Fig. 1

Comparison of genome quality among duck, chicken, and zebra finch. Assessment was carried out according to the following genome versions: duck SKLA1.0; our previous duck genome (BGI duck 1.0); the available duck genome with highest contiguity (ZJU1.0); two high-quality avian genomes (the chicken GRCg6a and zebra finch bTaeGut1.4.pri). a Treemaps of five genome assemblies scaled by contig length. b Mapping ratios of 83 RNA-seq data to three duck assemblies. c Mapping ratio of 1,625,932 transcripts to three duck assemblies. Transcripts were from de novo assembly of RNA-seq reads and corrected Pacbio Iso-seq reads. d Completeness of five assemblies and reference protein sets estimated by the BUSCO software. e Number of coding genes and transcripts annotated in the five assemblies. f Percentage of genes with gaps in flanking sequence