State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
Genome Biol Evol. 2019 Aug 1;11(8):2071-2077. doi: 10.1093/gbe/evz143.
As one economically important fish in the southeastern Himalayas, the giant devil catfish (Bagarius yarrelli) has been known for its extraordinarily large body size. It can grow up to 2 m, whereas the non-Bagarius sisorids only reach 10-30 cm. Another outstanding characteristic of Bagarius species is the salmonids-like reddish flesh color. Both body size and flesh color are interesting questions in science and also valuable features in aquaculture that worth of deep investigations. Bagarius species therefore are ideal materials for studying body size evolution and color depositions in fish muscles, and also potential organisms for extensive utilization in Asian freshwater aquaculture. In a combination of Illumina and PacBio sequencing technologies, we de novo assembled a 571-Mb genome for the giant devil catfish from a total of 153.4-Gb clean reads. The scaffold and contig N50 values are 3.1 and 1.6 Mb, respectively. This genome assembly was evaluated with 93.4% of Benchmarking Universal Single-Copy Orthologs completeness, 98% of transcripts coverage, and highly homologous with a chromosome-level-based genome of channel catfish (Ictalurus punctatus). We detected that 35.26% of the genome assembly is composed of repetitive elements. Employing homology, de novo, and transcriptome-based annotations, we annotated a total of 19,027 protein-coding genes for further use. In summary, we generated the first high-quality genome assembly of the giant devil catfish, which provides an important genomic resource for its future studies such as the body size and flesh color issues, and also for facilitating the conservation and utilization of this valuable catfish.
作为东南亚喜马拉雅山脉中一种重要的经济鱼类，巨型魔鬼鱼（Bagarius yarrelli）因其异常庞大的体型而闻名。它可以长到 2 米，而非 Bagarius 的 Sisorids 只能长到 10-30 厘米。Bagarius 物种的另一个显著特征是鲑鱼状的红色肉质。体型和肉质都是科学界有趣的问题，也是水产养殖中具有重要价值的特征，值得深入研究。因此，Bagarius 物种是研究鱼类肌肉体型进化和颜色沉积的理想材料，也是亚洲淡水水产养殖中广泛利用的潜在生物。在 Illumina 和 PacBio 测序技术的结合下，我们从头组装了一条来自总共 153.4Gb 清洁读数的巨型魔鬼鱼的 571Mb 基因组。支架和 contig N50 值分别为 3.1 和 1.6Mb。这个基因组组装通过 93.4%的基准通用单拷贝直系同源物完整性、98%的转录本覆盖度进行了评估，并且与基于染色体水平的斑点叉尾鮰（Ictalurus punctatus）基因组高度同源。我们检测到基因组组装的 35.26%由重复元件组成。利用同源性、从头预测和转录组预测注释，我们总共注释了 19027 个蛋白质编码基因，以供进一步使用。总之，我们生成了巨型魔鬼鱼的第一个高质量基因组组装，为其未来的研究提供了重要的基因组资源，例如体型和肉质问题，也为保护和利用这种有价值的鱼类提供了便利。
