Genome sequence rice breeding line COPSEMAR9

By combining Illumina and Pac-Bio sequencing, we generated a high-quality genome sequence of the blast-resistant breeding line COPSEMAR9. The pipeline for the de novo genome assembly consisted in the following steps: First, a de novo assembly was created only with the Pacbio reads using Canu. Second, a de novo assembly was created only with the Pacbio reads using wtdbg2. Finally, a consensus assembly was generated with the outputs of Canu and wtdbg2 using quickmerge. The Illumina reads were then mapped on the obtained assembly and the software pilon was used to correct misassemblies and errors performing 11 iterations of correction. The obtained assembly was composed of 335 scaffolds which were then anchored to the rice chromosomes using the software DGENIES and the Oryza sativa japonica genome as reference (GCA_000005425.2). Some scaffolds could not be anchored to the reference genome, so they were left as unanchored sequences. The final assembly is composed by the 12 expected rice chromosomes, the mitochondrial and chloroplast genomes and additional 9 unanchored scaffolds, totalling 393,859,641 bp.