Fig. 1

Comparative genomic analysis of the genome assemblies. a Image of GCO (left) and GSA (right). b Distribution of GCO in China. The magenta point represents current habitat of GCO in the Wuyuan area. The grayish blue indicates extinct GCO in Simiao area. c Genomic landscape of the GCO and GSA. The dark red numbers indicate the following: (1) Synteny blocks between the two species. (2) GC content (%). (3)–(8) Represent density of tandem repeats, TEprotein, Transposon, gene, INDELs, and SNPs within a 10-kb sliding window. (9) Assembled scaffolds, green for GCO and light yellow for GSA. The numbers outside the circle indicate the scaffold number of the assembled genome. The unit of (2) is the percentage, the scale of (3)–(8) is the frequency, and the unit (9) is Mb. The density distribution of Ks (d) and Ka/Ks (e) values. f A phylogentic tree was built on the 2391 shared single-copy gene families. Acanthisitta chloris (ACS) was the outgroup. The abbreviations of species correspond to Additional file 1: Table S13. The numerical value beside each node shows the estimated divergence time. The red and green numbers represent significantly expanded and contracted gene families, respectively (left). The classified homologous genes (right). Cre., Cretaceous; Pal., Paleocene; Eoc., Eocene; Oli., Oligocene; Mio., Miocene; Pli., Pliocene; Ple., Pleistocene