Yepes-Blandón Jonny Andrés, Bian Chao, Benítez-Galeano María José, Aristizabal-Regino Jorge Luis, Estrada-Posada Ana Lucía, Mir Daiana, Vásquez-Machado Gersson, Atencio-García Víctor Julio, Shi Qiong, Rodríguez-Osorio Nélida
GIPEN, Piscícola San Silvestre SA, Santander, Colombia.
Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong, China.
Front Genet. 2023 Jan 19;13:989788. doi: 10.3389/fgene.2022.989788. eCollection 2022.
We report the first draft genome assembly for , the leading representative species of the Prochilodontidae family in Colombia. This 1.2-Gb assembly, with a GC content of 42.0% and a repetitive content of around 31.0%, is in the range of previously reported characid species genomes. Annotation identified 34,725 nuclear genes, and BUSCO completeness value was 94.9%. Gene ontology and primary metabolic pathway annotations indicate similar gene profiles for and the closest species with annotated genomes: blind cave fish () and red piranha (). A comparative analysis showed similar genome traits to other characid species. The fully sequenced and annotated mitochondrial genome reproduces the taxonomic classification of and confirms the low mitochondrial genetic divergence inside the genus. Phylogenomic analysis, using nuclear single-copy orthologous genes, also confirmed the evolutionary position of the species. This genome assembly provides a high-resolution genetic resource for sustainable management in Colombia and, as the first genome assembly for the Prochilodontidae family, will contribute to fish genomics throughout South America.
我们报告了哥伦比亚脂鲤科主要代表物种的首个基因组草图组装结果。这个12亿碱基对的组装结果，GC含量为42.0%，重复序列含量约为31.0%，处于先前报道的脂鲤科物种基因组范围内。注释鉴定出34725个核基因，BUSCO完整性值为94.9%。基因本体论和主要代谢途径注释表明，该物种与已注释基因组的最接近物种：盲穴鱼（）和红腹食人鱼（）具有相似的基因谱。比较分析显示，其基因组特征与其他脂鲤科物种相似。完全测序和注释的线粒体基因组再现了该物种的分类地位，并证实了该属内线粒体遗传差异较低。使用核单拷贝直系同源基因进行的系统基因组分析也证实了该物种的进化位置。这个基因组组装为哥伦比亚的可持续管理提供了高分辨率的遗传资源，并且作为脂鲤科的首个基因组组装，将为整个南美洲的鱼类基因组学做出贡献。
