FEEDBACK  |  CONTACT  |  SITE MAP  |  ABOUT US   
Ask an account
You are here : Home / Home URGI / About us / Publications / An integrated information system dedicated to oak genomics and genetics

Publications

International,  COM (posters)

[Présentation orale]. PAG XXVI Plant and Animal Genome Conference (2018-01-13-2018-01-17) San Diego (USA). 2018. 27 slides

13 Jul 2018   An integrated information system dedicated to oak genomics and genetics

Amselem, J. ; Francillonne, N. ; Michotey, C. ; Letellier, T. ; Aury, J.-M. ; Da Silva, C. ; Duplessis, S. ; Ehrenmann, F. ; Faye, S. ; Gaspin, C. ; Klopp, C. ; Labadie, K. ; Lesur, I. ; Leroy, T. ; Murat, F. ; Rué, O. ; Bodenes, C. ; Leplé, J.-C. ; Le Provost, G. ; Faivre Rampant, P. ; Kremer, A. ; Martin, F. ; Quesneville, H. ; Salse, J. ; Plomion, C.

GnpIS is an information system designed to integrate and link genomic, genetic and environmental data into a single environment dedicated to plant (crops and forest trees) and fungi data. GnpIS is regularly improved with new functionalities answering specific needs raised by scientists and released several times a year. We propose to illustrate the integrated genome annotation system we set up with a focus on the interoperability between genomic and genetic data (e.g. Markers, QTL) present in GnpIS-core, through the use case Quercus robur (the pedunculate oak), a large, complex and highly heterozygous genome.
This genome annotation system relies on GMOD interfaces such as WebApollo/JBrowse and Intermine to make these data available under a user-friendly environment. All annotations and analysis results (Transposable Elements (TEs), genes, ncRNA ...) and functional annotation (protein-coding genes) were obtained using powerful and robust pipelines: (i) REPET used to detect, classify and annotate TEs representing 50% of the genome; (ii) Eugene which integrates ab initio and similarity gene finding softwares to predict gene models; (iii) ncRNA were annotated using different tools to annotate lncRNA, miRNA, rRNA, tRNA (iv) A functional annotation pipeline mainly based on Interproscan and comparative genomics was performed on the 25,808 highly confident predicted proteins. This system allows experts to analyze their protein families of interest and curate/validate gene structure.
All together these resources provide a framework to study the two key evolutionary processes that explain the remarkable diversity found within the Quercus genus: local adaptation and speciation.

2018_Amselem_Paper28541.pdf
In ProdINRA


Creation date: 31 Jul 2018
PLATFORM   RESEARCH   PROJECTS   DATA   TOOLS   SPECIES   ABOUT US   FEEDBACK   CONTACT US   REGISTER   EDIT