State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
University of Chinese Academy of Sciences, Beijing 100049, China.
Int J Mol Sci. 2023 May 6;24(9):8367. doi: 10.3390/ijms24098367.
Genome duplication supplies raw genetic materials and has been thought to be essential for evolutionary innovation and ecological adaptation. Here, we select () genes to study the evolution of the duplicated genes in the polyploid complex, including amphidiploid and amphitriploid . Phylogenetic, chromosomal location and read coverage analyses indicate that most of genes exhibit a 2:1 relationship with zebrafish orthologs and confirm two rounds of polyploidy, an allotetraploidy followed by an autotriploidy, occurred during evolution. The lineage-specific expansion and biased retention/loss of genes are also found in . Transcriptome analyses across eight adult tissues and seven embryogenesis stages reveal varied expression dominance and divergence between the two species. The expression of in response to herpesvirus 2 infection shows different expression changes corresponding to distinct herpesvirus resistances in three gynogenetic clones. Finally, we find that most genes possess three alleles except eight genes that have lost one or two alleles due to genome rearrangement. The allele expression bias is prosperous for genes and varies during embryogenesis owning to the sequential expression manner of the alleles. The current study provides global insights into the genomic and transcriptional evolution of duplicated genes in a given superfamily resulting from multiple rounds of polyploidization.
基因组复制提供了原始的遗传物质，被认为是进化创新和生态适应的关键。在这里，我们选择了 () 个基因来研究多倍体复合体中重复基因的进化，包括双二倍体 () 和双三倍体 ()。系统发育、染色体位置和读取覆盖度分析表明，大多数 () 基因与斑马鱼直系同源物呈 2:1 关系，并证实了在进化过程中发生了两轮多倍化，先是异源四倍体，然后是同源三倍体。在 () 中也发现了基因的谱系特异性扩张和偏向保留/丢失。在八个成年组织和七个胚胎发生阶段的转录组分析揭示了两个物种之间表达优势的差异和分歧。对 2 型单纯疱疹病毒感染的响应表明，在三个雌核发育克隆中，由于对单纯疱疹病毒的不同抗性，表达有不同的变化。最后，我们发现大多数 () 基因除了由于基因组重排而丢失一个或两个等位基因的八个基因外，都有三个等位基因。等位基因表达偏向在 () 基因中很丰富，并且由于等位基因的顺序表达方式，在胚胎发生过程中有所不同。本研究为在多轮多倍化作用下，特定超家族中重复基因的基因组和转录组进化提供了全面的见解。
