摘要
鲟鱼是全球现存鱼类中最为古老的种类之一,全基因组复制(Whole genome duplication,WGD)事件在鲟形目祖先中多次发生,导致鲟科物种普遍具有多倍性的复杂基因组,这使得鲟鱼成为研究基因组多倍化的理想模型。本研究使用流式细胞仪测定闪光鲟(Acipenser stellatus)、小体鲟(A. ruthenus)和欧鳇(Huso huso)3个四倍体鲟鱼的基因组大小分别为2.30、2.16和2.15 Gb,达氏鳇(H. dauricus)、施氏鲟(A. schrenckii)、俄罗斯鲟(A. gueldenstaedtii)和中华鲟(A. sinensis)4个八倍体鲟鱼的基因组大小分别为4.36、4.56、4.51和4.33 Gb。使用Illumina高通量测序对7种鲟鱼进行了全基因组survey测序和组装。基于这些鲟鱼survey基因组进行的系统发育分析表明,鲟科起源于3亿年前,在约1.55亿年前分化为大西洋和太平洋两个分支,不同地理分布的鲟鱼基因组中,免疫相关的基因都发生了快速扩增。基于不同物种多个同源基因和携带杂合单核苷酸多态性(Single nucleotide polymorphism,SNP)的同一基因编码序列的同义替换率计算结果证明,鲟鱼特有的第三轮WGD发生于1.18亿~1.96亿年前。本研究为鲟科基因组研究提供了重要的基础数据,为鲟科鱼类的起源与进化提供了新的研究视角。
Sturgeons represent one of the most ancient species among the existing fish species.Mul⁃tiple whole genome duplication(WGD)events have occurred in the ancestors of the Acipenseriformes,resulting in the widespread polyploidy and complex genomic architectures across sturgeon species.These characteristics make sturgeons an exceptional model for investigating genome polyploidization and vertebrate genome evolution.Flow cytometry was used to estimate the genome sizes of three tetraploid species,Acipenser stellatus,Acipenser ruthenus,and Huso huso,at 2.30,2.16,and 2.15 Gb,as well as four octoploid species,Huso dauricus,Acipenser schrenckii,Acipenser gueldenstaedtii,and Acipenser sinensis,at 4.36,4.56,4.51,and 4.33 Gb.The genome survey sequencing and assembly were constructed on seven sturgeon species using Illumina high-throughput technology.Phylogenetic analysis based on the survey genomes suggests that the Acipenseridae originates approximately 300 mil⁃lion years ago,and subsequently diverges into Atlantic and Pacific lineages around 155 million years ago.Notably,a lineage-specific expansion of immune-related genes is detected across geographically distinct species,implying adaptive evolution.Furthermore,synonymous substitution rates(Ks)are cal⁃culated both among orthologous genes across species and within heterozygous alleles of the same genes,supporting a lineage-specific third round of WGD in sturgeons occurring between 118 and 196 million years ago.This study provides fundamental genomic resources for the sturgeon family and sheds new light on the evolutionary history and polyploidization events of this ancient vertebrate lineage.
作者
黄沁怡
刘洁
孔玲玉
周艳
齐茜
陆颖
HUANG Qinyi;LIU Jie;KONG Lingyu;ZHOU Yan;QI Qian;LU Ying(Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources,Ministry of Education,Shanghai Ocean University,Shanghai 201306,China;Key Laboratory of Freshwater Aquatic Genetic Resources,Ministry of Agriculture and Rural Affairs,Shanghai Ocean University,Shanghai 201306,China;College of Animal Science and Technology,Henan University of Science and Technology,Luoyang 471023,China)
出处
《内蒙古大学学报(自然科学版)》
2025年第6期603-615,共13页
Journal of Inner Mongolia University:Natural Science Edition
基金
河南省自然科学基金项目(232300420201)。
关键词
鲟鱼
基因组测序
比较基因组学
全基因组复制
多倍体
sturgeon
genome sequencing
comparative genomics
whole genome duplication
polyploid
