Additional file 1 of Identification of regulatory factors promoting embryogenic callus formation in barley through transcriptome analysis
Creators: name: Jingqi Suo
name: Chenlu Zhou
name: Zhanghui Zeng
name: Xipu Li
name: Hongwu Bian
name: Junhui Wang
name: Muyuan Zhu
name: Han, Ning
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences

description: Additional file 1: Table S1. Statistics of the total reads from five libraries. Sample: sample name; Raw_reads: total number of reads in raw data; Raw_bases (G): total data volume of offline raw data; Valid_reads: number of valid reads after removing joints, low-quality reads, etc.; Dedup_reads: the number of reads after UMI deduplication; Valid_Q20 (%): Q20 value of valid reads; Valid_Q30 (%): Q30 value of valid reads; Valid_GC (%): GC content of reads after UMI deduplication; Valid2raw (%): valid reads accounted for the percentage of raw reads; Dedup2Valid (%): the percentage of valid reads after deduplication of the reads in the genome. Table S2. Summary of data cleaning and length distribution of tags. Table S3. List of primers for plasmid construction. The parts marked in red represents the adapter sequences. Fw: forward primer. Rev.: reverse primer. Table S4. List of primers used in the qRT-PCR. F: forward primer. R: reverse primer. Fig. S1. Pearson correlation between samples. a: Correlation heat map between samples. b: Principal component analysis of the three-dimensional map. Fig. S2. Fig. S2 Expression of a set of callus-inducing medium (CIM)--induced transcription factors during immature and mature embryo-derived callus formation. a-b: Pie chart of differentially expressed transcription factors in IME_0h/IME_48h and ME_0h/ME_24h. Numbers represent the gene members associated with a given TF family. c: The top 10 differentially expressed TFs in IME_0h/IME_48h ranked by fold change. Genes marked in blue are upregulated TFs, and transcription factors marked in black are downregulated. d: The top 10 differentially expressed TFs in ME_0h/ME_24h. Fig. S3. Transcript levels of ARF11, ARF16B, SUVH2A and SUVH3A in the five samples as revealed by qRT-PCR and RNA-seq data. The data shown are means ± S.D. of three biological replicates. Fig. S4. Phylogenetic tree of BBM and WUS genes in barley and other species. The phylogenetic tree was constructed in MEGA 4 by the Neighbor-Joining method. The gene IDs are HvBBM (HORVU2Hr1G087310.1), HvWUS (HORVU3Hr1G085050.1) from Hordeum vulgare, ZmBBM (Zm00001d042492), ZmWUS (Zm00001d026537) from Zea mays, SbBBM (SORBI_3003G390600), SbWUS (SORBI_3006G254900) from Sorghum bicolor, OsBBM (LOC_Os01g67410.1), OsWUS (LOC_Os04g56780.1) from Oryza sativa, TaBBM (TraesCS3B02G427300.1), TaWUS (TraesCS2A02G491900.1) from Triticum aestivum, BdBBM (BRADI_2g57747v3), BdWUS (BRADI_5g25113v3) from Brachypodium distachyon, and AtBBM (AT5G17430.1), AtWUS (AT2G17950.1) from Arabidopsis thaliana. Fig. S5. Expression analysis of candidate LEC1 gene during callus formation. a: Sequence alignment and domain analysis of the LEC1 in Arabidopsis, rice, maize and barley. b: Phylogenetic tree of LEC1 among barley and other species. The phylogenetic tree was constructed in MEGA 4 by the Neighbor-Joining method. The gene IDs are HvLEC1 (HORVU6Hr1G072110) from Hordeum vulgare, AtLEC1 (AT1G21970.1) from Arabidopsis thaliana, BnLEC1 (BnaA07g10770D) from Brassica napus, GmLEC1-A (GLYMA_07G268100), GmLEC1-B (GLYMA_17G005600) from Glycine max, and ZmLEC1 (Zm00001d017898_T001) from Zea mays, and OsLEC1 (LOC_Os02g49370.1) from Oryza sativa. Fig. S6. Phenotypes of plants regenerated from callus transformed with empty vectors and with WUS and BBM genes. Fig. S7. Expression analysis of candidate LBD genes potentially associated with callus formation in barley. The expression levels were visualised by using OmicStudio tools at https://www.omicstudio.cn/tool based on RNA-seq datasets (Additional file 4). Numbers beneath the heat map indicate the relative expression intensities, and the higher expression intensities are indicated by more reddish colors.