African rice genome projects: GLASS and IRIGIN

The GLASS project (GLAberrima ASSembly), joint project between Institut de recherche pour le développement (IRD) and AfricaRice, aims to sequence de novo the two African NERICA parents, CG14 and TOG5681, representing the two extremes of Oryza glaberrima variability. For that purpose, we chose a hybrid approach combining the illumina high-quality short reads and the PacificBioscience Long Reads technology. Tests were performed using Illumina data on TOG5307 and TOG5681, using AbySS short-reads assembler, with 19x and 25x total data, respectively. For TOG5307, we obtained 153,774 contigs (minimum size of 200b), mean size of 1.5 kb (N50 = 2.4kb, N90 = 637b). On TOG5681, we obtained 97,196 contigs (minimum size 200b), with a mean size of 2.8kb (N50 = 5kb, N90 = 1.3 kb). The overall assembly for each genome is 0.56x for TOG5307 and 0.69x for TOG5681. Just adding +6x of Illumina data almost doubled the assembly efficiency. PacBio data test on C2 and XL kits were also performed for CG14 data, providing, respectively, 143,456 and 99,488 contigs (mean size of 3140b and 3184b), with a 1.12x and 0.79x coverage. The C2 10x sequencing in PacBio for CG14 and TOG5681, and the 60x sequencing in Illumina for each is underway. The annotation will be transferred from the Nipponbare MSU7.0 reference genome using tools such as QOD and BLAST/BLAT based scripts. These sequences will be immediately available for the whole community without restriction. The IRIGIN project from France Genomique (International RIce Genomic INitiative) is headed by IRD and Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), and aims to provide valuable genetic stocks genomic data in the frame of the Global Rice Science Partnership (GRiSP). African rice (300 O. glaberrima and 100 O. barthii) will be deeply resequenced (25x) and aligned on their reference (from the GLASS project). At the same time, NAMs population (indica x tropical japonica) from AfricaRice and the International Center for Tropical Agriculture (CIAT) will be genotyped (using low-coverage sequencing), to provide the best genetic map ever created in plants, with the highest level of coverage ever seen. Thousand of terabytes of raw data and billions of polymorphic data will be gathered within this project, and will be distributed to the whole rice community as soon as possible.