Supporting data of genome assembly of the black tiger shrimp (Penaeus monodon)

The black tiger shrimp, <i>Penaeus monodon</i> (Fabricius, 1798) is a valuable commercial marine species in the inshore region of India Ocean and Southeast Asia. Even with extensive application of sequencing, genome resources are still lack in shrimp because of high heterozygosity and extremely high proportion of repeat sequences. In this study, the genome assembly of the black tiger shrimp was constructed in a hybrid strategy with Pacbio long reads and Illumna short reads. The contig N50 and scaffold N50 of the preliminary assembly were 116.8 kb and 268.5 kb, respectively. The scaffolds were anchored into chromosome-level assembly with Hi-C. The chromosome-level assembly was 2.1 Gb, accounting for 90.2% of the estimated genome size, and consisted of 53.7% of repeat sequences. A total of 29,387 protein-coding genes were predicted, 75.6% of which were successfully annotated with putative function. Furthermore, divergence between the black tiger shrimp and Pacific white shrimp was estimated to be 2.79 million years ago. And the population size of black tiger shrimp had been increasing since 50,000 years ago. This assembly is the second chromosome-level assembly in shrimp, and will be a valuable genomic resource for conservation and breeding studies of the black tiger shrimp in the future research.

斑节对虾（*Penaeus monodon*，Fabricius, 1798）是印度洋近岸区域及东南亚地区极具经济价值的商业海洋物种。尽管测序技术已得到广泛应用，但由于对虾基因组兼具高杂合度与极高的重复序列占比，其相关基因组资源仍较为匮乏。本研究采用PacBio长读长测序（Pacbio long reads）与Illumina短读长测序（Illumina short reads）相结合的混合组装策略，构建了斑节对虾的基因组组装序列。初步组装的重叠群N50（contig N50）与支架N50（scaffold N50）分别为116.8 kb与268.5 kb。研究人员通过Hi-C技术将所得支架锚定至染色体水平的基因组组装。该染色体水平组装的总长度为2.1 Gb，占预估基因组大小的90.2%，其中重复序列占比达53.7%。本研究共预测得到29387个蛋白质编码基因，其中75.6%的基因成功获得了推定功能注释。此外，研究估算得出斑节对虾与凡纳滨对虾（Pacific white shrimp）的分化时间约为279万年前。自5万年前起，斑节对虾的种群规模便持续扩张。该组装是虾类中第二个染色体水平的基因组组装，将为未来斑节对虾的种质保护与育种研究提供极具价值的基因组资源。