🧬 Plant genomics | 🍇 Vitis | ⏳ Ancient DNA

Grapevine genetics: clones, pangenomes, transposable elements, capture arrays, and tests of old population-genetic theory on modern data.

Annotation teaching pair (structure → function; TE lib is separate):

• 🏷️ gene-structure-annotation — primary gene-model layer (exons / CDS → GFF3 + proteins; TE soft-mask inside structure)
• 🏷️ gene-function-annotation — labels after proteins (GO / domains / names; no BRAKER / GFF edit / TE)
• 🧱 vitis-te — TE library build (not under function)

Annotation board: Project #2 (structure → function).

Also useful doors:

• 📜 genomics-theory-mining — classic genomics theory, one folder per note, tested on modern Vitis / clone data
• 🧰 gtbs-chip-service-kit — GBTS Chip Service Kit (species-agnostic scaffold + profile contract)
• 🍇 grapeancestry — grapevine 167K public walkthrough (GUIDELINE / demo HTML / step docs); chip design folder chip/
• 🧰 bioinfo-agent-skills — index of agent skills for plant genomics
• ✅ TrioConcordance — trio genotype QC
• 🧬 grapevine-adna — ancient-DNA methods and notes for Vitis
• 🕸️ vitis-pangenome — pangenome / graph line
• 🖼️ awesome-astra-science — GPT-6 Astra science gallery (wins + reality check)

• 🧰 gtbs-chip-service-kit — GBTS Chip Service Kit (generic scaffold)
• 🍇 grapeancestry — grapevine 167K walkthrough + chip/ design
• 🧬 grapevine-adna — ancient DNA
• 🕸️ vitis-pangenome — pangenome / graph
• 🧱 vitis-te — transposable elements
• 📊 vitis-popgen — population genetics
• 🟢 grapevine-plastid — plastid

• 🧰 bioinfo-agent-skills — public index (each skill is its own repo)
• 📜 genomics-theory-mining — one theory per folder; original paper first
• ⚠️ bioinfo-pitfalls — symptom-first traps for plant genomics pipelines
• 🔗 vitis-synteny — colinearity / synteny
• 🏷️ gene-structure-annotation — gene structure / models (ex plant-gene-annotation)
• 🏷️ gene-function-annotation — gene functional annotation (ex vitis-gene-annotation)
• 📚 plant-lit-review — literature review workflow
• 🗄️ plant-omics-db — plant multi-omics databases

• 👤 famous-people — one person, one checkable question
• 🌱 concept-learning — biology / evolution concept lessons
• 📄 paper-reading — one PDF to one Chinese L3 note

• 🖼️ paper-viz — paper figures
• 🖼️ awesome-astra-science — Astra science gallery (wins + 也就那回事)
• ✅ TrioConcordance — trio genotype QC

• Old theory, new data — lock the original paper, list the assumptions, then try to break them on grape clones and wild Vitis
• Capture panel — GBTS kit scaffold (gtbs-chip-service-kit) + grapevine 167K face (grapeancestry)
• Clonal genomes — aDNA, pangenomes, TE, and plastid as separate jobs, not one dump

VitisGDB is my grapevine database work. The public GitHub copy is currently published with a collaborator.

Read the original. Name the assumption that dies in clones. One theory per folder.