Isabelle Dufau

Arrival date : 2017

Status : Research Engineer

Roles :

- Management of genomic libraries conservation- Genome optical mapping project leader- Agreement management- Participation in CNRGV projects, especially High molecular DNA extraction

Last completed degree : Ph.D of Biochemistry - Biotechnology from an engineer school, INSA Toulouse

Professional experiences :

- 2013-2017 : Management of a technical platform (analytical area) at TWB, UMS INRA- 2003-2012 : Management of Drugs HTS (High Throughput Screening) projects at USR3388 CNS-Pierre Fabre (Pharmaceutical Industry)- 1998-2007 : Assistant Professor at Paul Sabatier University (Toulouse III), speciality : Molecular Pharmacology

    mimosa pudica


    The perennial legume Mimosa pudica fits in that category as it is a recalcitrant plant producing high amounts of secondary metabolites and polysaccharides...

    Added on : 09 July 2019

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    Since the Next Generation Sequencing revolution in 2005, whole genomes sequencing has become a routine activity for all types of species and for multiple research.

    The main limitation to take full advantage of long read sequencing and scaffolding technologies is the need for High Molecular Weight (HMW) DNA as starting material.

    While many protocols to obtain HMW DNA have been developed for mammals only few methods dedicated to plants exist and the quality of DNA obtained rarely meets the quality required for successful sequencing.


    The perennial legume Mimosa pudica fits in that category as it is a recalcitrant plant producing high amounts of secondary metabolites and polysaccharides.

    M. pudica is however of particular interest for several reasons : model for the study of mechanosensing systems in plants, formation of the nitrogen-fixing root nodule symbiosis (RNS), representative model of the legume subfamily Mimosoideae.

    A gold-standard M. pudica genome assembly is required, but multiple protocols tested for DNA extraction finally resulted in short fragment only suitable for Illumina-based sequencing.


    Failing to extract HMW gDNA for long-read sequencing is not specific to M. pudica, so the main goal of the gEXTRACT project will be to leverage the expertise of our three labs (CNRGV, LIPM, LRSV) to develop a universal protocol for plant HMW gDNA extraction.

    This protocol will be an essential resource for any laboratories interested in plant genome sequencing.


    The project is divided in three objectives:

    1) Optimisation of a HMW gDNA extraction protocol suitable for long-read sequencing on M. pudica samples

    2) Generation of a gold-standard genomic assembly for Mimosa pudica using PacBio (long-read sequencing) and Bionano (optical mapping).

    3) Extension of the HMW gDNA extraction protocol to a diversity of plant species (ex: the liverworts Marchantia paleacea, the fern Pteris vittata, the non-RNS forming legume Chaetocalyx brasilense, the Zygnematophyceae Spirogloea muscicola) to demonstrate the universal efficiency of the gEXTRACT protocol.



    • Project Partners


    - Remigi Philippe



    24 Chemin de Borde Rouge

    31320 Castanet tolosan


    - Delaux Pierre-Marc



    24 Chemin de Borde Rouge

    31320 Castanet tolosan





    • CNRGV implactions: HWM-DNA extraction, Optical Map