International Course On Plant Genome Sequencing using Oxford Nanopore technologies

Déc 1, 2023 | Issue

Faculty of Agronomy – National University of Rosario, Parque Villarino, Zavalla (Santa Fe, Argentina)

Participants : (from left to rigth) Giovani Gabelli (MAD member), Julien Serret (IRD, teaching), Olivier Leblanc (MAD member), Tomás Petiti, Sol Agostina Figueroa, Alicia Zelada, Celeste Arancibia, Florencia Rocío Turco, Larisa Altube, Liliana Alvarez, Mauro Debetti, Sofía Gischuck, Pilar Alda, Augusto Villalba (MAD member), François Sabot (IRD, teaching), Ingrid Georgina Orce, Julie Orjuela (IRD, teaching), Davide Perrone (MAD member), Francisco De Blas, Martín Raúl Quevedo (MAD member), Marie Couderc (IRD, teaching)

Objective: The aim of the course was to train plant biologists (mostly PhD students and post-docs) in Oxford Nanopore genomic sequencing and in sequence analysis. It consisted of practical laboratory (HMW DNA extraction, library preparation, sequencing) and bioinformatics (base calling, read quality and filtering, assembly) sessions, as well as of lectures.

Organizers: Olivier Leblanc (IRD, MAD coordinator) & Juan Pablo Ortiz (IICAR-CONICET-UNR)

Local organizers: Maricel Podio & Juliana Stein (FCA-UNR)

Lab team: Marie Couderc (IRD), Lorena Siena (IICAR), Carolina Colono (IICAR), & Julien Serret (IRD)

Bioinformatics team: Julie Orjuela (IRD), Maricel Podio (IICAR) & François Sabot (IRD)

Day one –  Introduction, HMW gDNA extraction, Library preparation and loading

Opening by Olivier Leblanc

Laboratory teachers, Maricel Podio (IICAR), Lorena Siena (IICAR), Marie Couderc (IRD), Julien Serret (IRD)

Lab work – HMW gDNA extraction

Day 2 – Practical DNA library preparation

The 7:30 a.m. shuttle from Rosario to Zavalla and Juan Pablo’s explanations. Special thanks to our drivers, Manuel and Roberto!

Lab work – ONT library preparation – Demo by Julien

MAD participants discussing library preparation. From left to rigth: Augustus Villalba, Sol Vega, Davide Perrone, Giovani Gabelli, Juan Manuel Vega & Lorena Siena

Nice flow cell!

Day 3 – Bioinformatics (base calling, quality control)

Time to join Linux!…

 

 

 

 

 

 

Does maté really boost bioinformatics skills?

Bioinformatics teachers, Julie Orjuela and Françcois Sabot, discussing the N50 metrics

Loosing connexion with the Minion….

Day 4 – Bioinformatics (genome assembly)

Maté does help….
THE code worked!…
Assembling genomes

Day 5 – Wrap-up & closing

Wrap-up session

Thanks again to the IICAR and IRD people involved in training and organization. Glad to see you all wearing your guardapolvo!

Carolina, Maricel, Marie, Julien, Francois, Lorena, Olivier, Julie, and Juan Pablo

 

 

Participants

Alda Pilar, Researcher,  CERZOS (CONICET-UNS), Bahia Blanca, Argentina

Altube Larisa V, Researcher, IUNIR, Rosario, Argentina

Arancibia Celeste, Post doc, IBAM (CONICET-UNCUYO), Mendoza, Argentina

Alvarez, Liliana

Bedetti Mauro, PhD student , IICAR (CONICET-UNR), Rosario, Argentina

Bianchi Julieta, Researcher, ICAR (CONICET-UNR), Rosario, Argentina

De Blas Francisco, Researcher, IBONE (CONICET-UNNE), Corrientes, Argentina

Figueroa Sol Agostina, PhD student, IPROBYQ (CONICET-UNR) Rosario, Argentina

Gabelli Giovanni, Post doc, University of Padova, Italy

Gischuck Sofía, PhD student, UNCo, Neuquén, Argentina

Godoy Federico, PhD student, IICAR (CONICET-UNR), Rosario, Argentina

Orce Ingrid Georgina, Researcher , CREAS (CONICET-UNCA), Catamarca, Argentina

Petiti Tomás, PhD student, IPROBYQ (CONICET-UNR) Rosario, Argentina

Perrone Dávide, PhD Student, University of Milan, Italy

Turco Florencia Rocío, PhD student, UNC, Córdoba, Argentina

Quevedo Martín Raúl, PhD student, CERZOS (CONICET-UNS), Bahia Blanca, Argentina

Villalba Augusto Ivan, PhD student, IBONE (CONICET-UNNE), Corrientes, Argentina

Vega María Sol, PhD student, IICAR (CONICET-UNR), Rosario, Argentina

Vega Juan Manuel, PhD student, IICAR (CONICET-UNR), Rosario, Argentina

Zelada Alicia, Researcher, UBA, Buenos Aires, Argentina