De novo gene birth and the conundrum of ORFan genes in bacteria

IF 6.2 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Genome research Pub Date : 2025-07-10 DOI:10.1101/gr.280157.124

Md. Hassan uz-Zaman, Howard Ochman

引用次数: 0

Abstract

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.

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细菌中新生基因的诞生和ORFan基因的难题

细菌基因组值得注意的是，它们含有大量的谱系限制（“ORFan”）基因，这些基因被认为起源于水平转移，与已有基因的快速分化，或者来自非编码序列的从头出现。我们评估了探索这些假设的研究主体，并证明细菌ORFans起源的奥秘仍未解决。尽管如此，细菌为研究基因诞生的过程和机制提供了一些独特的途径，而这些途径在其他生物体中是不可行的。它们对实验进化分析的适应性，以及它们在基因含量上的品系水平差异，都促进了对非编码序列如何获得表达并转变为功能的研究——这些问题是表型新颖性起源的核心问题。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Genome research 生物-生化与分子生物学

CiteScore

12.40

自引率

1.40%

发文量

140

审稿时长

6 months

期刊介绍： Launched in 1995, Genome Research is an international, continuously published, peer-reviewed journal that focuses on research that provides novel insights into the genome biology of all organisms, including advances in genomic medicine. Among the topics considered by the journal are genome structure and function, comparative genomics, molecular evolution, genome-scale quantitative and population genetics, proteomics, epigenomics, and systems biology. The journal also features exciting gene discoveries and reports of cutting-edge computational biology and high-throughput methodologies. New data in these areas are published as research papers, or methods and resource reports that provide novel information on technologies or tools that will be of interest to a broad readership. Complete data sets are presented electronically on the journal''s web site where appropriate. The journal also provides Reviews, Perspectives, and Insight/Outlook articles, which present commentary on the latest advances published both here and elsewhere, placing such progress in its broader biological context.