Assembly of the Pea Genome by Integration of High Throughput Sequencing (PacBio and Illumina) and Whole Genome Profiling (WGPTM) Data

Pea (Pisum sativum) is one of the most cultivated grain legume crops in the world, however the pea crop encounters recurrent abiotic and biotic stresses that decrease its competitiveness. To increase our capacity to efficiently breed new cultivars and to better understand pea genome differentiation in different ecotypes, the International Consortium for Pea Genome Sequencing gathered their efforts to produce a high quality pea genome reference sequence. The pea genome being very large (4.5 Gb) and highly repetitive, the consortium strategy  is based on the integration of different and complementary data such as whole genome sequencing data (short and long reads), physical map, optical map and genetic map data.

Whole genome shotgun DNA libraries of Pisum sativum var. Cameor with fragment sizes ranging from 160 bp to 17 kb were built and sequenced using the Illumina technology. A de novo assembly of the genome was done using a de Bruijn graph approach, contigs were scaffolded with the large insert reads and gap closed with PacBio reads. In parallel, whole genome profiling (WGP™) was used to create a physical map covering the entire genome. Based on the initial assembly, the WGP and the sequencing data, we improved the genome assembly continuity thanks to the MaGuS method (https://github.com/institut-de-genomique/MaGuS). The quality of the assembly was investigated by checking the collinearity with the genetic map and by using chromosome specific sequences obtained from chromosome sorting.