Constructing the putative chromosome
To infer the putative autosome of the black-faced spoonbill, we usedSatsuma v2.1(Grabherr et al., 2010) to align our reference genome assembly to the chicken genome (GRCg6a; GCA_000002315.5(Warren et al., 2017)) with option “l (minimum alignment length) = 100”. Scaffolds embedded within other scaffolds were removed. If the same scaffold was repeatedly aligned to different chromosomes, we kept the longest alignment. 486 scaffolds with a total length 1.10 Gb (93% of total draft genome) of the black-faced spoonbill genome were aligned to seven macro-chromosomes, 30 intermediate and micro-chromosomes and the mitochondrial DNA of the chicken genome. We classified unaligned scaffolds as “unlocalized” (Table S4).