Epigenetic modifications play important roles in plant and animal development. DNA methylation impacts the transposable element (TE) silencing, gene imprinting and expression regulation. Through a genome-wide analysis, DNA methylation peaks were characterized and mapped in maize embryo and endosperm genome, respectively. Distinct methylation level was observed across maize embryo and endosperm. The maize embryo genome contained more DNA methylation than endosperm. Totally, 985,478 CG islands (CGIs) were identified and most of them were unmethylated. More CGI shores were methylated than CGIs in maize suggested that DNA methylation level was not positively correlated with CpG density. The promoter sequence and transcriptional termination region (TTR) were more methylated than the gene body (intron and exon) region based on peak number and methylated depth. Result showed that 99% TEs were methylated in maize embryo, but a large portion of them (34.8%) were not methylated in endosperm. Maize embryo and endosperm exhibit distinct pattern/level of methylation. The most differentially methylated region between embryo and endosperm are CGI shores. Our results indicated that DNA methylation is associated with both gene silencing and gene activation in maize. Many genes involved in embryogenesis and seed development were found differentially methylated in embryo and endosperm. We found 41.5% imprinting genes were similarly methylated and 58.5% imprinting genes were differentially methylated between embryo and endosperm. Methylation level was associated with allelic silencing of only a small number of imprinting genes. The expression of maize DEMETER-like (DME-like) gene and MBD101 gene (MBD4 homolog) were higher in endosperm than in embryo. These two genes may be associated with distinct methylation levels across maize embryo and endosperm. Through MeDIP-seq we systematically analyzed the methylomes of maize embryo and endosperm and results indicated that the global methylation status of embryo was more than that of the endosperm. Differences could be observed at the total number of methylation peaks, DMRs and specific methylated genes which were tightly associated with development of embryo and endosperm. Our results also revealed that many DNA methylation regions didn’t affect transcription of the corresponding genes.

Peanut zygotes typically divide a few times to form a pre-embryo before further embryonic development halts under normal day/night photoperiods. Ovary elongation, however, continuesforming a downward growing peg-like structure. When the peg is buried in the soil, embryo development resumes in the darkness. The embryo-located region (ER) of the peg begins to enlarge and form a pod, while the basal region (BR) of the peg has a distinct fate. The molecular mechanisms governing these unique embryo development processes are unknown. In this study, histological analysis demonstrated that from 4 days after pollination to 3 days after soil penetration, the peanut pre-embryo remained morphologically similar. By 9 days after soil penetration, the embryo had changed to a globular embryo. Transcriptome analysis revealed differentially expressed genes in the ER and BR before and after peg soil penetration. In addition to light signaling and plant hormone metabolism genes, we identified differentially expressed genes in the ER that contribute to embryo development and pod formation processes, including MADS-box transcription factors, xyloglucan endotransglucosylase/hydrolase protein, cellulose synthase, homeobox-leucine zipper (HD-Zip) protein family genes, amino acid permease, and seed growth and embryo morphogenesis regulators (DA1, TCP3, and YABBY). A large number of genes were found to be differentially expressed in the ER and BR across three developmental peg stages. Exact changes in gene expression were also identified in the ER during early embryo and pod development. This information provides an expanded knowledgebase for understanding the mechanisms of early peanut pod formation.

Early peanut pod development is an important process of peanut reproductive development. Modes of DNA methylation during early peanut pod development are still unclear, possibly because its allotetraploid genome may cause difficulty for the methylome analysis. To investigate the functions of the dynamic DNA methylation during the early development of the peanut pod, global methylome and gene expression analyses were carried out by Illumina high throughput sequencing. A novel mapping strategy of reads was developed and used for methylome and gene expression analysis. Differentially methylated genes, such as nodulin, cell number regulator-like protein, and senescence-associated genes, were identified during the early developmental stages of the peanut pod. The expression levels of gibberellin-related genes changed during this period of pod development. From the stage one (S1) gynophore to the stage two (S2) gynophore, the expression levels of two key methyltransferase genes, DRM2 and MET1, were up-regulated, which may lead to global DNA methylation changes between these two stages. The differentially methylated and expressed genes identified in the S1, S2, and stage 3 (S3) gynophore are involved in different biological processes such as stem cell fate determination, response to red, blue, and UV light, post-embryonic morphogenesis, and auxin biosynthesis. The expression levels of many genes were co-related by their DNA methylation levels. In addition, our results showed that the abundance of some 24-nucleotide siRNAs and miRNAs were positively associated with DNA methylation levels of their target loci in peanut pods. A novel mapping strategy of reads was described and verified in this study. Our results suggest that the methylated modes of the S1, S2, and S3 gynophore are different. The methylation changes that were identified during early peanut pod development provide useful information for understanding the roles of epigenetic regulation in peanut pod development.

Mixed broad-leaved trees are particularly effective in addressing ecological issues such as soil degradation and biodiversity loss caused by the dense planting of Chinese fir. Understanding the changes in soil bacterial communities in fir–broadleaf mixed forests as a function of fir retention density may offer new insights for optimizing management practices and enhancing the ecological functions of the underground components of forest ecosystems. In this study, the diversity and composition of soil bacterial communities in mixed Cunninghamia lanceolata and Betula luminifera forests (CFBFs) with diverse retention densities of Chinese fir (1250, 1560, and 1690 trees/hm²) were analyzed. The results suggested that the soil characteristics and microbial communities’ diversity and structure are significantly influenced by the retention densities of Chinese fir in CFBFs. At the aggregate scale, the CFBFs with a retention density of 1560 trees/hm² presented the greatest soil bacterial community diversity (based on the Chao 1 (3562.75) and Shannon indices (6.58)), and the diversity and richness of soil bacteria initially increase and then decrease as the retention density decreases. In CFBFs, regardless of the retention density, bacterial communities in soil were mainly composed of Acidobacteria, Proteobacteria, and Planctomycetes. The relative abundance of soil Acidobacteria first elevated and afterwards decreased as the retention density decreased, with the highest levels (47.15%) observed in the stand with 1560 trees/hm² of Chinese fir. The Principal Coordinates Analysis (PCoA) showed that the soil microbial community structure in CFBEs with a retention density of 1560 trees/hm² is significantly different from CFBEs with a retention density of 1260, and 1690 trees/hm². Moreover, with different retention densities of Chinese fir, soil organic C, total N concentrations, and soil pH also significantly affected the diversity and composition of CFBF soil bacterial communities. Our results show that the choice of retention densities significantly influences soil microbial diversity and composition in CFBFs. Optimal retention densities (1560 trees/hm²) of Chinese fir in CFBFs can maximize bacterial diversity and stability, providing management guidance for thinning for sustainable management of the soil microenvironment of CFBFs.

In June 2018, symptoms consisting of leaf blight and rot were observed on interior foliage margin of immature Chun Da Wang, a Chinese cabbage (Brassica rapa pekinensis) cultivar, grown in Shandong province China (Figure 1). Microscopic examination of symptomatic tissue samples revealed characteristic of bacterial streaming. Once Chinese cabbage leaves were infected, the leaf head could not grow and decay, resulting loss of economic value. Infected leaves were collected, lesions surface-sterilized, and washed in sterile water. Upon plating on nutrient-agar medium, yellow-pigmented bacterium was consistently isolated. Bacteria were gram negative, positive tests for citrate utilization and Voges-Proskauer, and produced acid from D-glucose, α-lactose, sucrose, D-fructose and L-rhamnose, but not maltose. DNA was extracted and 16S rRNA gene sequence was amplified using universal primers, 27F and 1492R (Lane, 1991). 16S rRNA DNA sequence (MK880378) analysis indicated that the bacteria were phylogenetically close...

Chinese cabbage tipburn is characterized by the formation of necrotic lesions on the margin of leaves, including on the insides of the leafy head. This physiological disorder is associated with a localized calcium deficiency during leaf development. However, little information is available regarding the molecular mechanisms governing Ca-deficiency-triggered tipburn. This study comprehensively analysed the transcriptomic comparison between control and calcium treatments (CK and 0 mM Ca) in Chinese cabbage to determine its molecular mechanism in tipburn. Our analysis identified that the most enriched gene ontology (GO) categories are photosynthesis, thylakoid and cofactor binding. Moreover, the KEGG pathway was most enriched in photosynthesis, carbon metabolism and carbon fixation. We also analyzed the co-expression network by functional categories and identified ten critical hub differentially expressed genes (DEGs) in each gene regulatory network (GRN). These DEGs might involve abiotic stresses, developmental processes, cell wall metabolism, calcium distribution, transcription factors, plant hormone biosynthesis and signal transduction pathways. Under calcium deficiency, CNX1, calmodulin-binding proteins and CMLs family proteins were downregulated compared to CK. In addition, plant hormones such as GA, JA, BR, Auxin and ABA biosynthesis pathways genes were downregulated under calcium treatment. Likewise, HATs, ARLs and TCP transcription factors were reported as inactive under calcium deficiency, and potentially involved in the developmental process. This work explores the specific DEGs’ significantly different expression levels in 0 mM Ca and the control involved in plant hormones, cell wall developments, a light response such as chlorophylls and photosynthesis, transport metabolism and defence mechanism and redox. Our results provide critical evidence of the potential roles of the calcium signal transduction pathway and candidate genes governing Ca-deficiency-triggered tipburn in Chinese cabbage.