S1_VarData

Compiled table of evolved variants used to produce Figure 1. Columns refer to sample number (sample_number), whether the clone had evolved in a population with or without the plasmid (plasmid_trt, pQBR57 = plasmid-containing, plasmid- = plasmid free), with or without the other species (cul, ss = single-species, co=co-culture), the level of mercury treatment (mer, in µg/g), replicate (rep), species (spc, Pf = P. fluorescens, Pp = P. putida), whether the clone was carrying a plasmid (plasmid, P = plasmid+, T = contained Tn5042 but not the plasmid, 0 = contained neither plasmid nor Tn5042), the chromosome in which the variant was detected (chr, numbers are as the EMBL database with AM181176 referring to the P. fluorescens SBW25 chromosome, AE015451 to the P. putida KT2440 chromosome and LN713926 referring to pQBR57), the position of the variant (position and position.1, where the variant is a SNV/indel these numbers are identical and refer to the first base in question, where the variant is a TE insertion these numbers refer to the boundaries of the direct repeat caused on insertion, where the variant is a duplication or deletion these numbers refer to the start and end of the event respectively), the target gene (target, where the target it intergenic the upstream and downstream genes are given, separated by a dash), the type of mutation (type, either SNV/indel, or, if a TE insertion, the name of the TE), and the predicted effect of the mutation (effect, as determined by snpEff).

用于生成图1的进化变异体编译表格。各列信息说明如下：样本编号（sample_number）；质粒处理条件（plasmid_trt，pQBR57=携带质粒组，plasmid-=无质粒组）；培养模式（cul，ss=单物种培养，co=共培养）；汞处理浓度（mer，单位为µg/g）；生物学重复编号（rep）；菌株物种（spc，Pf=荧光假单胞菌P. fluorescens，Pp=恶臭假单胞菌P. putida）；克隆携带遗传元件情况（plasmid，P=携带质粒，T=携带Tn5042但无质粒，0=既无质粒也无Tn5042）；变异体所在染色体（chr，编号参考欧洲分子生物学实验室（EMBL）数据库：AM181176对应荧光假单胞菌SBW25染色体，AE015451对应恶臭假单胞菌KT2440染色体，LN713926对应pQBR57质粒）；变异体位置（position和position.1：若为单核苷酸变异/插入缺失（SNV/indel），二者数值一致，指向目标碱基的首位；若为转座因子（TE）插入，二者对应插入时产生的正向重复序列的边界；若为片段重复或缺失，二者分别对应该事件的起始与终止位点）；靶基因（target，若靶区域为基因间区，则以短横线分隔的上下游基因名称标注）；突变类型（type，可为SNV/indel；若为转座因子插入，则标注对应转座因子的名称）；突变预测效应（effect，由snpEff软件分析得到）。