Tooluniverse Plant Genomics

Key principles:

1. Plant-specific pathways — photosynthesis, secondary metabolism, hormone signaling are unique to plants
2. PlantReactome as foundation — curated plant pathway database with cross-species coverage (Oryza, Arabidopsis, Zea mays, etc.)
3. Ensembl Plants for genomics — use Ensembl with plant species names for gene lookup and annotation
4. KEGG for metabolism — KEGG has plant-specific organism codes (ath=Arabidopsis, osa=rice, zma=maize)
5. Evidence grading — T1: functional validation (mutant phenotype), T2: expression/localization data, T3: ortholog-based prediction, T4: computational annotation only

When to Use

• "What pathway is [plant gene] involved in?"
• "Find genes in the flavonoid biosynthesis pathway"
• "Compare [gene] across Arabidopsis and rice"
• "What species is [plant name]?"
• "Plant hormone signaling pathways"
• "Photosynthesis gene annotation"

Not this skill: For general pathway analysis (human/mouse), use tooluniverse-systems-biology. For phylogenetics, use tooluniverse-phylogenetics.

Core Tools

Workflow

Phase 0: Species & Gene Identification
  Species name → POWO taxonomy; Gene symbol → Ensembl/UniProt IDs
    |
Phase 1: Gene Function & Annotation
  UniProt function, Ensembl annotation, InterPro domains
    |
Phase 2: Pathway Analysis
  PlantReactome → plant-specific pathways; KEGG → metabolism
    |
Phase 3: Cross-Species Comparison
  Ensembl Compara → orthologs in other plant species
    |
Phase 4: Literature & Report
  PubMed → published studies; synthesis

Phase 1: Gene Function

# Look up an Arabidopsis gene
ensembl_lookup_gene(gene_symbol="CHS", species="arabidopsis_thaliana")
# Get protein function
UniProt_search(query="CHS AND taxonomy_id:3702 AND reviewed:true")

Phase 2: Plant Pathway Analysis

Key plant-specific KEGG pathways:

# Search PlantReactome for flavonoid pathway
PlantReactome_search_pathways(query="flavonoid")
# Get genes in Arabidopsis flavonoid biosynthesis
KEGG_get_pathway_genes(pathway_id="ath00941")

Phase 3: Species Comparison

KEGG organism codes for major crops:

Phase 4: Interpretation Framework

Evidence grading: T1 = mutant phenotype confirms function; T2 = expression/localization data; T3 = ortholog has validated function in model species; T4 = computational annotation only (domain/GO term). Prioritize T1/T2 evidence; treat T3/T4 as hypotheses requiring further validation.

Synthesis Questions

1. Is the gene plant-specific or conserved? (Plant-specific genes often in secondary metabolism; conserved genes in primary metabolism)
2. Which tissues/developmental stages express it? (Root vs shoot vs flower vs seed)
3. Is there a crop improvement application? (Yield, stress tolerance, nutritional quality)
4. What regulatory mechanisms control it? (Hormone-responsive, light-regulated, circadian)
5. Are there natural variants with known phenotypes? (Accession diversity in Arabidopsis 1001 Genomes)

Limitations

• No TAIR tool — The Arabidopsis Information Resource has no public REST API. Use Ensembl Plants and UniProt as alternatives for Arabidopsis gene data.
• PlantReactome coverage — Focused on Oryza sativa (rice) with cross-references to Arabidopsis. Not all plant species equally covered.
• No crop breeding tools — This skill covers gene/pathway analysis, not marker-assisted selection or breeding simulation.
• POWO is taxonomy-focused — Plants of the World Online provides species identification and distribution, not genomics data.