滚环转座元件的富集，表明它们可能在塑造 C. gigas 基因组的进化中发挥了作用。
这个新的染色体水平组装将成为遗传学和基因组学研究的基础资源，以支持对双壳类生物学的基础洞察，以及在水产养殖中对 C. gigas 的选择性繁殖。
