BioProject

There had a total number of 804 genes with transcript difference, including 482 up-regulated genes and 322 down-regulated genes. Enrichment analysis of those 804 different transcript gene sets was performed to explore the biological effects and the corresponding pathways that are significantly associated on GO and KEGG (Padj <0.05 as the threshold for significant enrichment). In the GO functional enrichment analysis, all differential genes were significantly enriched into 65 GO Terms, among them there had 50 GO terms belonging to BP (Biological Process). Among these BP 50 terms, organonitrogen compound metabolic process (44 genes), organonitrogen compound biosynthetic process (44 genes), and oxidation-reduction process (58 genes) had most different transcript gene sets. While in the MF (Molecular Function), there had 3 GO terms involved transcript changes, which including coenzyme binding (31 genes), structural constituent of ribosome (17 genes) and structural molecule activity (17 genes). In the KEGG pathways enrichment analysis, all differential genes were significantly enriched mainly into 4 pathways, including efq03010 (Ribosome, 30 genes), efq01212 (Fatty acid metabolism, 10 genes), efq00061 (Fatty acid biosynthesis, 10 genes), and efq02010 (ABC transporters, 19 genes), where efq03010 (Ribosome), efq01212 (Fatty acid metabolism), efq00061 (Fatty acid biosynthesis) were up-transcripted pathways, and efq02010 (ABC transporters) was the down-transcripted pathway. Based on transcriptome data analysis in selenium-enriched E. durans A8-1 compared with E. durans A8-1, a total of 19 genes were screened for significant up- transcripted that may be associated with selenium metabolic processes Overall design: RNA was extracted from E. durans A8-1 grown in MRS broth containing 60 μg/ml selenite using a bacteria RNA kit (Tiangen Biotech Co. Ltd, Beijing, China). E. durans A8-1 grown in MRS broth without selenite was used as negative control, the control and treatment were all in triplicates. A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Through qualified RNA samples, the cDNA library was constructed, and then transcriptome sequencing was performed at Novogen Co. Ltd (Beijing, China). The raw data passed the quality control and mapped to the reference genome, differential expression analysis of two groups (three biological replicates per group) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distributio. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value<0.05 found by DESeq were assigned as differentially expressed. Corrected P-value of 0.005 and log2(Fold change) of 1 were set as the threshold for significantly differential expression. For the differentially expressed genes, the GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment were analyzed.