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P. tremula x P. alba, clone INRA 717-1B4 draft genome sequence

Clone INRA 717-1B4

Clone INRA 717-1B4 whole-genome draft assembly v0.9

 
 

Overview

Here we focus on the clone INRA 717-1B4, a female P. tremula x P. alba (P. x canescens) interspecific hybrid. The clone INRA 717-1B4 is a female clone, originating from a cross between a female Populus tremula tree (tree # 5903) harvested on March 3, 1959 in the Parroy forest (Meurthe Moselle, France) and a male Populus alba tree (tree # 6072) harvested on February 22, 1960 close to the Pont du Gard (France). This hybrid was part of a breeding program initiated by Dr. Michel Lemoine in the 1960’s (Lemoine 1973, PhD thesis). Trees 5903 and 6072, installed in the nurseries of Nancy, were lost during storms in 1999, and unfortunately vegetative copies of the parents are not available.

Due to its high susceptibility to Agrobacterium tumefaciens infection, this clone is universally used by scientists worldwide as a model woody species in transgenic experiments to discover gene expression and function. We assembled draft genomic scaffolds by a combination of de novo assembly and reference-based assembly.


Statistics

Clone INRA 717-1B4 was sequenced 30 times over and assembled to produce 419,969 scaffolds. The scaffolds were sorted by size (starting with largest), successively numbered and stored in a FASTA file available for download here .

 

Blast tool

Here you can blast your favorite sequences on 717-1B4 draft genome sequence and get matching scaffold sequences.

 

Contributors

Malte Mader1, Marie-Christine Le Paslier2, Rémi Bounon2, Aurélie Bérard2, Patricia Faivre Rampant2, Matthias Fladung1, Jean-Charles Leplé3,4, and Birgit Kersten1

1 Thünen Institute of Forest Genetics, Grosshansdorf, Germany

2 EPGV US 1279, INRA, CEA, IG-CNG, Université Paris-Saclay, 91000 Evry, France

3 AGPF, INRA, 45075, Orléans, France

4 present address: BIOGECO, INRA, Université Bordeaux, 33610 Cestas, France

 

Reference Publication

Mader M, Le Paslier MC, Bounon R, Berard A, Faivre Rampant P, Fladung M, Leple J-C, Kersten B. 2016. Whole-genome draft assembly of Populus tremula x Populus alba clone INRA 717-1B4. Silvae Genetica 65(2): 74-79

 

Publications citing the clone INRA 717-1B4

Download citations (updated in september 2018) :

In order to help keeping this list up to date, please could you send missing references to JC Leplé .

Thanks in advance.

Update: 29 Oct 2018
Creation date: 05 May 2017