Additional file 1 of Population transcriptomic analysis identifies the comprehensive lncRNAs landscape of spike in wheat (Triticum aestivum L.)

Additional file 1: Table S1. Summary of all lncRNAs. Table S2. Summary of all lncRNA-mRNA pairs. Table S3. GO and KEGG enrichment of all target mRNAs. Table S4. Homologous lncRNAs between wheat and other species. Table S5. Sequence conservation of wheat lncRNAs based on results of whole-genome alignment. Table S6. Message of samples in population analysis. Table S7. Nucleotide diversity in each group. Table S8. Detail information of haplotype in lncRNA or target mRNA. (Yellow annotation indicates that gene has different haplotypes in different populations). Table S9. Interrelationship of ceRNA network between lncRNA, miRNA and mRNA. Table S10. Overlap between lncRNA or target mRNA and GWAS signals. Table S11. Overlap between lncRNA or target mRNA and known QTLs. Table S12. Overlap between lncRNA or target mRNA and introgression regions. Table S13. Information of 93 wheat lines. Table S14. Primers used for qRT-PCR analysis

Additional file 2 of Population transcriptomic analysis identifies the comprehensive lncRNAs landscape of spike in wheat (Triticum aestivum L.)

Additional file 2: Figure S1. Enrichment analysis of mRNA targets of lncRNAs. (a) GO enrichment analysis of target mRNAs. Different colors represent different GO term categories. (b) KEGG enrichment analysis of mRNA targets. Pathways were sorted by rich factor on the x-axis, which is determined by rich factor = (significant gene count of GO term)/(total gene count of GO term). Figure S2. Phylogenetic relationships of lncRNAs and target mRNAs on A subgenome. (a) Phylogenetic tree of lncRNA-mRNA pairs on A subgenome. (b) Phylogenetic tree of lncRNAs on A subgenome. (c). Phylogenetic tree of mRNAs on A subgenome. Figure S3. Phylogenetic relationships of lncRNAs and target mRNAs in B subgenome. (a) Phylogenetic tree of lncRNA-mRNA pairs on B subgenome. (b) Phylogenetic tree of lncRNAs on B subgenome. (c). Phylogenetic tree of mRNAs on B subgenome. Figure S4. Phylogenetic relationships of lncRNAs and target mRNAs in D subgenome. (a). Phylogenetic tree of lncRNA-mRNA pairs on D subgenome. (b) Phylogenetic tree of lncRNAs on D subgenome. (c). Phylogenetic tree of mRNAs on D subgenome. Figure S5. Expression and functional enrichment of lncRNAs and target mRNAs in chromosome 1BS. (a). Heatmap of expression levels of lncRNAs and target mRNAs in the 1B1R region. (b). Boxplots of expression levels of lncRNAs and target mRNAs in the 1B1R region in the two groups of samples. (c). GO and KEGG enrichment analysis of target mRNAs within 1B1R region. Figure S6. qRT-PCR validation of lncRNAs between 1B1R samples and non-1B1R samples. (a). qRT-PCR validation of 1B1R lineage-specific lncRNAs. (b). qRT-PCR validation of non-1B1R lineage-specific lncRNAs. The significance of expression level between 1B1R and non-1B1R groups was statistically analyzed by student's t-test. Figure S7. Phylogenetic relationships of TraesCS2A02G518500 in A subgenome. Figure S8. Genome-wide average LD decay estimated from 93 samples