HAL Id: hal-01839185
https://hal.archives-ouvertes.fr/hal-01839185
Submitted on 5 Jun 2020
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Joëlle Amselem, Nicolas Francillonne, Célia Michotey, Thomas Letellier,
Jean-Marc Aury, Corinne da Silva, Sébastien Duplessis, François Ehrenmann,
Sébastien Faye, Christine Gaspin, et al.
To cite this version:
Joëlle Amselem, Nicolas Francillonne, Célia Michotey, Thomas Letellier, Jean-Marc Aury, et al.. An integrated information system dedicated to oak genomics and genetics. PAG XXVI Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.27 slides. �hal-01839185�
An Integrated Information System Dedicated to Oak Genomics and Genetics
01
joelle.amselem@inra.fr
Digital Tools and Resources Session 1 Saturday, January 13, 2018
GnpIS: A Genetic and genomic Information System
2 https://urgi.versailles.inra.fr/gnpis GnpIS architecture (ETL) URGI format standards (Ex: VCF) GnpIS core DB Standart GFF3
Physical size: 1.5 Gb (Kremer et al. 2007)
12 pairs of chromosomes
genetic size: 933 cM
12 linkage groups from 5.5k SNP-based genetic linkage maps (Bodénès et al. 2016)
Assembly and annotation
Diploïd version (2N): 8,827 scaffolds covering 1.45 Gb
Haploïd version (1N): 1,409 scaffolds covering 814 Mb
• 871 scaffolds ordered in 12 pseudomolecules and assigned to the 12 linkage groups of the genetic map
• 533 unassigned scaffold
• 25,808 high-quality protein-coding gene models (4% manually curated/validated) • 52% of diverse Transposable Elements
Plomion et al. under review
Quercus robur genome in numbers
4
Structural annotation pipelines
5 Transposable Elements REPET package https://urgi.versailles.inra.fr/Tools/REPET TEdenovo TEannot Genes prediction Eugene http://eugene.toulouse.inra.fr/
Functional annotation pipeline
6 Blast similarities KOG rpsBlast Conserved domains Predicted polypeptides
Protein domain identification
TMHMM
SignalP TargetP
Localization Targeting
Coils, Patternscan, Profilescan, Scanregexp, seg …
Protein definition* based on results of
KOG
EC Number Orthology
Oak resources
7
Markers, QTLs Genetic maps Phenotypes (in progress)
GnpIS core DB
8 Navigating oak genomic and genetic data
Pseudomolecules … to JBrowse
9
https://urgi.versailles.inra.fr/WebApollo_oak_PM1N/PseudoMolecule.html
https://urgi.versailles.inra.fr/WebApollo_oak_PM1N/jbrowse
Jbrowse overview and cross references
10 TEs Genes Transcripts Proteins RNA-Seq Scaffolds Markers ncRNA QTL OakMine portal 11
OakMine_PM1N central object: the gene card
12 Genome features
Integrated JBrowse
Functional annotation QTLs overlapping this gene
13 Gene Ontology Pfam KEGG Panther Interpro
Functional annotation : cross references to external DBs
panther
14 Interoperability with other features in OakMine
Gene ontology parent terms
Other genes sharing the same ontology term
15 Interoperability with other features in the database
QTL infos
Genes overlapped by this QTL
Several ways to query data
16 Blast search Keyword based quick search Predicted protein_ID A selection of Query templates Query templates
Search for genes in genome regions Advanced search using
Query the builder
Search box: chromosome region, genes, markers IDs… GnpIS keyword based
quick search
OakMine
17 Oak assemblies
Oak coding sequences
Use list to store and/or improve complex queries
18 Domains Description contains “xylanase” Save results in list Blast Description contains “xylanase” Save results in list 134 proteins 66 proteins X <X
The LISTs
19 Interoperability between
Genomics and Genetics
From Gbrowse to Markers in GnpIS
20
021
List of QTL Overlapping this marker
22
Link to the QTL card
23
List of markers overlapped by this QTL Link to a genetic map card
024
Open the Genetic map with BioMercator (java webstart)
From GnpIS QTL card to JBrowse
25
From JBrowse to the same QTL card
26 Acknowledgments C Plomion C Klopp J Salse F Martin JM Aury C Gaspin P Faivre-rampant
LabEx Genoak Treepeace
S Duplessis F Ehrenmann JC Leplé T Leroy I Lesur C Bodénès G Le Provost A Kremer F Murat C Da Silva K Labadie Faye S O Rué Funding H Quesneville N Francillonne C Michotey T Letellier J Amselem R Flores
