Anas platyrhynchos breed:Ji'an red duck Genome sequencing. Anas platyrhynchos breed:Ji'an red duck

The Ji'an red duck, a representative native dual-purpose type breed from Ji'an city of Jiangxi province of China, is the only domestic duck with the characteristics of red plumage. To de novo assemble the Ji'an red duck genome, we generated 713.35 Gb of reads with about 589.55 fold sequence coverage. The 126 Gb ( 114.55 fold) PacBio ultralong reads were used for self-corrected and then de novo assembled into initial contigs, which were further polished using high-quality Illumina short reads (133 Gb, 120.91 fold). Subsequently, a hybrid scaffolding was implemented by 10X Genomics (185 Gb, 153.16 fold) and BioNano optical mapping (147 Gb, 133.64 fold) to elongate the initial assembly. After clustering of high-throughput chromosome conformation capture (Hi-C) data (120 Gb, 109.09 fold), approximately 93.57% of all sequences (1.11 Gb) were assigned to 40 pseudo-chromosomes, which is consistent with previous karyotype analysis and the latest constructed chromosome-scale genome of improved duck breeds.