# JXB Figures Specification — V14.2
## Transcriptional streamlining and translational control drive the liquid-to-solid transition in coconut endosperm
### Target: Journal of Experimental Botany

---

## Overview: 4 Main + 2 Supplementary Figures

| Fig | Type | Panels | Tool | Data Source |
|-----|------|--------|------|-------------|
| **Fig 1** | Bar + heatmap | A/B/C | Python (matplotlib) | edgeR DEG results |
| **Fig 2** | Scatter/volcano + bar | A/B | Python (matplotlib) | Proteomics vs transcriptomics |
| **Fig 3** | Paired bar chart | Single | Python (matplotlib) | Metabolomics (Hou 2025) |
| **Fig 4** | Mechanistic model | A/B/C | BioRender or draw.io | Conceptual |
| **S1** | Multi-panel bar | 3 panels | Python (matplotlib) | CT phenotyping data |
| **S2** | Schematic | Single | BioRender | Batch correction method |

---

## Fig 1 — Transcriptional Streamlining (3 panels)

**Legend (punchline first):**
> **A progressive 13.3-fold reduction in mid-developmental DEG counts reveals transcriptional streamlining across the coconut domestication series.** (A) DEG counts at the mid-developmental stage relative to early stage for CK (11,247), W6 (1,993), and W5 (846) (edgeR QL F-test, |log₂FC| > 1, FDR < 0.05). (B) KEGG pathway enrichment of upregulated genes showing proportional reduction across cultivars. (C) Late-stage attenuation: 5,769 DEGs in CK vs. 2 (W5) and 0 (W6), indicating earlier program completion in domesticated dwarfs.

### Panel A — DEG Bar Chart
- **Type:** Stacked bar (up in green, down in red)
- **X-axis:** Three cultivars (CK, W6, W5)
- **Y-axis:** Number of DEGs (0–12,000)
- **Data:**
  | Cultivar | Up | Down | Total |
  |----------|-----|------|-------|
  | CK (wild-type tall) | 6,182 (55%) | 5,065 (45%) | **11,247** |
  | W6 (intermediate dwarf) | 1,721 (86%) | 272 (14%) | **1,993** |
  | W5 (domesticated dwarf) | 378 (45%) | 468 (55%) | **846** |
- **Highlight:** Add total number as bold annotation above each bar
- **Arrow/label:** Add bracket with "13.3×" spanning CK→W5
- **Color:** CK = dark gray (#555), W6 = medium blue (#3498db), W5 = orange (#e67e22)

### Panel B — KEGG Pathway Enrichment
- **Type:** Horizontal bar chart (top 5 pathways per cultivar)
- **X-axis:** Gene count
- **Y-axis:** KEGG categories (same order for all three for comparison)
- **Data (upregulated genes):**

  | KEGG Category | CK | W6 | W5 |
  |---------------|-----|-----|------|
  | Plant hormone signal transduction | 163 | 59 | 9 |
  | Plant–pathogen interaction | 101 | 29 | — |
  | Starch and sucrose metabolism | 63 | 22 | — |
  | Phenylpropanoid biosynthesis | 61 | 25 | — |
  | Flavonoid biosynthesis | 38 | — | — |
  | Endocytosis | — | — | 7 |
  | Amino sugar/nucleotide sugar metabolism | — | — | 5 |
  | Carotenoid biosynthesis | — | — | 5 |

- **Design:** Three mini-panels side by side (CK | W6 | W5), each with proportional bar length
- **Color:** Use same category color across all three panels for visual comparison
- **Annotation:** Add "% of total" note to show proportional similarity

### Panel C — Late-Stage Attenuation
- **Type:** Paired bar (mid→early vs late→mid per cultivar)
- **X-axis:** Three groups (CK, W6, W5), each with two bars
- **Y-axis:** DEG count
- **Data:**
  | Transition | CK | W6 | W5 |
  |------------|-----|-----|------|
  | Mid → Early | 11,247 | 1,993 | 846 |
  | Late → Mid | 5,769 (51%) | 0 (0%) | 2 (0.2%) |
- **Color:** Mid→Early = solid fill, Late→Mid = hatched/dotted
- **Annotation:** "% retained" label above each late→mid bar

### Fig 1 Layout
- Single column width (85 mm) or 1.5 columns (114 mm)
- A + B across top row, C full width below
- Or: A left 40%, B right 60%, C full width below

---

## Fig 2 — Transcript–Protein Divergence (2 panels)

**Legend (punchline first):**
> **Transcript–protein divergence reaches 1.3-fold at the mid-developmental stage between two dwarf cultivars (2,851 DEPs vs. 2,183 DEGs).** (A) Comparison of transcriptomic and proteomic differential abundance between W5 and W6, showing 2,851 DEPs against 2,183 DEGs at the mid-stage (fold-change > 1.5, FDR q < 0.05). (B) Pathway enrichment of DEPs, with cell wall, chloroplast/plastid, and cytochrome P450 categories prominently represented.

### Panel A — DEP/DEG Comparison
- **Type:** Scatter plot with marginal bars
- **X-axis:** Transcript (DEG) group
- **Y-axis:** Protein (DEP) group
- **Data:**
  - **4,956 DEPs** at early stage (W5 vs W6)
  - **2,851 DEPs** at mid stage (W5 vs W6)
  - **2,183 DEGs** at mid stage (W5 vs W6)
  - Overlap: genes that are both DEG and DEP
- **Alternative design:** Two-panel bar:
  - Left: DEP counts (early=4,956 → mid=2,851) + DEG comparison
  - Right: Scatter of log₂FC(protein) vs log₂FC(RNA) for all genes
- **Annotation:** Draw bracket spanning DEP/DEG with "1.3×" label
- **Color:** DEP = purple (#8e44ad), DEG = teal (#16a085), Overlap = gold (#f39c12)

### Panel B — Pathway Enrichment of DEPs
- **Type:** Dot plot (GO/KEGG enrichment)
- **X-axis:** Gene ratio or -log₁₀(P)
- **Y-axis:** Pathway categories
- **Categories to include:**
  - Cell wall (cellulose synthase, XTH, pectin methylesterase)
  - Chloroplast/plastid
  - Cytochrome P450
  - Stress/defense (down in W5)
- **Color:** Dot size = count, color = enrichment significance

### Fig 2 Layout
- A left (50%), B right (50%)
- Single column width (85 mm) or page width (174 mm)

---

## Fig 3 — Metabolic Reversal (single panel)

**Legend (punchline first):**
> **Eight of 12 metabolite classes (67%) reverse direction between liquid and solid endosperm phases, with Bayesian posterior P(θ > 0.5 | 8/12) = 0.91 supporting non-random metabolic reprogramming.** Paired bar chart showing log₂ fold-change during development for 12 major compound classes in coconut water (blue) and coconut kernel (magenta, W6). Gold stars mark the 8 classes with opposite directional trends. Two-tailed binomial test: P = 0.194; Beta-Binomial P(θ > 0.5) = 0.91.

### Single Panel — Paired Bar Chart
- **Type:** Paired bar (water vs kernel for each compound class)
- **X-axis:** 12 compound classes
- **Y-axis:** log₂ fold-change (developmental)
- **Data (8 reversing classes, mark with ★):**

  | Compound Class | Water (log₂FC) | Kernel (log₂FC) | Reverse? |
  |----------------|----------------|-----------------|----------|
  | Sugars | ↑ | ↓ | ★ |
  | Amino acids | ↑ | ↓ | ★ |
  | Nucleotides | ↑ | ↓ | ★ |
  | Lipids | ↓ | ↑ | ★ |
  | Cell wall components | ↓ | ↑ | ★ |
  | Secondary metabolites | ↓ | ↑ | ★ |
  | Organic acids | ↓ | ↑ | ★ |
  | Vitamins | ↓ | ↑ | ★ |
  | [4 non-reversing classes] | [same direction] | [same direction] | — |

- **Design:**
  - Water bars: light blue (#5dade2)
  - Kernel bars: magenta (#c0392b)
  - Gold star (★) above each reversing pair
  - Error bars shown
- **Annotation:** 
  - Bottom-left: "P = 0.194 (binomial)"
  - Bottom-right: "P(θ > 0.5) = 0.91 (Bayesian)"
  - Box around reversing pairs with "8/12 reverse" label

### Fig 3 Layout
- Full page width (174 mm)
- Landscape orientation preferred for readability

---

## Fig 4 — ABC1K7 Causal Cascade Model (3 layers) ⭐ SOUL FIGURE ⭐

**Legend:**
> **ABC1K7 impairment orchestrates a causal cascade from genotypic variation to molecular rewiring to phenotypic divergence across the coconut domestication gradient.** (A) Genotypic layer: ABC1K7 locus on Chromosome 5, with a Y→F substitution reaching 92% homozygosity in domesticated W5 vs. wild-type CK (You et al., in preparation). (B) Molecular layer: ABC1K7 encodes a chloroplast-localized kinase; its impairment in W5 relaxes chloroplast stress signaling (downregulation of chloroplast movement proteins, cytochrome P450s) and releases cell wall biosynthesis (cellulose synthase, XTH, pectin methylesterase) from transcriptional and translational constraint. Key quantitative landmarks: transcriptional streamlining (13.3-fold, 11,247→846 DEGs) and translational divergence (1.3-fold, 2,851 DEPs vs. 2,183 DEGs). (C) Phenotypic layer: domesticated W5 executes accelerated liquid-to-solid transition (thin shell, early solidification, sweet water) relative to CK (thick shell, late solidification). Model integrates population genomics (companion), proteomics, transcriptomics, metabolomics, and CT phenotyping.

### Tool: BioRender or draw.io

### Layout — Three vertical layers × Two columns (CK | W5)

| | CK (wild-type) | W5 (domesticated) |
|--|----------------|-------------------|
| **(A) Genotype** | ABC1K7 (wild-type kinase) | ABC1K7 (Y→F, 92% homozyg.) |
| **(B) Molecular** | Stress signaling ON → defense active → 11,247 DEGs | Stress signaling OFF → defense relaxed → 846 DEGs |
| **(C) Phenotype** | Thick shell, late solid. (9-11m), less sweet | Thin shell, early solid. (7m), sweet water |

### Layer A — Genotypic (20% of canvas height)
- **CK side (left):** 
  - Blue rectangle labeled "ABC1K7"
  - Below it: "Wild-type kinase" in smaller text
  - Chromosome 5 icon (short line with locus marker)
- **W5 side (right):**
  - Orange/red rectangle labeled "ABC1K7^{Y→F}"
  - Below: "92% homozygous • 17-yr selection"
  - Small mutation annotation: "Y→F substitution"
- **Center:** Dashed gray arrow labeled "Domestication gradient" pointing left → right

### Layer B — Molecular (50% of canvas height) ← INFORMATION DENSE
- **CK side (left) — "Defense program active" theme:**
  - Top: Chloroplast icon (green oval) with "Stress signaling ON" badge (red)
  - Middle: Network of red nodes labeled "Defense metabolism" (P450, pathogen interaction, flavonoid biosynthesis)
  - Nodes connected by many lines (representing 11,247 DEGs)
  - Right side of CK: Small cell wall nodes (grayed out, inactive)
  - Bottom annotation: "**11,247 DEGs**" in bold red
- **W5 side (right) — "Cell wall program released" theme:**
  - Top: Chloroplast icon with "Stress signaling OFF" badge (gray)
  - Middle: Defense nodes grayed out/dimmed → arrow pointing to...
  - Right side: Green highlighted nodes: "Cell wall biosynthesis" (CESA, XTH, PME, starch synthase)
  - Oil droplets (small yellow circles) accumulating
  - Bottom annotation: "**846 DEGs**" in bold green
- **Center connector:** 
  - Large annotation box with two lines:
    - "Transcriptional streamlining: **13.3×** (11,247 → 846 DEGs)"
    - "Translational divergence: **1.3×** (2,851 DEPs vs 2,183 DEGs)"
  - Use bold, large font for the numbers

### Layer C — Phenotypic (30% of canvas height)
- **CK side (left):**
  - Coconut cross-section: thick shell, large liquid cavity, thin solid layer
  - Time tag: "9-11 months"
  - Labels: "Thick shell • Late solidification • Less sweet"
- **W5 side (right):**
  - Coconut cross-section: thin shell, smaller liquid cavity, thick solid layer
  - Time tag: "7 months"
  - Labels: "Thin shell • Early solidification • Sweet water"
- **Arrow between:** "Accelerated by ~2 months"

### Color Scheme
| Element | Color | Hex |
|---------|-------|-----|
| CK genotype box | Steel blue | #2c5f74 |
| W5 genotype box | Burnt orange | #d35400 |
| CK molecular (active) | Red tones | #c0392b |
| W5 molecular (active) | Green tones | #27ae60 |
| W5 molecular (inactive) | Gray | #95a5a6 |
| Cell wall nodes | Bright green | #2ecc71 |
| Oil droplets | Gold | #f1c40f |
| Background | White / light gray | #fafafa |

### Bottom Footer
- Translucent gray bar spanning full width:
  "Model integrates population genomics, proteomics, transcriptomics, metabolomics, and CT phenotyping"

### Font & Size
- Canvas: Full page width for JXB (174 mm)
- Font: Arial or Helvetica
- Title text: 12pt bold
- Body text: 9pt
- Annotation numbers (13.3×, 1.3×): 14pt bold, color matched to theme

---

## Supplementary Fig S1 — Three-Gradient Phenotype Quantification

**Motivation:** The manuscript repeatedly invokes "early solidification / thin shell / sweet water" in W5, but no quantified phenotypic data appears in the main figures. This figure provides the CT-based evidence.

### Panels (3 vertical)

**Panel A — Shell Thickness (mm)**
- **Type:** Bar chart with error bars
- **X-axis:** CK | W6 | W5
- **Y-axis:** Shell thickness (mm)
- **Data:** 3-5-7-9 month time series
- **Expected pattern:** CK > W6 > W5 at all time points

**Panel B — Solid-to-Liquid Ratio**
- **Type:** Line chart with time course
- **X-axis:** Months post-anthesis (3, 5, 7, 9)
- **Y-axis:** Solid-to-liquid ratio
- **Data:** CK (slow rise), W6 (intermediate), W5 (early rise reaching plateau ~7 months)
- **Annotation:** Dashed vertical line at W5's solidification time point

**Panel C — Water Sugar Content (Brix)**
- **Type:** Bar or line chart
- **X-axis:** CK | W6 | W5
- **Y-axis:** Brix or sugar concentration

**Legend:**
> **CT-quantified phenotypic divergence across the coconut domestication gradient confirms accelerated development in domesticated W5.** (A) Shell thickness. (B) Solid-to-liquid ratio over development. (C) Water sugar content. Data from CT phenotyping (Sun et al., companion study). Error bars: SD, n = 3.

---

## Supplementary Fig S2 — Ratio-Based Batch Correction Schematic

**Motivation:** The Methods describe a ratio-based batch correction (W5/W6 = (W5/CK) / (W6/CK)). This is an unusual but clever approach; a schematic helps reviewers understand it without reading the dense Methods text.

### Single Schematic Panel

**Layout — 3×3 matrix:**
| | CK | W5 | W6 |
|---|---|---|---|
| **Early** | Sample E_CK | Sample E_W5 | Sample E_W6 |
| **Mid** | Sample M_CK | Sample M_W5 | Sample M_W6 |

- **CK column highlighted** with dashed border and label: "Internal Reference (same batch)"
- **Arrows:** For each row, W5/CK → ratio1, W6/CK → ratio2 → W5/W6 = ratio1/ratio2
- **Annotation box:** "Ratio-based correction cancels inter-batch variation using shared CK reference in each batch"

**Legend:**
> **Schematic of ratio-based batch correction strategy.** CK serves as the common internal reference for each developmental stage, allowing inter-batch variation to be cancelled when comparing W5 and W6 across different mass spectrometry runs.

---

## File Format & Submission Specifications

| Requirement | Value |
|-------------|-------|
| Resolution | 300 dpi minimum |
| Format | TIFF (preferred) or high-quality PNG |
| Fig 1-3 (main) | Grayscale + 1-2 spot colors OR RGB |
| Fig 4 (model) | Full color (BioRender export as TIFF) |
| Width (single col) | 85 mm |
| Width (1.5 col) | 114 mm |
| Width (full page) | 174 mm |
| Font | Arial/Helvetica, ≥ 6 pt |
| Line weight | ≥ 0.5 pt |
| JXB requirement | Each figure as separate file |

---

## Key Decisions for Your External Figure Maker

1. **Fig 1 Panel B:** The KEGG data is sparse for W5 (only 5 categories with ≥5 genes). Consider merging minor categories into "Other" for cleaner presentation.

2. **Fig 4:** This is the MOST IMPORTANT figure. It must look professional (BioRender premium or equivalent). The reviewers will judge the paper's ambition by this figure.

3. **S1:** Use actual CT data not shown in main figures. If CT data isn't ready as a companion, replace with simple cartoon showing timeline differences.

4. **Color consistency:** Use the same color for the same cultivar across all figures:
   - CK = dark gray or steel blue
   - W6 = medium blue
   - W5 = orange/burnt orange

---

*Specification prepared for JXB V14.2 — July 2026*
*Figures to be generated externally, reviewed by AI assistant, verified by corresponding author*