Gao Zijian, You Xinxin, Zhang Xinhui, Chen Jieming, Xu Tengfei, Huang Yu, Lin Xueqiang, Xu Junmin, Bian Chao, Shi Qiong
BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
Genomics. 2021 Sep;113(5):3349-3356. doi: 10.1016/j.ygeno.2021.07.026. Epub 2021 Jul 31.
Striped catfish (Pangasianodon hypophthalmus), belonging to the Pangasiidae family, has become an economically important fish with wide cultivation in Southeast Asia. Owing to the high-fat trait, it is always considered as an oily fish. In our present study, a high-quality genome assembly of the striped catfish was generated by integration of Illumina short reads, Nanopore long reads and Hi-C data. A 731.7-Mb genome assembly was finally obtained, with a contig N50 of 3.5 Mb, a scaffold N50 of 29.5 Mb, and anchoring of 98.46% of the assembly onto 30 pseudochromosomes. The genome contained 36.9% repeat sequences, and a total 18,895 protein-coding genes were predicted. Interestingly, we identified a tandem triplication of fatty acid binding protein 1 gene (fabp1; thereby named as fabp1-1, fabp1-2 and fabp1-3 respectively), which may be related to the high fat content in striped catfish. Meanwhile, the FABP1-2 and -3 isoforms differed from FABP1-1 by several missense mutations including R126T, which may affect the fatty acid binding properties. In summary, we report a high-quality chromosome-level genome assembly of the striped catfish, which provides a valuable genetic resource for biomedical studies on the high-fat trait, and lays a solid foundation for practical aquaculture and molecular breeding of this international teleost species.
条纹鲶鱼（Pangasianodon hypophthalmus）属于鲶科，已成为一种具有重要经济价值的鱼类，在东南亚广泛养殖。由于其高脂肪特性，它一直被视为油性鱼类。在我们目前的研究中，通过整合Illumina短读长、Nanopore长读长和Hi-C数据，生成了高质量的条纹鲶鱼基因组组装。最终获得了一个731.7 Mb的基因组组装，其重叠群N50为3.5 Mb，支架N50为29.5 Mb，并且98.46%的组装序列被锚定到30条假染色体上。该基因组包含36.9%的重复序列，共预测到18,895个蛋白质编码基因。有趣的是，我们鉴定出脂肪酸结合蛋白1基因（fabp1）存在串联三倍体（因此分别命名为fabp1-1、fabp1-2和fabp1-3），这可能与条纹鲶鱼的高脂肪含量有关。同时，FABP1-2和-3亚型与FABP1-1存在几个错义突变差异，包括R126T，这可能会影响脂肪酸结合特性。总之，我们报道了高质量的条纹鲶鱼染色体水平基因组组装，为高脂肪特性的生物医学研究提供了宝贵的遗传资源，并为这种国际硬骨鱼类的实际水产养殖和分子育种奠定了坚实基础。
