From 4f835baef0aac0ad3a7f1124b1a33d197d28f78d Mon Sep 17 00:00:00 2001
From: Viktoria Petrova <vipet103@hhu.de>
Date: Sun, 10 Nov 2024 13:35:58 +0100
Subject: [PATCH] add figures and descriptions in readme
---
.../README.md | 14 ++++++++++++++
.../dataset/gr2.jpg | 3 +++
.../dataset/gr4.jpg | 3 +++
.../isa.assay.xlsx | Bin 6917 -> 6916 bytes
.../AmpliconSequencingDataAnalysis/README.md | 6 ++++++
.../dataset/gr1.jpg | 3 +++
.../README.md | 7 +++++++
.../dataset/gr5.jpg | 3 +++
.../isa.assay.xlsx | Bin 6913 -> 6912 bytes
assays/GUSHistochemicalStaining/README.md | 5 +++++
.../GUSHistochemicalStaining/dataset/gr3.jpg | 3 +++
.../isa.assay.xlsx | Bin 6912 -> 6911 bytes
12 files changed, 47 insertions(+)
create mode 100644 assays/ANOVAForDifferentialEnrichmentOfMetabolites/dataset/gr2.jpg
create mode 100644 assays/ANOVAForDifferentialEnrichmentOfMetabolites/dataset/gr4.jpg
create mode 100644 assays/AmpliconSequencingDataAnalysis/dataset/gr1.jpg
create mode 100644 assays/CorrelationBetweenMicrobesAndMetabolites/dataset/gr5.jpg
create mode 100644 assays/GUSHistochemicalStaining/dataset/gr3.jpg
diff --git a/assays/ANOVAForDifferentialEnrichmentOfMetabolites/README.md b/assays/ANOVAForDifferentialEnrichmentOfMetabolites/README.md
index e69de29..0319b42 100644
--- a/assays/ANOVAForDifferentialEnrichmentOfMetabolites/README.md
+++ b/assays/ANOVAForDifferentialEnrichmentOfMetabolites/README.md
@@ -0,0 +1,14 @@
+<img src=./dataset/gr2.jpg width=60%>
+
+**Figure 2. Diversity and region-specificity of metabolites along the root axis**
+
+(A) Principal-component analysis (PCA) of metabolites extracted from the full-length root, and segments 0–2, 2–4, and 4–6 cm from the root tip. The colors of clusters correspond to regions of the root depicted in the plant cartoon in Figure 1A. Centroids are indicated for each cluster of root region.
+(B) Heatmap depicting the enrichment or depletion of indicated metabolites in respective root segments. Clustering performed based on average linkage Pearson hierarchical clustering of metabolites. Clusters are indicated in red roman numbers. Colors on the scale bar indicate the level of enrichment or depletion of each metabolite across the root segments.
+
+<img src=./dataset/gr4.jpg width=60%>
+
+**Figure 4. Metabolite profiles of root segments from *sweet2, sweet4*, and *swee11;12* are distinct from WT**
+
+(A) Principal-component analysis (PCA) of total metabolites extracted from the whole root and root segments 2, 4, and 6 cm above the root tip of *sweet2, sweet4, sweet11;12*, and WT plants. WT: N = 16, *sweet2*: N = 19, *sweet4*: N = 20, *sweet11;12*: N = 21.
+(B) Relative abundance of metabolite superclasses significantly (p value < 0.05) enriched and depleted in each root segment of sweet mutants compared with corresponding segments of WT.
+(C) Heatmap depicting the enrichment (or depletion) of indicated metabolites in respective root segments for WT and sweet plants (abbreviated as *swt*). Heatmap generated based on average linkage Pearson hierarchical clustering of metabolites and root segments. Clusters are indicated in red roman numbers. Colors indicate the level of enrichment or depletion of each metabolite across the plant genotypes and root segments.
\ No newline at end of file
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diff --git a/assays/AmpliconSequencingDataAnalysis/README.md b/assays/AmpliconSequencingDataAnalysis/README.md
index e69de29..a15ccc5 100644
--- a/assays/AmpliconSequencingDataAnalysis/README.md
+++ b/assays/AmpliconSequencingDataAnalysis/README.md
@@ -0,0 +1,6 @@
+<img src=./dataset/gr1.jpg width=60%>
+
+**Figure 1. Differential spatial colonization by root microbiota along the longitudinal root axis**
+
+(A) Phenotype of wild-type *A. thaliana* Col-0 grown on CD-Rhizotron, with root segments marked. CPCoA of the Bray-Curtis dissimilarities of endospheric (n = 63) or rhizosphere samples (n = 65), constrained by the distance to the tip from which they were harvested. Different colors represent respective longitudinal segments or whole root samples, with colors of clusters corresponding to the root segments depicted in the plant cartoon. Centroids are indicated for each cluster of root region.
+(B) Phenotype of wild-type *A. thaliana* Col-0 grown on ArtSoil. CPCoA of the Bray-Curtis dissimilarities of root endosphere (n = 39) or rhizosphere samples (n = 40), constrained by the distance to the tip from which they were harvested. Colors of clusters correspond to segments of the root depicted in the plant cartoon. Centroids are indicated for each cluster of root region.
\ No newline at end of file
diff --git a/assays/AmpliconSequencingDataAnalysis/dataset/gr1.jpg b/assays/AmpliconSequencingDataAnalysis/dataset/gr1.jpg
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diff --git a/assays/CorrelationBetweenMicrobesAndMetabolites/README.md b/assays/CorrelationBetweenMicrobesAndMetabolites/README.md
index e69de29..3e916ef 100644
--- a/assays/CorrelationBetweenMicrobesAndMetabolites/README.md
+++ b/assays/CorrelationBetweenMicrobesAndMetabolites/README.md
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+<img stc=./dataset/gr5.jpg width=60%>
+
+**Figure 5 Loss of spatial microbiota colonization in roots of *sweet2, sweet4*, and *sweet11;12***
+
+(A) CPCoA of the Bray-Curtis dissimilarities of endospheric bacteria derived from full-length roots of WT, *sweet2, sweet4*, and *sweet11;12* plants, constrained by plant genotype. Different colors represent plant genotypes with centroids indicated for each cluster of genotype. WT: N = 60, *sweet2*: N = 40, *sweet4*: N = 41, *sweet11;12* and N = 42.
+(B) Bray-Curtis dissimilarities distances of endospheric bacteria derived from the 0–2, 2–4, and 4–6 cm segments from the root tip of WT, *sweet2, sweet4*, and *sweet11;12* plants (sweet abbreviated as “swtâ€) compared with each other. The colors and sizes of the dots correspond to the mean of the Bray-Curtis distance.
+(C) Spearman correlation for metabolite-microbe (class level) pairs. Metabolites ranked based on Spearman average hierarchical clustering. The color of each point indicates the degree of correlation. Highlights indicate the class of metabolite: blue, sugar/carbohydrate; red, organic acid; and yellow, lipid. Spearman correlations significance, p < 0.05.
\ No newline at end of file
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diff --git a/assays/GUSHistochemicalStaining/README.md b/assays/GUSHistochemicalStaining/README.md
index e69de29..81a7b24 100644
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+++ b/assays/GUSHistochemicalStaining/README.md
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+<img src=./dataset/gr3.jpg width=60%>
+
+**Figure 3. Accumulation of SWEETs along the root in the absence or presence of sugar and soil microbes**
+
+Accumulation of respective SWEETs fused with a translational GUS reporter gene in 14-days-old A. thaliana seedlings grown on ½ MS-salt media supplemented with or without 1% sucrose (½ MS-salt −suc: ½ MS media without sucrose supplementation, ½ MS-salt +suc: ½ MS media with sucrose supplementation), on microbiome-inoculated or microbiome-killed ArtSoil (ArtSoil −microbes: ArtSoil inoculated with heat-killed soil microbes, ArtSoil +microbes: ArtSoil inoculated with soil microbes). The root segment depicted for SWEET2-GUS is <0.2 cm, and the root segments depicted for SWEET12-GUS and SWEET4-GUS are >2 cm. Scale bars, 500 μm. The yellow arrow indicates the accumulation of SWEET2-GUS in the root zone of interest. Green arrows indicate the sporadic accumulation of SWEET4-GUS. Representative image for each genotype from N > 10.
\ No newline at end of file
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