Department of Botany, University of British Columbia, Vancouver, BC, Canada.
Division of Biological Sciences, University of Montana, Missoula, MT, USA.
Mol Biol Evol. 2022 Jul 2;39(7). doi: 10.1093/molbev/msac153.
Prokaryotic genomes are usually densely packed with intact and functional genes. However, in certain contexts, such as after recent ecological shifts or extreme population bottlenecks, broken and nonfunctional gene fragments can quickly accumulate and form a substantial fraction of the genome. Identification of these broken genes, called pseudogenes, is a critical step for understanding the evolutionary forces acting upon, and the functional potential encoded within, prokaryotic genomes. Here, we present Pseudofinder, an open-source software dedicated to pseudogene identification and analysis in bacterial and archaeal genomes. We demonstrate that Pseudofinder's multi-pronged, reference-based approach can detect a wide variety of pseudogenes, including those that are highly degraded and typically missed by gene-calling pipelines, as well newly formed pseudogenes containing only one or a few inactivating mutations. Additionally, Pseudofinder can detect genes that lack inactivating substitutions but experiencing relaxed selection. Implementation of Pseudofinder in annotation pipelines will allow more precise estimations of the functional potential of sequenced microbes, while also generating new hypotheses related to the evolutionary dynamics of bacterial and archaeal genomes.
原核基因组通常密集排列着完整且功能正常的基因。然而，在某些情况下，例如最近的生态转变或极端种群瓶颈之后，破碎的和无功能的基因片段会迅速积累并形成基因组的重要部分。鉴定这些被称为假基因的断裂基因是理解作用于原核基因组的进化力量以及编码的功能潜力的关键步骤。在这里，我们介绍了 Pseudofinder，这是一款专门用于细菌和古菌基因组中假基因鉴定和分析的开源软件。我们证明，Pseudofinder 的多管齐下的基于参考的方法可以检测到各种各样的假基因，包括那些高度降解且通常被基因调用管道遗漏的假基因，以及仅包含一个或几个失活突变的新形成的假基因。此外，Pseudofinder 可以检测到缺乏失活替换但经历松弛选择的基因。在注释管道中实现 Pseudofinder 将允许更精确地估计测序微生物的功能潜力，同时也产生与细菌和古菌基因组进化动态相关的新假设。
