Fig. 2

Chromosome profiles of previously missing protein-coding genes recovered in the VGP zebra finch assembly. a Circos plot of chromosomes greater than 10 Mb in size. b Circos plot of chromosomes less than 10 Mb in size. In the zebra finch, previously 20 or 40 Mb were used to classify micro- and macro-chromosomes [23], but we used 10 Mb for effective visualization. The two plots are not to scale. Shown from the outer to inner circle are the following: Chromosome number name (u: unlocalized) with previously present labelled in green, newly assembled and assigned labelled in purple, and assembly gaps labelled in gray lines in the outermost circle; % ratio of missing genes in the previous assembly; GC content, over the average of 42% in red and under in gray; Repeat content, over the average of 20% in blue and under in gray; Gene density in non-overlapping 200 kbp windows, orange line; Loci of totally missing genes in the prior assembly, black bars; Alignment with the previous assembly, with red bars as unaligned regions. Circos plots were generated with R package OmicCircos [24]. Chromosome-level scaffolds were sorted in descending order by size. Each scaffold was binned in consecutive 10 kbp blocks. Missing ratio of protein-coding genes was calculated by dividing the number of completely missing genes with the number of all genes on each scaffold. Gene density was calculated with BEDtools [25] makewindows and intersect