Additional file 2: Figure S2. of Transcriptome-wide identification and expression profiles of the WRKY transcription factor family in Broomcorn millet (Panicum miliaceum L.)

Sequence logos of PmWRKY domain. The PmWRKY proteins domain submitted to MEME server. The total height of stack was used to shows ‘information content’ of that position in the motif. Height of letters in stack suggests probability of each amino acids at that position. (DOC 558 kb

Additional file 3: Table S1. of Transcriptome-wide identification and expression profiles of the WRKY transcription factor family in Broomcorn millet (Panicum miliaceum L.)

The identified PmWRKY proteins in Broomcorn millet and their putative orthologous gene in rice. (DOC 47 kb

Additional file 6: of Genome-wide identification, phylogeny and expressional profiles of mitogen activated protein kinase kinase kinase (MAPKKK) gene family in bread wheat (Triticum aestivum L.)

Detail information of the network of TaMAPKKK with other wheat genes. (XLSX 42 kb

Additional file 4: Figure S3. of Transcriptome-wide identification and expression profiles of the WRKY transcription factor family in Broomcorn millet (Panicum miliaceum L.)

Expression level of 32 PmWRKY genes in different tissues. Actin was an internal reference gene. (DOC 797 kb

Additional file 1: Figure S1. of Transcriptome-wide identification and expression profiles of the WRKY transcription factor family in Broomcorn millet (Panicum miliaceum L.)

Multiple-sequence alignment of the WRKY protein domain from PmWRKYs and OsWRKYs. Conserved amino acids were indicated by blank background, conserved WRKY domains and zinc-finger motifs were indicated by red box. (DOC 1365 kb

Additional file 2: of Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in Brachypodium distachyon

The detailed sequence information of all the BdAP2/ERF genes, including genomic, transcript, CDS and protein as well as 2 kb upstream sequence. (RAR 245 kb

Additional file 1: Table S1. of Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in Brachypodium distachyon

The primers used in RT-PCR analysis. Table S2. Summary of functional domains presented in the BdAP2/ERF proteins. Table S3. Detail information of motifs identified in BdAP2/ERF proteins. Table S4. Characteristics of cis-regulatory elements in the promoter region of BdAP2/ERF genes. Table S5. Annotations of 278 putative cis-acting regulatory DNA elements identified in 141 BdERF genes in B. distachyon by PLACE. Table S6. List of putative miRNAs targeted BdAP2/ERF predicted by psRNATarget tool. Table S7. The Ka/Ks ratios and estimated divergence time for tandemly duplicated BdAP2/ERF genes. Table S8. The Ka/Ks ratios and estimated divergence time for segmentally duplicated BdAP2/ERF genes. Table S9. The Ka/Ks ratios and estimated divergence time for orthologous BdAP2/ERF proteins between B. distachyon and rice. Table S10. The Ka/Ks ratios and estimated divergence time for orthologous BdAP2/ERF proteins between B. distachyon and maize. Table S11. The Ka/Ks ratios and estimated divergence time for orthologous BdAP2/ERF proteins between B. distachyon and sorghum. Table S12. Detail information of network of BdAP2/ERF with other genes. Table S13. Detail information of alternative splicing variants. (XLSX 412 kb

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

Percent identity plot for comparison of six Asteraceae chloroplast genomes using mVISTA program.

<p>Top line shows genes in order (transcriptional direction indicated with arrow). Sequence similarity of aligned regions between <i>A. adenophora</i> and other five species is shown as horizontal bars indicating average percent identity between 50–100% (shown on y-axis of graph). The x-axis represents the coordinate in the chloroplast genome. Genome regions are color coded as protein-coding (exon), rRNA, tRNA and conserved non-coding sequences (CNS).</p