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Project goal: To produce an improved structural annotation of the A. thaliana Col-0 genome based on a 2022 community consensus genome assembly

Project phases:

Dec2022Jan2023FebMarAprMayJunJulAugSepOctNovDecJan2024PAG30 meeting in San DiegoASPB meeting in Georgia, USAICAR meeting in Chiba, Japan
TAIR
Schneeberger lab
NCBI
Subject Matter Experts

Install WebApollo

Run training session for WebApollo

Practice annotation submission to GenBank

Finish & submit CC-assembly to NCBI

Dec2022Jan2023FebMarAprMayJunJulAugSepOctNovDecJan2024Update @ PAG30 in Sa…Update @ ICAR (Chiba, Japan)Update @ ASPB i…Update @ PAG31 in Sa…Status updateStatus updateStatus update
Genome Assembly
Automated Annotation
Manual Review
NCBI/RefSeq Submission
Dissemination/Integration

Schneeberger group to submit to NCBI

Schneeberger group to complete CC assembly

NCBI to run annotation pipeline

NCBI to provide gene lists for review

TAIR to set up WebApollo

TAIR to set up review training

Community to conduct manual review

Status update

Status update

Status update

TAIR to test NCBI submission with dummy data

TAIR to submit final annotation to GenBank

TAIR to run QC checks on final annotation

Write manuscript about community effort

Poster and/or talk at conference

Poster and/or talk at conference

TAIR to prepare update

Timeline: 12 months, starting Nov. 2022

Participants: 

  • globally distributed scientists (UK, Germany, China, Canada, US, so far)
  • varying areas of expertise relevant to different phases of the project, not all participants are involved in all phases
  • TAIR will provide coordination/project management and hosting of the software for manual review

Benefits:

  • product will be widely welcomed, adopted, and used by the plant biology community
  • publication about effort will credit all who contributed
  • sets a precedent and workflow for subsequent updates


Challenges:

  • volunteer effort, contributions are in kind (expertise)- this may lead to difficulties in sticking to a timeline and reaching milestones
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