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Pea Genome project

The reference genome sequence of pea
 
 

With its large and complex genome (ca 4.45 Gb), pea represented a real challenge to genome sequencing. In 2013, the Pea Genome International Consortium launched a program dedicated to the development of a quality reference draft sequence for pea.

‘Caméor’ a French cultivar released in 1973 was chosen as the reference genotype, because a number of enabling resources were available for this genotype, including a BAC library (INRA), a gene expression atlas (DOI:10.1111/tpj.12967), inter-connected recombinant inbred lines and high-density genetic maps ( https://doi.org/10.1111/tpj.13070 ).

Several complementary strategies conducted by the different groups of the consortium were undertaken in order to produce this reference sequence.

 

The Pea Genome Consortium

INRA Dijon managed the Consortium.

A close INRA-GENOSCOPE cooperation, under the France-Génomique project, produced plant material, whole genome shot-gun Illumina sequences, and a whole genome bionano map, assembled, and annotated the genome. Whole genome resequencing of 35 Pisum accessions was done under the ANR GENOPEA and the Région Bourgogne-France-Comté PARI projects. Additional funds were granted by AVRIL and FP7 LEGATO.

This was completed with 13X PacBio sequencing from Washington State University under fundings from the NSF. Resequencing data for 3 accessions were also provided.

The University of Saskatchewan contributed a physical map of the pea genome, with Keygene, under fundings from the Saskachewan Pulse Growers.

The University of Western Australia provided chromosome sequences and an ultra-high density skimGBS map, under a GRDC project.

The Institute of Experimental Botany of Olomouc used advanced flow-cytometry sorting of chrosmosomes to produce single chromosome samples. These were used for the development of bionano maps and for resequencing at GENOSCOPE and University of Western Australia.

The Institute of Plant Molecular Biology, at České Budějovice contributed to repeated sequence analysis and FISH.

Curtin University contributed RNA-seq data for annotation and legume genome evolution analysis, under a GRDC project.

Summary statistics:

The genome assembly length is 3,920,161,095 bp, composed of 24,623 scaffolds, from which 10,237 are anchored on the seven pseudomolecules. The number of genes is 44,756. In total, 294 X genome sequencing reads were produced to obtain this sequence.

 

> Pea reference genome sequence : Access to the Pisum sativum v1a JBrowse   / Download the sequences of Pisum sativum v1a   

> BLAST tool : run BLAST against the Pisum sativum v1a banks  

Update: 17 May 2019
Creation date: 14 Dec 2018
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