Chromosome-Level Assembly of Farmer Preferred Cassava Varieties Using Single – Molecule Sequencing (SMRT) Technology and Chromosome-Conformation Capture

Cassava is an important food security crop for the poorest communities in sub-Saharan Africa. Due to the clonal propagation of cassava, genetic diversity is limited and narrow facilitating the spread of different diseases. Here we present a diploid aware, chromosome scale de novo genome assembly of farmer preferred cassava (Manihot esculenta) varieties. Through the combination of SMRT PacBio sequencing and high-throughput chromosome conformation capture sequencing (Hi-C), cassava genomes have been sequenced and assembled to a high degree of completeness. Starting with PacBio raw reads, we integrated the FALCON assembler and the Quiver genome finishing tool to produce assemblies each composed of approximately 5700 contigs with a contig N50 size of >200 Kb. The genomes were scaffolded with the composite genetic map of cassava released by the International Cassava Genetic Map Consortium (ICGMC). Finally, cis-chromosome associations were determined by Hi-C, yielding reconstructions of all 18 chromosomes into single scaffolds. The new high quality assemblies enable novel comparative insights into the genome evolution of cultivated African cassava varieties.