In vitro and in planta data on the phosphonate sensitivity and fitness of Phytophthora nicotianae isolates from citrus orchards and nurseries across South Africa

All sheet names preceded by a number '2' contain data from Chapter 2, while those preceded by a number '3' contains data from Chapter 3. The data from the sheet named "2 All isolates" includes the identity of all isolates from the sample and supplementary information on the province from where they were sourced (MP = Mpumalanga; WC = Western Cape; EC = Eastern Cape; NW = North West; LP = Limpopo; NC = Northern Cape; Unknown = Samples from South Africa with unknown province of origin). The identity was determined by PCR Restriction fragment length polymorphism and sequencing of the internal transcribed spacer (ITS) region. The sheet named "2 In vitro isolates" contains only the Phytophthora nicotianae isolates that were screened for their in vitro sensitivity to phosphonates using an agar dilution method. Additional data provided for these isolates include the BLASTn identity of their respective ITS sequences, their province of origin, and previous phosphonate exposure history. The history of phosphonate exposure was ascertained through interviews with growers at sampled orchards and nurseries.

The sheet named "2 In vitro trials" contains the data collected from the in vitro phosphonate sensitivity trials conducted by an agar dilution method, using 50 identified P. nicotianae isolates, two different phosphonates namely ammonium phosphite (NH4-P) and potassium phosphite (K-P), five different concentrations of these phosphonates (0, 25, 75, 150, 600, 1250 ug/ml), three replicates and two trials. The average of two perpendicular measurements of radial colony diameter (minus the 8mm diameter agar plug) was used to calculate percentage inhibition, which was then logit transformed and regressed against the concentrations to calculate EC50 from the regression equation. 

The data in the sheet named "2 In vitro trials EC50" represents the post-hoc analysis, specifically the Fisher’s protected t-LSD (Least Significant Difference) that was calculated to compare the EC50 means of significant effect. Means that do not share t-groupings, or t-grouping ranges, are significantly different at the 5% significance level. The sheet named "2 In planta trials soil CFU" contains data from the in planta phosphonate sensitivity trials on soil colony forming units of P. nicotianae in different pots (subsamples) per block of different treatments (NH4-LS = Ammonium phosphite sprayed plants inoculated with the pooled least sensitive isolates; NH4-MS = Ammonium phosphite sprayed plants inoculated with the pooled most sensitive isolates; NH4-uninoculated = Ammonium phosphite sprayed plants that are not inoculated; K-LS = Potassium phosphite sprayed plants inoculated with the pooled least sensitive isolates; K-MS = Potassium phosphite sprayed plants inoculated with the pooled most sensitive isolates; K-uninoculated = Potassium phosphite sprayed plants that are not inoculated; Unsprayed-LS = Unsprayed plants that have been inoculated with the pooled least sensitive isolates; Unsprayed-MS = Unsprayed plants that have been inoculated with the pooled most sensitive isolates; Unsprayed-Uninoculated = Unsprayed plants that have not been inoculated). The sheet named "2 In planta trials root collars" contains data from the in planta phosphonate sensitivity trials on root dry mass, root wet mass, and root collar diameter measurements of two plants (subsamples) per block for the same treatments listed under the In planta trials soil CFU data. 

The sheet named "2 In planta trials qPCR" contains the data on P. nicotianae DNA concentrations in harvested plant roots for the same treatments listed under the in planta trials above. DNA concentrations refer to concentrations of the ras-related protein (Ypt1) gene, as determined by qPCR. The given concentrations (column F) were those of standards used in standard curve construction. The quantification cycle (Cq) (column D), calculated concentration (column G), and % variation (column H) data, as well as the slope and y-intercept, were generated by Q-qPCR version 1.0.2. The sample DNA was diluted by a factor of five (column I) to reduce the effect of qPCR inhibitors. The actual concentrations (column J) of three single-sample biological replicates of the same treatments listed under the in planta trials, were calculated by multiplying the calculated concentrations by the dilution factor. Statistical analysis was performed on the actual concentrations. The sheet named "2 In planta trials temperatures" contains the temperature data recorded with a HOBO data logger throughout the in planta trials. The sheet named "3 In vitro mycelial growth", contains data from the in vitro assay of mycelial growth rate. The average of two perpendicular measurements of the radial colony growth (minus the 8mm agar plug diameter) was calculated for each of three petri dishes (subsamples), together representing a replicate. Isolates 137, 121, and 146 were categorised as 'Sensitive' and isolates 89, 302, and 193 as 'Reduced Sensitivity'. 

The sheet named "3 In vitro sporangia", contains data from the in vitro assay of sporangium production capacity of the same six isolates from the in vitro assay of mycelial growth rate. The number of sporangia at the edge of the upper surface of an agar plug (subsample), of which there were 4 on a microscope slide (representing a replicate), were counted. The sheet named "3 In vitro stability", contains data from the in vitro assay of the stability of reduced phosphonate sensitivity. The same six isolates from the previously described sheet were subcultured onto new non-selective media for 10 successive generations and subsequently, these 10th generation isolates, along with their original 'parent' strains (indicated by a letter 'P' following the isolate number), had their EC50 values to ammonium phosphite determined by an agar dilution method, as previously described. The sheet named "3 In planta soil CFU" contains soil CFU data from the in planta trials that compared the fitness of the same six isolates (137, 121, 146, 89, 302, 193). However, due to Fusarium oxysporum overgrowth (column G) on the media, no reliable data was generated for this variable. The sheet named "3 In planta root reisolati", contains data on the reisolation of P. nicotianae from root pieces from the in planta trials that compared the fitness of the same six isolates. However, due to Fusarium oxysporum overgrowth (column H) on the media, no reliable data was generated for this variable. 

The sheet named "3 In planta Fusarium id" contains data on the identity of the Fusarium contaminant mentioned above. The translation elongation factor 1-α (tef1) gene was sequenced and compared to sequences in the Genbank database using the BLASTn tool. The sheet named "3 In planta root mass coll" contains data on root wet mass and root collar diameter measurements taken during the in planta trials that compared the fitness of the aforementioned six isolates. There were two plants (subsamples) per treatment (isolate) per block. The sheets named "3 In planta qPCR Trial 1" and "3 In planta qPCR Trial 2" contain the data on P. nicotianae DNA concentrations in harvested plant roots for the same in planta trials that compared the fitness of the aforementioned six isolates. DNA concentrations were determined by qPCR, as previously described. The sheet named "3 In planta temperatures" contains the temperature data recorded with a HOBO data logger throughout the in planta trials that compared the fitness of the aforementioned six isolates.

所有以数字'2'开头的电子表格名称包含第2章的数据，而以数字'3'开头的表格则包含第3章的数据。名为'2 All isolates'的表格包含了所有样本中分离物的身份信息，以及这些分离物来源省份的补充信息（MP = 马普托兰；WC = 西部省；EC = 东部省；NW = 北部省；LP = 林波波省；NC = 北开普省；未知 = 来自南非且来源省份不明的样本）。身份通过PCR限制性片段长度多态性和内部转录间隔区（ITS）区域的测序来确定。名为'2 In vitro isolates'的表格仅包含经过琼脂稀释法筛选其对磷化物的体外敏感性测试的Phytophthora nicotianae分离物。为这些分离物提供的附加数据包括它们各自的ITS序列的BLASTn身份、来源省份和既往的磷化物暴露历史。磷化物暴露历史是通过采访样本果园和苗圃的种植者来确定的。

名为'2 In vitro trials'的表格包含了使用琼脂稀释法进行的体外磷化物敏感性试验的数据，试验使用了50个已确定的P. nicotianae分离物，两种不同的磷化物（即氨磷和磷酸钾），这些磷化物的五种不同浓度（0，25，75，150，600，1250微克/毫升），三个重复和两个试验。通过计算两个垂直测量值的平均半径菌落直径（减去8毫米直径的琼脂塞）来计算抑制百分比，然后将其对数转换并回归到浓度以计算回归方程的EC50。

名为'2 In vitro trials EC50'的表格代表了事后分析，特别是为了比较显著效应的EC50均值而计算的Fisher保护t-LSD（最小显著差异）。在5%的显著性水平上，不共享t分组或t分组范围的均值显著不同。名为'2 In planta trials soil CFU'的表格包含了在盆栽（亚样本）的不同处理块中进行的植物体内磷化物敏感性试验的P. nicotianae土壤形成单位的数据。名为'2 In planta trials root collars'的表格包含了在相同的处理下，每块中两个植物（亚样本）的根干质量、根湿质量和根颈直径测量的数据。

名为'2 In planta trials qPCR'的表格包含了关于收获植物根中P. nicotianae DNA浓度的数据，这些数据与上述植物体内试验中的相同处理相对应。DNA浓度是指ras相关蛋白（Ypt1）基因的浓度，由qPCR确定。所提供的浓度（F列）是在标准曲线构建中使用的标准品的浓度。定量循环（Cq）（D列）、计算浓度（G列）、%变化（H列）的数据，以及斜率和y截距，均由Q-qPCR版本1.0.2生成。样本DNA通过五倍稀释（I列）以减少qPCR抑制剂的效应。通过将计算浓度乘以稀释因子，计算了相同处理下植物体内试验中的三个单样本生物重复的实际浓度（J列）。对实际浓度进行了统计分析。名为'2 In planta trials temperatures'的表格包含了在整个植物体内试验期间用HOBO数据记录器记录的温度数据。

名为'3 In vitro mycelial growth'的表格包含了关于菌丝生长速率的体外试验数据。对于每个三个培养皿（亚样本）的平均垂直菌落生长测量值（减去8毫米琼脂塞直径），计算了代表重复的数据。分离物137、121和146被归类为'敏感型'，而分离物89、302和193被归类为'降低敏感性'。

名为'3 In vitro sporangia'的表格包含了关于同六个分离物从菌丝生长速率体外试验中产生的囊泡生产能力的体外试验数据。在一个琼脂塞的上表面边缘的囊泡数量（亚样本），在显微镜载玻片上有4个（代表重复），被计数。名为'3 In vitro stability'的表格包含了关于降低磷化物敏感性的稳定性的体外试验数据。之前描述的表格中的相同六个分离物被转接到新的非选择性培养基上，连续进行了10代，随后，这些第10代分离物以及它们的原始'亲本'菌株（通过分离物编号后的字母'P'表示），通过琼脂稀释法确定了它们对氨磷的EC50值，方法与之前所述相同。

名为'3 In planta soil CFU'的表格包含了与上述六个分离物比较的适应性的植物体内试验的土壤形成单位数据。然而，由于培养基上Fusarium oxysporum的过度生长，没有生成该变量的可靠数据。

名为'3 In planta root reisolati'的表格包含了关于从植物体内试验中比较的六个分离物的根片段中重新分离P. nicotianae的数据。然而，由于培养基上Fusarium oxysporum的过度生长，没有生成该变量的可靠数据。

名为'3 In planta Fusarium id'的表格包含了上述提到的Fusarium污染物的身份数据。通过BLASTn工具对延伸因子1-α（tef1）基因进行测序，并将其与Genbank数据库中的序列进行比较。名为'3 In planta root mass coll'的表格包含了在比较上述六个分离物的适应性的植物体内试验期间进行的根湿质量和根颈直径测量的数据。每个处理（分离物）的每个块中有两个植物（亚样本）。名为'3 In planta qPCR Trial 1'和'3 In planta qPCR Trial 2'的表格包含了关于相同植物体内试验中P. nicotianae DNA浓度的数据，这些试验比较了上述六个分离物的适应性。DNA浓度通过qPCR确定，方法如前所述。名为'3 In planta temperatures'的表格包含了在整个植物体内试验期间用HOBO数据记录器记录的温度数据。