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Abstract Alternative transcription initiation (ATI) appears to be a ubiquitous regulatory mechanism of gene expression in eukaryotes. However, the extent to which it affects the products of gene expression and how it evolves and is regulated remain unknown. Here, we report genome-wide identification and analysis of transcription start sites (TSSs) in various soybean (Glycine max) tissues using a survey of transcription initiation at promoter elements with high-throughput sequencing (STRIPE-seq). We defined 193,579 TSS clusters/regions (TSRs) in 37,911 annotated genes, with 56.5% located in canonical regulatory regions and 43.5% from start codons to 3′ untranslated regions, which were responsible for changes in open reading frames of 24,131 genes. Strikingly, 6,845 genes underwent ATI within coding sequences (CDSs). These CDS-TSRs were tissue-specific, did not have TATA-boxes typical of canonical promoters, and were embedded in nucleosome-free regions flanked by nucleosomes with enhanced levels of histone marks potentially associated with intragenic transcriptional initiation, suggesting that ATI within CDSs was epigenetically tuned and associated with tissue-specific functions. Overall, duplicated genes possessed more TSRs, exhibited lower degrees of tissue specificity, and underwent stronger purifying selection than singletons. This study highlights the significance of ATI and the genomic and epigenomic factors shaping the distribution of ATI in CDSs in a paleopolyploid eukaryote. 

Abstract Phytophthora sansomeana is an emerging oomycete pathogen causing root rot in many agricultural species including soybean. However, as of now, only one potential resistance gene has been identified in soybean, and our understanding of how genetic and epigenetic regulation in soybean contributes to responses against this pathogen remains largely unknown. In this study, we performed whole genome bisulfite sequencing (WGBS) on two soybean lines, Colfax (resistant) and Williams 82 (susceptible) in response to P. sansomeana at two time points: 4 and 16 hours post inoculation to compare their methylation changes. Our findings revealed that there were no significant changes in genome-wide CG, CHG (H = A, T, or C), and CHH methylation. However, we observed local methylation changes, specially an increase in CHH methylation around genes and transposable elements (TEs) after inoculation, which occurred earlier in the susceptible line and later in the resistant line. After inoculation, we identified differentially methylated regions (DMRs) in both Colfax and Williams 82, with a predominant presence in TEs. Notably, our data also indicated that more TEs exhibited changes in their methylomes in the susceptible line compared to the resistant line. Furthermore, we discovered 837 DMRs within or flanking 772 differentially expressed genes (DEGs) in Colfax and 166 DMRs within or flanking 138 DEGs in Williams 82. These DEGs had diverse functions, with Colfax primarily showing involvement in metabolic process, defense response, plant and pathogen interaction, anion and nucleotide binding, and catalytic activity, while Williams 82 exhibited a significant association with photosynthesis. These findings suggest distinct molecular responses to P. sansomeana infection in the resistant and susceptible soybean lines. 

Abstract Phytophthora root rot, caused by oomycete pathogens in the Phytophthora genus, poses a significant threat to soybean productivity. While resistance mechanisms againstPhytophthora sojaehave been extensively studied in soybean, the molecular basis underlying immune responses toPhytophthora sansomeanaremains unclear. In this study, we investigated transcriptomic and epigenetic responses of two resistant (Colfax and NE2701) and two susceptible (Williams 82 and Senaki) soybean lines at four time points (2, 4, 8, and 16 h post inoculation [hpi]) afterP. sansomeanainoculation. Comparative transcriptomic analyses revealed a greater number of differentially expressed genes (DEGs) upon pathogen inoculation in resistant lines, particularly at 8 and 16 hpi. These DEGs were predominantly associated with defense response, ethylene, and reactive oxygen species‐mediated defense pathways. Moreover, DE transposons were predominantly upregulated after inoculation, and more of them were enriched near genes in Colfax than other soybean lines. Notably, we identified a long non‐coding RNA (lncRNA) within the mapped region of the resistance gene that exhibited exclusive upregulation in the resistant lines after inoculation, potentially regulating two flankingLURP‐one‐relatedgenes. Furthermore, DNA methylation analysis revealed increased CHH (where H = A, T, or C) methylation levels in lncRNAs after inoculation, with delayed responses in Colfax compared to Williams 82. Overall, our results provide comprehensive insights into soybean responses toP. sansomeana, highlighting potential roles of lncRNAs and epigenetic regulation in plant defense.