Additional file 2 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 2: Table S1. An overview of the sequencing data for Mallard genomes. Table S2. An overview of the sequencing data for Silkie genomes. Table S3. RNA-seq data was utilized for gene annotation in the Silkie and Mallard genomes. Table S4. Annotation of non-coding RNA within the Silkie and Mallard genomes. Table S5. Annotation of repetitive sequences within the Silkie and Mallard genomes. Table S6. A comparison of contigs continuity during the assembly process of the Mallard genome. Table S7. A comparison of contigs continuity during the assembly process of the Silkie genome. Table S8. A continuity comparative analysis of chicken and duck genomes. Table S9. A description of the chromosomal status of the Silkie genome. Table S10. The length of newly assembled sequences relative to the version 1.0 genome across each chromosome of Silkie and Mallard genomes. Table S11. A description of the chromosomal status of the Mallard genome. Table S12. The location of centromeric regions in the Mallard genome. A description of the chromosomal status of the Silkie genome. Table S13. Distribution of centromeric regions in Silkie genome identified via CENPA ChIP-seq. Table S14. The BUSCO scores of newly assembled genomes and reference genomes. Table S15. Genes annotated in the Silkie and Mallard genomes across various databases. Table S16. BUSCO scores of annotation from Silkie and Mallard genomes. Table S17. Gene annotation of the ZW chromosomes in the Mallard. Table S18. Genes annotated to ChrZ and ChrW from CAU_Wild_2.0 and CAU_Wild_1.0. Table S19. Review of the 'missing genes' with Silkie and the Mallard genomes. Table S20. The RNA-seqs are used in the quantification of gene expression.