Bian Chao, Hu Changxing, He Zhe, Li Zigang, Shi Qiong
Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518057, China.
State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
Sci Data. 2025 Mar 24;12(1):496. doi: 10.1038/s41597-025-04824-0.
X-ray tetra (Pristella maxillaris) originates from the lower Amazon basin in South America. It is renowned for its strikingly transparent body, which has drawn significant interests in biomedical research and the world ornamental fish industry. Nevertheless, genomic resources for this interesting fish species remains scarce, hindering exploration of the molecular basis behind its unique transparency. To address this gap, we constructed the first complete telomere-to-telomere (T2T) chromosome-scale genome assembly of the X-ray tetra by integration of PacBio HiFi, ONT ultra-long, and Hi-C sequencing technologies. This haplotypic assembly spans approximately 1.1 Gb, with a contig N50 of 42.8 Mb. It is anchored onto 25 chromosomes, highlighting a complete set of 50 telomeres and 25 centromeres. We predicted 514.3 Mb of repetitive sequences and annotated 28,456 protein-coding genes in the assembled genome. Subsequent BUSCO analysis discovered high genome completeness (98.0%). This high-quality T2T genome assembly provides a valuable genetic resource for investigating the molecular mechanisms underlying transparency, and supporting in-depth studies on functional genomics, genetic diversity, and selective breeding for this economically important species.
X射线鱼（Pristella maxillaris）原产于南美洲亚马逊河下游流域。它以其惊人的透明身体而闻名，这引起了生物医学研究和全球观赏鱼产业的极大兴趣。然而，这种有趣的鱼类的基因组资源仍然稀缺，阻碍了对其独特透明度背后分子基础的探索。为了填补这一空白，我们通过整合PacBio HiFi、ONT超长和Hi-C测序技术，构建了首个X射线鱼的从端粒到端粒（T2T）染色体水平的基因组组装。这个单倍型组装体跨度约为1.1Gb，重叠群N50为42.8Mb。它被锚定到25条染色体上，突出显示了一套完整的50个端粒和25个着丝粒。我们在组装的基因组中预测了514.3Mb的重复序列，并注释了28456个蛋白质编码基因。随后的BUSCO分析发现基因组完整性很高（98.0%）。这种高质量的T2T基因组组装为研究透明度背后的分子机制提供了宝贵的遗传资源，并支持对这种经济上重要的物种进行功能基因组学、遗传多样性和选择性育种的深入研究。
