Additional file 1 of Near telomere-to-telomere genome assemblies of Silkie Gallus gallus and Mallard Anas platyrhynchos restored the structure of chromosomes and “missing” genes in birds

Additional file 1: Fig. S1. Summary of sequencing data from CAU_Wild_2.0 and CAU_Silkie_2.0. Fig. S2. Genome assembly pipeline of CAU_Silkie_2.0. Fig. S3. Genome assembly pipeline of CAU_Wild_2.0. Fig. S4. The collinearity between chromosome W of CAU_Silkie_2.0 and scaffolds from CAU_Silkie_1.0. Fig. S5. Hi-C interaction signal heatmap of CAU_Silkie_2.0. Fig. S6. Average GC content of chromosomes and new sequences of a. CAU_Wild_2.0 and b. CAU_Silkie_2.0 compared with the previous assembly version. Fig. S7. Hi-C interaction signal heatmap of CAU_Wild_2.0. Fig. S8. Locations of centromeres, telomeres, and gaps on chromosomes of CAU_Wild_1.0. Fig. S9. Locations of centromeres, telomeres, and gaps on chromosomes of SKLA1.0. Fig. S10. The gene collinearity of sex chromosomes between CAU_Wild_2.0 and CAU_Wild_1.0 and comparison of annotated genes. Fig. S11. Similarity heatmap of the centromere of Chr5 of CAU_Wild_2.0. Fig. S12. Locations of "missing" genes found on chromosomes of CAU_Silkie_2.0. Fig. S13. Locations of "missing" genes found on chromosomes of CAU_Wild_2.0. Fig. S14. The expression levels of TNFA in 19 different duck tissues.