A universal and constant rate of gene content change traces pangenome flux to LUCA.

IF 2.2 4区生物学 Q3 MICROBIOLOGY

Fems Microbiology Letters Pub Date : 2024-01-09 DOI:10.1093/femsle/fnae068

Katharina Trost, Michael R Knopp, Jessica L E Wimmer, Fernando D K Tria, William F Martin

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引用次数: 0

Abstract

Prokaryotic genomes constantly undergo gene flux via lateral gene transfer, generating a pangenome structure consisting of a conserved core genome surrounded by a more variable accessory genome shell. Over time, flux generates change in genome content. Here, we measure and compare the rate of genome flux for 5655 prokaryotic genomes as a function of amino acid sequence divergence in 36 universally distributed proteins of the informational core (IC). We find a clock of gene content change. The long-term average rate of gene content flux is remarkably constant across all higher prokaryotic taxa sampled, whereby the size of the accessory genome-the proportion of the genome harboring gene content difference for genome pairs-varies across taxa. The proportion of species-level accessory genes per genome, varies from 0% (Chlamydia) to 30%-33% (Alphaproteobacteria, Gammaproteobacteria, and Clostridia). A clock-like rate of gene content change across all prokaryotic taxa sampled suggest that pangenome structure is a general feature of prokaryotic genomes and that it has been in existence since the divergence of bacteria and archaea.

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基因含量变化的普遍性和恒定性追踪了泛基因组到 LUCA 的变化。

原核生物基因组通过横向基因转移不断发生基因变异，形成了由保守的核心基因组和可变的附属基因组外壳组成的泛基因组结构。随着时间的推移，通量会导致基因组内容发生变化。在这里，我们测量并比较了 5 655 个原核生物基因组的基因组通量速率与 36 个普遍分布的信息核蛋白（IC）的氨基酸序列差异的函数关系。我们发现了基因内容变化的时钟。在所有取样的高等原核生物类群中，基因内容变化的长期平均速率非常稳定，而附属基因组的大小--即基因组对中携带基因内容差异的基因组比例--则在不同类群中各不相同。每个基因组中物种级附属基因的比例从 0%（衣原体）到 30-33%（扁平蛋白杆菌、伽马蛋白杆菌、梭菌）不等。在所有取样的原核生物类群中，基因含量的变化率类似于时钟，这表明庞基因组结构是原核生物基因组的一个普遍特征，而且自细菌和古细菌分化以来就一直存在。

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

Fems Microbiology Letters 生物-微生物学

CiteScore

4.30

自引率

0.00%

发文量

112

审稿时长

1.9 months

期刊介绍： FEMS Microbiology Letters gives priority to concise papers that merit rapid publication by virtue of their originality, general interest and contribution to new developments in microbiology. All aspects of microbiology, including virology, are covered. 2019 Impact Factor: 1.987, Journal Citation Reports (Source Clarivate, 2020) Ranking: 98/135 (Microbiology) The journal is divided into eight Sections: Physiology and Biochemistry (including genetics, molecular biology and ‘omic’ studies) Food Microbiology (from food production and biotechnology to spoilage and food borne pathogens) Biotechnology and Synthetic Biology Pathogens and Pathogenicity (including medical, veterinary, plant and insect pathogens – particularly those relating to food security – with the exception of viruses) Environmental Microbiology (including ecophysiology, ecogenomics and meta-omic studies) Virology (viruses infecting any organism, including Bacteria and Archaea) Taxonomy and Systematics (for publication of novel taxa, taxonomic reclassifications and reviews of a taxonomic nature) Professional Development (including education, training, CPD, research assessment frameworks, research and publication metrics, best-practice, careers and history of microbiology) If you are unsure which Section is most appropriate for your manuscript, for example in the case of transdisciplinary studies, we recommend that you contact the Editor-In-Chief by email prior to submission. Our scope includes any type of microorganism - all members of the Bacteria and the Archaea and microbial members of the Eukarya (yeasts, filamentous fungi, microbial algae, protozoa, oomycetes, myxomycetes, etc.) as well as all viruses.