tooluniverse-plant-genomics

name tooluniverse-plant-genomics description Plant genomics and biology research — PlantReactome pathways, Ensembl Plants gene structure, POWO species taxonomy, UniProt annotation, KEGG plant pathways. Handles polyploidy (wheat hexaploidy etc.) and homeologous gene copies. Use for crop-gene annotation, plant secondary metabolism queries, and plant-disease/stress-response biology. disable-model-invocation true Plant Genomics & Biology Pipeline for investigating plant genes, metabolic pathways, species taxonomy, and comparative plant biology using ToolUniverse tools. Reasoning Strategy Plant genomes are large (wheat is ~17 Gb, vs. 3 Gb for human) and often polyploid — wheat is hexaploid (AABBDD), meaning there are three homeologous copies of most genes. When comparing plant genes to Arabidopsis, always account for whole-genome duplications: a single Arabidopsis gene may have 2–4 paralogs in a crop species, all potentially with diverged functions. Gene families are massively expanded in plants relative to animals (e.g., receptor-like kinases, cytochrome P450s, transcription factors) — a BLAST hit does not mean functional equivalence. Arabidopsis thaliana is the primary model, but its small genome and rapid life cycle mean some features (wood formation, nitrogen fixation symbiosis, C4 photosynthesis) are absent and must be studied in other species. LOOK UP DON'T GUESS : Do not assume gene function by sequence similarity alone in polyploid species; look up functional validation evidence via UniProt (reviewed entries) or PlantReactome. Do not assume KEGG organism codes — use the table or query kegg_search_pathway with the species name to confirm availability. Key principles : Plant-specific pathways — photosynthesis, secondary metabolism, hormone signaling are unique to plants PlantReactome as foundation — curated plant pathway database with cross-species coverage (Oryza, Arabidopsis, Zea mays, etc.) Ensembl Plants for genomics — use Ensembl with plant species names for gene lookup and annotation KEGG for metabolism — KEGG has plant-specific organism codes (ath=Arabidopsis, osa=rice, zma=maize) 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 Tool Use For PlantReactome_search_pathways Search plant-specific pathways by keyword PlantReactome_get_pathway Get pathway details (genes, reactions, species) PlantReactome_list_species List all species covered by PlantReactome POWO_search_plants Search Plants of the World Online (taxonomy, distribution) USDA_plants_get_profile US plant profile by PLANTS symbol (e.g., symbol="ABBA" ) — taxonomy, growth habit, duration, native status; use for North American flora USDA_plants_get_characteristics Morphology/physiology trait records for a PLANTS symbol — use when a question needs growth-form or physiological traits ensembl_lookup_gene Gene lookup — use with plant species (e.g., species="arabidopsis_thaliana" ) kegg_search_pathway Search KEGG pathways (use plant organism codes: ath, osa, zma) KEGG_get_pathway_genes Get genes in a plant pathway (e.g., pathway_id="ath00941" for flavonoid in Arabidopsis) UniProt_search Search plant protein sequences (add taxonomy_id:3702 for Arabidopsis) UniProt_get_function_by_accession Get protein function annotation PubMed_search_articles Plant biology literature EnsemblCompara_get_orthologues Cross-species plant gene comparison 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 : Pathway KEGG ID (Arabidopsis) Biological Significance Photosynthesis ath00195 Light reactions, electron transport Carbon fixation (Calvin cycle) ath00710 CO2 → sugar Flavonoid biosynthesis ath00941 UV protection, pigmentation, defense Carotenoid biosynthesis ath00906 Photoprotection, vitamin A precursors Auxin signaling ath04075 Growth, tropisms Brassinosteroid signaling ath04712 Cell elongation, stress response Circadian rhythm (plant) ath04712 Photoperiod, flowering time Terpenoid backbone ath00900 Secondary metabolite precursors Starch/sucrose metabolism ath00500 Carbon partitioning Nitrogen metabolism ath00910 Nitrogen assimilation # 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 : Species Code Common Name Arabidopsis thaliana ath Thale cress (model plant) Oryza sativa osa Rice Zea mays zma Maize/corn Triticum aestivum tae Wheat Glycine max gmx Soybean Solanum lycopersicum sly Tomato Nicotiana tabacum nta Tobacco Medicago truncatula mtr Barrel medic (legume model) 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 Is the gene plant-specific or conserved? (Plant-specific genes often in secondary metabolism; conserved genes in primary metabolism) Which tissues/developmental stages express it? (Root vs shoot vs flower vs seed) Is there a crop improvement application? (Yield, stress tolerance, nutritional quality) What regulatory mechanisms control it? (Hormone-responsive, light-regulated, circadian) 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.