Prophage maintenance is determined by environment-dependent selective sweeps rather than mutational availability

Prophages, viral sequences integrated into bacterial genomes, can confer fitness benefits and costs. Despite the risk of prophage activation and subsequent bacterial death, active prophages are present in most bacterial genomes. However, our understanding about the selective forces that maintain prophages in bacterial populations is scarce. Combining experimental evolution with stochastic modelling we found that prophage maintenance and loss are primarily determined by environmental conditions that amplify the net fitness effect of the prophage. Whole genome sequencing revealed that prophage loss occurs through environment-specific sequences of selective sweeps, leading to rapid prophage loss when prophages are costly. However, conflicting selection pressures that select against the prophage but for a prophage-encoded accessory gene can prolong prophage maintenance. The extent of prolonged maintenance depends on the sociality of this accessory gene. Selection for non-cooperative genes i..., We initiated a selection experiment to observe prophage maintenance over time in four different selection regimes using three bacterial genotypes, i.e., n_lys, s_lys and r_lys in a full-factorial design. With six biological replicates, each originating from single colonies, our design resulted in a total of 72 populations. We used the following selection regimes: (i) Amp at IC50 (i.e., 6.4 ug/ml) selecting for the prophage encoded AmpR present in the r_lys population, (ii) Mitomycin C (MMC) at a concentration of 0.1 ug/ml which induces the lytic cycle of prophages causing massive cell death due to host lysis and increases the costs of prophage carriage for the s_lys and r_lys populations, (iii) a combination of Amp and MMC at the same concentrations as above, to create opposing selective pressures on the r_lys populations and two competing selective pressures on s_lys populations, and (iv) LB broth as control. Unless otherwise stated, all bacteria were grown at 37° C and constant shakin..., , # Data from: Prophage maintenance is determined by environment-dependent selective sweeps rather than mutational availability

This database contains the data relevant to performing the analysis described in \"Prophage maintenance is determined by environment-dependent selective sweeps rather than mutational availability\" by Zachary M. Bailey, Claudia Igler, and Carolin C. Wendling

Here is a brief description of the data files located in this dataset:

## 01\_pfus\_phage\_dynamics\_Figure\_1.csv

This file contains the data for figure 1 of the manuscript.

genotype_treatment - the combination of both genotype and the treatment of the population

replicate_population - the biological replicate numbered 1-6 for each combination of genotype and population

time - the number of days since the beginning of the selection experiment

total_pfus - the absolute number of plaque forming units (free phages) per population (in PFUs/ml)

log10_pfus - the log base 10 value of the absolute values of p...

前噬菌体（Prophage）是整合于细菌基因组内的病毒序列，可赋予宿主细菌适合度收益与代价。尽管存在前噬菌体激活并导致宿主细菌死亡的风险，但大多数细菌基因组中仍存在活性前噬菌体。然而，目前学界对维持细菌种群中前噬菌体的选择压力机制尚缺乏深入理解。本研究将实验进化与随机建模相结合，发现前噬菌体的保留与丢失主要由放大其净适合度效应的环境条件所决定。全基因组测序结果显示，前噬菌体的丢失通过环境特异性的选择性清除（selective sweep）序列发生，当携带前噬菌体存在适合度代价时，会快速引发前噬菌体丢失。然而，存在冲突的选择压力：一方面对前噬菌体本身产生负选择，另一方面对前噬菌体编码的附属基因产生正选择，这一情况可延长前噬菌体的保留时长。该延长保留的程度取决于该附属基因的社会性。针对非合作基因的选择…… 我们启动了一项选择实验，以三种细菌基因型（即n_lys、s_lys和r_lys）为研究对象，采用全因子实验设计，在四种不同的选择处理方案下，随时间观测前噬菌体的保留情况。每个组合设置6个生物学重复，均起源于单菌落，最终共得到72个种群群体。本研究采用以下四种选择处理方案：(i) 浓度为半数抑制浓度（IC50，即6.4 μg/ml）的氨苄青霉素（Amp），用于筛选r_lys种群中由前噬菌体编码的氨苄青霉素抗性基因（AmpR）；(ii) 浓度为0.1 μg/ml的丝裂霉素C（Mitomycin C，MMC），该试剂可诱导前噬菌体进入裂解周期，引发宿主细胞大量裂解死亡，并提升s_lys与r_lys种群携带前噬菌体的适合度代价；(iii) 联合使用上述浓度的氨苄青霉素与丝裂霉素C，对r_lys种群形成相互拮抗的选择压力，同时对s_lys种群形成两种竞争性选择压力；(iv) 以LB肉汤培养基作为空白对照。除另有说明外，所有细菌均在37℃下恒温振荡培养…… # 数据来源："Prophage maintenance is determined by environment-dependent selective sweeps rather than mutational availability" 本数据库包含与Zachary M. Bailey、Claudia Igler及Carolin C. Wendling发表的上述研究中数据分析相关的全部数据。 以下是本数据集内各数据文件的简要说明： ## 01_pfus_phage_dynamics_Figure_1.csv 该文件包含论文图1对应的实验数据。 genotype_treatment：基因型与处理组的组合信息，即种群对应的细菌基因型与施加的处理方案 replicate_population：每个基因型-处理组合下的生物学重复编号，范围为1-6 time：自选择实验启动以来的培养天数 total_pfus：每个种群中每毫升的噬菌斑形成单位（plaque forming units, PFU）绝对数量 log10_pfus：总噬菌斑形成单位绝对数量的以10为底的对数值……