Uz-Zaman Md Hassan, Ochman Howard
Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA.
Genome Res. 2025 Aug 1;35(8):1679-1688. doi: 10.1101/gr.280157.124.
Bacterial genomes are notable in that they contain large numbers of lineage-restricted ("ORFan") genes, which have been postulated to originate from either horizontal transfer, rapid divergence from pre-existing genes, or de novo emergence from noncoding sequences. We assess the body of research that explores each of these hypotheses and demonstrate that the mystery of the origin of bacterial ORFans still remains unresolved. Nonetheless, bacteria offer several unique avenues for research into the process and mechanics of gene birth at a resolution not feasible in other organisms. Both their amenability to experimental evolutionary analysis and their strain-level variation in gene content foster investigations of how noncoding sequences acquire expression and transition into functionality-questions central to the origin of phenotypic novelty.
细菌基因组的显著特点是它们包含大量谱系受限的（“孤儿”）基因，这些基因被推测起源于水平转移、从现有基因的快速分化，或从非编码序列中从头出现。我们评估了探索这些假设的各项研究，并表明细菌孤儿基因的起源之谜仍未得到解决。尽管如此，细菌为研究基因诞生的过程和机制提供了几条独特的途径，这是在其他生物体中无法实现的分辨率。它们对实验进化分析的适应性以及基因含量的菌株水平差异，都有助于研究非编码序列如何获得表达并转变为功能性——这些问题是表型新奇性起源的核心。
