Additional file 1 of Differential subgenome expression underlies biomass accumulation in allotetraploid Pennisetum giganteum

Additional file 1: Table S1. Summary of DNA sequencing data for Pennisetum giganteum. Table S2. Genome size estimation result of P. giganteum based on k-mer frequency analysis. Table S3. Statistics of the P. giganteum genome assembly. Table S4. The number of contigs and gaps in chromosomes of P. giganteum. Table S5. Statistics of chromosome-anchored contigs in subgenomes of P. giganteum. Table S6. BUSCO analysis of P. giganteum genome assembly. Table S7. The mapping rate of RNA-seq data to the P. giganteum genome. Table S8. Summary of homozygous SNPs detected in genome resequencing data of P. giganteum. Table S9. Statistics of repeat contents in the A and B subgenomes of P. giganteum. Table S10. Overview of protein-coding genes and transposable elements on chromosomes of A and B subgenomes. Table S11. Summary of intact LTR-RTs identified in the P. giganteum genome. Table S12. Statistics of gene annotation in P. giganteum. Table S13. Functional annotation of the predicted P. giganteum genes. Table S14. Mapping rates of pearl millet short reads on chromosomes of P. giganteum. Table S15. Summary of subgenome-specifically enriched 13-mers in P. giganteum. Table S16. Orthologous groups identified in P. giganteum and other plant species. Table S17. Distribution of different categories of gene families in P. giganteum and other plant species. Table S18. GO enrichment analysis of expanded genes of subgenome A and B in P. giganteum. Table S19. KEGG enrichment analysis of expanded genes of subgenome A and B in P. giganteum. Table S20. GO enrichment analysis of conserved genes of subgenome A in P. giganteum. Table S21. GO enrichment analysis of conserved genes of subgenome B in P. giganteum. Table S22. GO enrichment analysis of unique genes P. giganteum A and B compared with C. americanus. Table S23. GO enrichment analysis of unique genes in P. giganteum A and B compared with S. viridis. Table S24. GO enrichment analysis of unique genes in P. giganteum A and B compared with S. bicolor. Table S25. GO enrichment analysis of unique genes in P. giganteum A and B. Table S26. Statistics of number and length of SVs between different plant species. Table S27. Summary of highly conversed genes of A and B subgenome in P. giganteum relative to C. americanus and S. viridis. Table S28. Summary of the ratio of 3D chromatin A/B compartments between the syntenic gene pairs of A and B subgenomes. Table S29. Comparison of gene and exon in different tissues of P. giganteum. Table S30. The number of highly expressed genes in subgenomes of P. giganteum. Table S31. Summary of differentially expressed genes in inter-tissue comparison groups. Table S32. Summary of expressed homoeologous genes in different tissues of the AB subgenome. Table S33. Summary of homoeolog-specific genes in different tissues of the AB subgenome. Table S34. Summary of cellulose synthase related gene families in P. giganteum and S. viridis. Table S35. Summary of expression levels of cellulose synthesis related genes in different tissues of P. giganteum. Table S36. Distribution of cellulose synthase genes on chromosomes of P. giganteum. Table S37. Comparison of expression levels of homoeologous gene pairs between the A and B subgenomes in P. giganteum. Table S38. Summary of differentially expressed genes in seven stages of P. giganteum. Table S39. GO enrichment analysis of DEGs in leaves at seven stages in P. giganteum. Table S40. GO enrichment analysis of DEG in stems at seven stages in P. giganteum.Table S41. Statistics of all and full-length LTRs in A5-B14 syntenic regions. Table S42. Homoeolog expression dominance in P. giganteum and three other polyploid species.