Gene Annotation Jamboree

(Geneboree)

April 26, 27, May 4, 2023, 1 – 5 pm 

BPRI-wide Objectives: Annotate as many genes as possible across 6 Schistocerca species to identify those that might be involved in phase change and those that most likely are not involved. The annotation results will also be used later on to create phylogeny trees, RNAi targets, and CRISPR/Cas9 primers for genome editing.

Participant Goals: Each participant should learn how to validate a gene model and propose changes if required. Each participant that successfully achieves this goal will be listed as co-author on the genome paper where the gene annotation data will be presented. The participant annotating correctly the highest number of genes will win a $50 Amazon gift card (selected by the Research Committee).

Learning Resources:

  • BPRI-specific i5k video introduction to annotation and slides
  • i5k tutorial video (passcode: hm3tu1A@) and slides on manual annotation tools
  • i5k tutorial video (passcode: 1%yC!#w#) and slides on in-depth annotation techniques
  • Herman Dierick’s NCBI primer
  • Fringy’s presentation on ‘Why annotate locust genomes’
  • Apollo Training:

Supporting Documents:

  • List of candidate genes selected for annotation and result-tracking spreadsheet
  • i5K workspace registration link

Procedure

  • Participants need to register with the i5k workspace before the Geneboree 
  • Participants should take advantage of the learning resources before the Geneboree 
  • We will meet via Zoom on three days from 1 to 5 pm (central time) to help guide the process 
  • It is recommended that participants from each institution gather in a common room to facilitate interactions, the answering of questions, and so that local experts can help beginners 
  • Zoom breakout rooms will be created as needed to help participants remotely 
  • After a tutorial introduction, each participant will be assigned one gene to annotate. The first step will be to do this in Schistocerca gregaria. Next, annotation of the same gene will be carried out in the other 5 species
  • An expert will check the work from each participant 
  • The annotation results will be entered in the Result-tracking spreadsheet
  • Following the initial gene annotation, participants will be assigned additional genes to annotate to the extent possible 
  • At the end of the Geneboree, each participant will give a lightening talk about his/her results 
  • Groups of participants working on similar genes will write a summary of their results in one paragraph that will be used for future work by BPRI members and to help during the writing of the genome paper.  

Rough Agenda Day 1

Wed April 26, 1 – 5 pm central time

Session 1 Zoom ID: 997 0938 2481, Passcode: 124838  

  • 1:00 – 1:30 pm: Introduction to NCBI, Uniprot, i5k Workspace (Hojun) 
  • 1:30 – 2:15 pm: Gene annotation example (Anna) 
  • 2:15 – 2:30 pm: Review and assignment of genes to be annotated 
  • 2:30 – 3:15 pm: Annotate your first gene in S. gregaria 
  • 3:15 – 4:15 pm: Get back together and show your results
  • 4:15 – 5:00 pm: Your next steps  

Rough Agenda Day 2

Thu April 27, 1 – 5 pm central time

Session 2 Zoom ID: 951 7918 9384, Passcode: 581979

  • 1:00 – 1:15 pm: Check-in – answering questions 
  • 1:15 – 2:00 pm: Work on your next assigned genes 
  • 2:00 – 2:15 pm: Progress report 
  • 2:15 – 3:00 pm: Work on your next assigned genes 
  • 3:00 – 3:15 pm: Progress report 
  • 3:15 – 4:00 pm: Work on your assigned genes 
  • 4:00 – 4:15 pm: Progress report 
  • 4:15 – 4:45 pm: Discussion on annotated genes, tutorial on trees, answering questions (Hojun) 
  • 4:45 – 5:00 pm: Your next steps 

Rough Agenda Day 3

Thu May 4, 1 – 5 pm central time

Session 3 Zoom ID: 999 3945 8020, Passcode: 003461

  • 1:00 – 1:15 pm: Check-in – answering questions 
  • 1:15 – 2:00 pm: Work on your genes 
  • 2:00 – 2:15 pm: Progress report 
  • 2:15 – 3:00 pm: Work on your genes 
  • 3:00 – 3:30 pm: Check-in on goals, did everyone annotate one gene?, prepare for lightening talks 
  • 3:30 – 4:00 pm: lightening talks 
  • 3:30 – 4:00 pm: Write one report paragraph summarizing the work 
  • 4:00 – 5:00 pm: Tree generation for a specific annotated gene example (Hojun) 

References

Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community. Saha et al., Database, Volume 2017, 2017, bax032.

A quick guide for student-driven community genome annotation. Hosmani et al., PLoS Comput Biol 15(4): e1006682.

Asian citrus psyllid community annotation article collection.

Organizing committee

Stephen Richards (fringy), Anna Childers, Herman Dierick, Maeva Techer, Fabrizio Gabbiani, Hojun Song, Richard Dewell