Anas platyrhynchos domestica (Pekin duck) bAnaPla1

Pekin duck (Z2 strain) has a haploid genome size estimated to be 1.41 Gb(Nakamura et al. 1990; Tiersch and Wachtel 1991), and a karyotype of 9 pairs of macrochromosomes (from chr1 to chr8, chrZ/chrW) and 31 pairs of microchromosomes (chr9 to chr39)(Takagi and Makino 1966). To de novo assemble the new genome, we generated 143-fold of PacBio long reads (read N50 14.3 kb) and 142-fold of 10x linked-read data from a female individual, 56-fold of BioNano map and 82-fold of Hi-C reads from a male individual. To identify the female-specific chrW sequences, we also generated 72-fold Illumina reads from a male individual and 92-fold Illumina reads from a female individual. Our primary assembly of PacBio long reads have assembled the entire genome into 1645 gapless contigs. To extend the contigs, we first corrected their sequence errors with 92-fold female Illumina reads, then oriented and connected them into 942 scaffolds with linked-reads, BioNano optical maps and Hi-C reads. As Hi-C data provides linkage but not orientation information, at our final step of chromosome anchoring, we incorporated RH linkage map and reduced the scaffold number further down to 789. This new genome has assembled 95.6% (1.13 Gb) sequences into 31 autosomes and a pair of sex chromosomes, leaving only 4.4% (62.1 Mb) of the genome unanchored due to their repetitive sequence composition or lack of linkage markers.