College of marine Sciences, Ningbo University, Ningbo, China.
School of Civil & Environmental Engineering and Geography Science, Ningbo University, Ningbo, China.
Sci Data. 2024 Oct 8;11(1):1100. doi: 10.1038/s41597-024-03914-9.
Pampus argenteus is a highly commercial marine fish whose population is declining sharply. Here, we generated a female P. argenteus genome, spanning 536.33 Mb with contig N50 of 1.79 Mb; 24070 genes (99.50% of 24,182) were functionally annotated. To improve quality of it, we assembled a 553.79 Mb genome of male fish with contig N50 of 24.75 Mb through HiFi and ultra-long ONT sequence technologies; 550.82 Mb were anchored onto 24 gap-free chromosomes; 22,892 genes (98.1% of 23,346) were functionally annotated; the QV value was 51.55 with 98.9% of BUSCO and 99.39% coverage of Illumina reads. Finally, we compared this genome with previous published one, revealing 37,301 SVs. 52.82 Mb and 18.05 Mb SDs were characterized in our and published assemblies, respectively, and 48.96 Mb PURs were constructed. Thus, this genome assembly exhibits excellent completeness, continuity and accuracy comparing to the published one, which can be current preferred reference genome. Overall, these works help aquaculture and wild resources recovery of P. argenteus and provide a valuable genetic resource for study.
银鲳是一种极具商业价值的海洋鱼类，其种群数量正在急剧下降。本研究生成了一个雌性银鲳基因组，大小为 536.33Mb，N50 为 1.79Mb；注释到了 24070 个基因（24182 个基因的 99.50%）。为了提高其质量，我们通过 HiFi 和超长 ONT 序列技术组装了一个雄性银鲳基因组，大小为 553.79Mb，N50 为 24.75Mb；550.82Mb 被锚定到 24 条无间隙染色体上；注释到了 55082 个基因（23346 个基因的 98.1%）；QV 值为 51.55，BUSCO 的 98.9%和 Illumina reads 的 99.39%都得到了覆盖。最后，我们将这个基因组与之前发表的基因组进行了比较，发现了 37301 个 SVs。我们和已发表的组装中分别有 52.82Mb 和 18.05Mb 的 SDs，构建了 48.96Mb 的 PURs。与已发表的基因组相比，这个基因组组装具有更好的完整性、连续性和准确性，可以作为当前首选的参考基因组。总的来说，这些工作有助于银鲳的水产养殖和野生资源恢复，并为研究提供了有价值的遗传资源。
