Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary

Mechanisms of HAHV-1 Interaction with Hemocytes in Haliotis diversicolor supertexta: An In Vitro Study

Haliotid herpesvirus 1 (HAHV-1) causes significant damage to the abalone aquaculture industry. Knowledge of HAHV-1 invasion and host defense mechanisms is limited due to the lack of stable molluscan cell lines. The present study established an in vitro infection model of HAHV-1 using the primary suspension cultures of hemocytes from Haliotis diversicolor supertexta and Haliotis discus hannai. The cytopathic effects of HAHV-1 on adherent-cultured hemocytes of both species were also investigated. The HAHV-1 DNA loads were firstly monitored by means of quantitative PCR during the development of viral infection, and subsequently the mechanism of interaction between HAHV-1 and hemocytes was explored by means of a transcriptome analysis. H. diversicolor supertexta hemocytes exhibited a high degree of susceptibility to HAHV-1, with viral loads reaching a peak of 4.0 × 10⁷ copies/ng DNA. In contrast, no significant replication was observed in H. discus hannai hemocytes. Transcriptome analysis revealed that HAHV-1 evades the host immune response in the early stages of infection, and hijacks the host's energy and redox metabolism to promote its replication at the late stages. Consequently, this study provides a valuable reference point for the investigation of virus-host interaction between HAHV-1 and abalone in vitro.

Physio-biochemical and molecular mechanisms of low nitrogen stress tolerance in peanut (Arachis hypogaea L.)

Nitrogen (N) is a major plant nutrient and its deficiency can arrest plant growth. However, how low-N stress impair plant growth and its related tolerance mechanisms in peanut seedlings has not yet been explored. To counteract this issue, a hydroponic study was conducted to explore low N stress (0.1 mM NO3-) and normal (5.0 mM NO3-) effects on the morpho-physiological and molecular attributes of peanut seedlings. Low-N stress significantly decreased peanut plant height, leaf surface area, total root length, and primary root length after 10 days of treatment. Meanwhile, glutamate dehydrogenase, glutamine oxoglutarate aminotransferase activities, chlorophyll, and soluble protein contents were substantially decreased. Impairment in these parameters further suppressed photochemical efficiency (Fv/Fm), and chlorophyll fluorescence parameters (PIABS), under low-N stress. Transcriptome sequencing analysis showed a total of 2139 DEGs were identified between the two treatments. KEGG enrichment annotation analysis of DEGs revealed that 119 DEGs related to 10 pathways, including N assimilation, photosynthesis, starch, and sucrose degradation, which may respond to low-N stress in peanuts. Combined with transcriptome, small RNA, and degradome sequencing, we found that PC-3p-142756_56/A.T13EMM (CML3) and PC-5p-43940_274/A.81NSYN (YTH3) are the main modules contributing to low N stress tolerance in peanut crops. Peanut seedlings exposed to N starvation exhibited suppressed gene expression related to nitrate transport and assimilation, chlorophyll synthesis, and carbon assimilation, while also showing improved gene expression in N compensation/energy supply and carbohydrate consumption. Additionally, low N stress tolerance was strongly associated with the miRNA.

Molecular and Biochemical Mechanisms of Scutellum Color Variation in Bactrocera dorsalis Adults (Diptera: Tephritidae)

Bactrocera dorsalis (Hendel) is an invasive fruit and vegetable pest, infesting citrus, mango, carambola, etc. We observed that the posterior thoracic scutella of some B. dorsalis adults are yellow, some light yellow, and some white in China. Compared with the B. dorsalis races with a yellow scutellum (YS) and white scutellum (WS), the race with a light-yellow scutellum (LYS) is dominant in citrus and carambola orchards. To reveal genetic correlates among the three races, the genomes of 22 samples (8 with YS, 7 with LYS, and 7 with WS) were sequenced by high-throughput sequencing technology. Single-nucleotide polymorphism (SNP) annotation showed that there were 17,580 non-synonymous mutation sites located in the exonic region. Principal component analysis based on independent SNP data revealed that the SNPs with LYS were more similar to that with YS when compared with WS. Most genes associated with scutellum color variation were involved in three pathways: oxidative phosphorylation, porphyrin and chlorophyll metabolism, and terpenoid backbone biosynthesis. By comparing the sequences among the three races, we screened out 276 differential genes (DGs) in YS vs. WS, 185 DGs in LYS vs. WS, and 104 DGs in YS vs. LYS. Most genes determining color variation in B. dorsalis scutella were located on chromosomes 2-5. Biochemical analysis showed that β-carotene content in YS and LYS was significantly higher than that in WS at any stage of adult days 1, 10, and 20. No significant differences were observed in cytochrome P450 or melanin content in YS, LYS, or WS. Our study provides results on aspects of scutellum color variation in B. dorsalis adults, providing molecular and physiological information for revealing the adaptation and evolution of the B. dorsalis population.

Gibberellin-3 induced dormancy and suppression of flower bud formation in pitaya (Hylocereus polyrhizus)

BACKGROUND

Flowering is a complex, finely regulated process involving multiple phytohormones and transcription factors. However, flowering regulation in pitaya (Hylocereus polyrhizus) remains largely unexamined. This study addresses this gap by investigating gibberellin-3 (GA3) effects on flower bud (FB) development in pitaya. Our findings reveal that GA3 application induces significant bud dormancy and suppresses FB formation, highlighting GA3's role in modulating flowering in this species.

RESULTS

GA3 application during peak flowering period significantly altered hormone levels, reducing auxin (AUX), cytokinin (CTK) active forms dihydrozeatin riboside (dhZR), zeatin riboside (ZR), N6-isopentenyladenosine (iPA), and brassinosteroid (BR), while increasing jasmonic acid (JA), GA3, and gibberellin-4 (GA4) levels, with abscisic acid (ABA) levels remaining unchanged compared to control. Conversely, FB formation was associated with increased levels of AUX, dhZR, ZR, iPA, ABA, and JA, and decreased GA3 and GA4 levels. Transcriptomic analysis revealed batches of differentially expressed genes (DEGs) associated with phytohormone signal transduction, aligning with observed hormone changes. Notably, except four CONSTANS-like (CO) (HU06G02633, HU10G00019, HU04G00234, and HU02G01458), all other CO genes were preferentially active in GA3-treated buds. GA3 treatment inhibited genes linked to the ABC model (AP1, AP2, MADS-box, AGL, SPL) and floral identity genes (LFY, FT), favoring dormancy and clean sweep of FB formation.

CONCLUSION

These findings underscore the potential of GA3 as a powerful modulator of flowering and bud dormancy in pitaya. By elucidating the hormonal and genetic responses to GA3 treatment, this study contributes to our understanding of flowering regulation in pitaya and highlights the significant impact of GA3 on bud developmental pathways.

Orogeny and High Pollen Flow as Driving Forces for High Genetic Diversity of Endangered Acer griseum (Franch.) Pax Endemic to China

Acer griseum (Franch.) Pax is an endangered species endemic to China, mainly scattered in the Qinling-Daba Mountains. The genetic diversity of 17 natural populations were analyzed by nuclear DNA (nDNA) and chloroplast DNA (cpDNA) to explore the driving forces for its microevolution. A high level of genetic diversity (nDNA: He = 0.296, cpDNA: Ht = 0.806) was found in A. griseum. Genetic variation was mainly within populations (92.52%) based on nDNA, while it was mainly among populations (96.26%) based on cpDNA. The seventeen populations were divided into two groups, corresponding to the subtropical zone (Group I) and temperate zone (Group II), with haplotype 4 (Hap4) and Hap5 being the most common haplotypes, respectively. Consequently, genes associated with heat and heavy metal stress were identified in Group I, while genes related to salt and drought stress were identified in Group II. Haplotype differentiation was driven by the heterogeneous microenvironment caused by the uplifting of the Qinling-Daba Mountains, which was a vital source of its high genetic diversity. Furthermore, the uplifted Qinling-Daba mountains may bridge high pollen flow among populations, whereas rivers can result in low seed flow among populations, which has led to the incongruent genetic structure between nDNA and cpDNA. This study represents a new perspective that geological events, especially orogeny, play an important role in plant microevolution through the establishment of maternal genetic structure and provides a meaningful conservation strategy for A. griseum. Overall, the Qinling-Daba Mountains not only are cradles for the genetic diversity of A. griseum but also provided refugia for it during the Quaternary glacial period.

Multiomics analysis provides insights into musk secretion in muskrat and musk deer

BACKGROUND

Musk, secreted by the musk gland of adult male musk-secreting mammals, holds significant pharmaceutical and cosmetic potential. However, understanding the molecular mechanisms of musk secretion remains limited, largely due to the lack of comprehensive multiomics analyses and available platforms for relevant species, such as muskrat (Ondatra zibethicus Linnaeus) and Chinese forest musk deer (Moschus berezovskii Flerov).

RESULTS

We generated chromosome-level genome assemblies for the 2 species of muskrat (Ondatra zibethicus Linnaeus) and musk deer (Moschus berezovskii Flerov), along with 168 transcriptomes from various muskrat tissues. Comparative analysis with 11 other vertebrate genomes revealed genes and amino acid sites with signs of adaptive convergent evolution, primarily linked to lipid metabolism, cell cycle regulation, protein binding, and immunity. Single-cell RNA sequencing in muskrat musk glands identified increased acinar/glandular epithelial cells during secretion, highlighting the role of lipometabolism in gland development and evolution. Additionally, we developed MuskDB (http://muskdb.cn/home/), a freely accessible multiomics database platform for musk-secreting mammals.

CONCLUSIONS

The study concludes that the evolution of musk secretion in muskrats and musk deer is likely driven by lipid metabolism and cell specialization. This underscores the complexity of the musk gland and calls for further investigation into musk secretion-specific genetic variants.

Time-Course Transcriptomics Analysis Reveals Molecular Mechanisms of Salt-Tolerant and Salt-Sensitive Cotton Cultivars in Response to Salt Stress

Salt stress is an environmental factor that limits plant seed germination, growth, and survival. We performed a comparative RNA sequencing transcriptome analysis during germination of the seeds from two cultivars with contrasting salt tolerance responses. A transcriptomic comparison between salt-tolerant cotton cv Jin-mian 25 and salt-sensitive cotton cv Su-mian 3 revealed both similar and differential expression patterns between the two genotypes during salt stress. The expression of genes related to aquaporins, kinases, reactive oxygen species (ROS) scavenging, trehalose biosynthesis, and phytohormone biosynthesis and signaling that include ethylene (ET), gibberellin (GA), abscisic acid (ABA), jasmonic acid (JA), and brassinosteroid (BR) were systematically investigated between the cultivars. Despite the involvement of these genes in cotton's response to salt stress in positive or negative ways, their expression levels were mostly similar in both genotypes. Interestingly, a PXC2 gene (Ghir_D08G025150) was identified, which encodes a leucine-rich repeat receptor-like protein kinase (LRR-RLK). This gene showed an induced expression pattern after salt stress treatment in salt-tolerant cv Jin-mian 25 but not salt-sensitive cv Su-mian 3. Our multifaceted transcriptome approach illustrated a differential response to salt stress between salt-tolerant and salt-sensitive cotton.

Integrated microRNA study and pathological analysis provides new insights into the immune response of Ruditapes philippinarum under Vibrio anguillarum challenge

Manila clam (Ruditapes philippenarum) is an important shellfish aquaculture product. The large-scale breeding of clams is often affected by V. anguillarum and causes large-scale death. However, the pathogenesis, immune response and metabolic pathway of V. anguillarum are still unclear. In this study, we found that the bacterial load in the hepatopancreas of R. philippinarum peaked at 48 h after V. anguillarum infection, and then gradually decreased, while the activity of lysozyme reached the peak at 12 h. Tissue section observation reveals that the infected hepatopancreas cells lost normal structure or necrosis. Additionally, six small RNA libraries were constructed using hepatopancreas of clams. A total of 15 differentially expressed (DE) microRNA (miRNA) were identified at 48 h after V. anguillarum infection, including 8 upregulated and 7 downregulated miRNAs. GO and KEGG enrichment results indicated the prediction of 48 known miRNAs and 127 new miRNAs, with functional annotation suggests that endocytosis pathway and bacterial recognition proteins may play key roles in immune response. The sequencing results were basically consistent with the qRT-PCR validation, indicating the accuracy of the data. This study provides a new idea to explore the immune regulation mechanism of shellfish after V. anguillarum infection, which brings important reference significance for modern immunological research.

Life-history traits trade-off in gecko (Gekko japonicus) under the influence of climate warming and spirotetramat: Different adaptations to stressors in female and male

Global warming and rising surface temperatures are adversely affecting organisms. As the use of pesticides increases, concerns about their impacts on non-target organisms are growing. However, climate warming and pesticides may interact to produce combined effects on organisms. In this study, we exposed the geckos (Gekko japonicus) to different doses of spirotetramat (0, 15, and 30 mg/kg) and at different temperatures (25 °C and 30 °C) for 30 days. To investigate the effects of warming and spirotetramat on the trade-off in life-history traits of G. japonicus, we analyzed the energy allocation of the geckos under environmental stress. The results showed that females tended to allocate a significant amount of energy for self-maintenance and reduce investment in reproduction, which is a "conservative" life-history strategy. In contrast, males adopted a "risky" life-history strategy, tending to increase investment in reproduction while reducing immunity. However, in the long run, both reducing energy allocation towards reproduction and reducing investment in immunity can have adverse effects on the sustainable development of the population.

CRISPR/Cas9-mediated CHS2 mutation provides a new insight into resveratrol biosynthesis by causing a metabolic pathway shift from flavonoids to stilbenoids in Vitis davidii cells

Resveratrol is an important phytoalexin that adapts to and responds to stressful conditions and plays various roles in health and medical therapies. However, it is only found in a limited number of plant species in low concentrations, which hinders its development and utilization. Chalcone synthase (CHS) and stilbene synthase (STS) catalyze the same substrates to produce flavonoids and resveratrol, respectively. However, it remains unclear how CHS and STS compete in metabolite synthesis. In this study, two CHS2 mutant cell lines (MT1 and MT2) were generated using CRISPR/Cas9 genome editing. These CHS2 mutant cell lines exhibited abundant mutations in CHS2, leading to the premature termination of protein translation and subsequent CHS2 knockout. Amplicon sequencing confirmed comprehensive CHS2 knockout in MT1, whereas the wild-type sequence remained predominant in the MT2 cell line. Transcriptome and RT-qPCR results showed a significant downregulation of genes involved in flavonoid biosynthesis, including CHS2, CHS3, F3H, F3'H, DFR, FLS, LDOX, among others, resulting in decreased flavonoid accumulation, such as anthocyanins, proanthocyanidins, quercetin, and kaempferol. Conversely, STS genes involved in stilbenoid biosynthesis were upregulated competing with the flavonoid pathway. Consequently, there was a marked increase in stilbenoids, including resveratrol, piceatannol, piceid, and pterostilbene, with a 4.1-fold increase in resveratrol and a 5.3-fold increase in piceid (a derivative of resveratrol) observed in CHS2 mutant cell lines. This research demonstrates that CHS2 mutation induces a shift from flavonoid biosynthesis towards stilbenoid biosynthesis, offering new insights into metabolite biosynthesis and regulation, as well as an alternative solution for natural resveratrol production, and a novel breeding approach for eliminating non-target agronomic traits using CRISPR-Cas9.

Drought Adaptation and Responses of Stipa krylovii Vary Among Different Regions: Evidence From Growth, Physiology, and RNA-Seq Transcriptome Analysis

In the context of global climate change, exploring how plant adaptation and responses to drought vary among different regions are crucial to understanding and predicting its geographic distribution. In this study, to explore the drought adaptation and responses of the dominant species in the semi-arid Eurasian Steppes and their differences among the different regions in terms of growth, physiology, and RNA-seq transcriptome, Stipa krylovii was chosen as the study material, and a seed source (three regions: eastern, middle, and western regions) × soil moisture treatment (three treatments: control, light drought, and heavy drought) two-factor experiment was conducted. (1) Four growth traits for individuals from the western region were significantly lower than those from the other two regions. By Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis on gene expressions of individuals from each treatment, unique enriched pathways were found under heavy drought. (2) The decrease in the number of tillers with the increasing drought was much lower for individuals from the western region than those from the other two regions. The differentially expressed genes (DEGs) of individuals from the eastern, middle, and western regions between heavy drought versus control were 4887, 1900, and 4896. By KEGG functional enrichment analysis, individuals from the eastern and middle regions mainly regulated energy metabolism and metabolism of other amino acids; and those from the western region mainly regulated biosynthesis of other secondary metabolites and carbohydrate metabolism. (3) Clustering analysis based on gene expressions separated the western region from the other two regions under the same drought treatment. This study indicates that drought adaptation and responses of S. krylovii vary among different regions, especially between individuals from the western region and the other two regions. These findings are essential to understanding the adaptive evolution of population and germplasm resource protection for this important species.

Protective effect of ginseng extract and total ginsenosides on hematopoietic stem cell damage by inhibiting cell apoptosis and regulating the intestinal microflora

Ginseng may improve the myelosuppression and intestinal microbiota disorder induced by cyclophosphamide (CY); however, the effect of ginseng components on hematopoietic stem cell (HSC) damage remains largely unexplored. The present study aimed to assess the protective effect of ginseng extract (GE), total ginsenosides (TG) and total polysaccharides (TP) from ginseng on the intestinal microflora and HSCs of model mice. In the present study, a mouse model of HSC damage induced by CY was constructed, intestinal microflora of fecal samples were sequenced using the 16S ribosomal RNA (rRNA) sequencing techniques, the differentially expressed genes (DEGs) of HSCs were analyzed using high‑throughput RNA‑sequencing, cell apoptosis and erythroid differentiation were detected using flow cytometry and the blood cell parameters were analyzed using a hematology analyzer. Analysis of the 16S rRNA in fecal samples showed that GE, TG and TP improved an imbalanced intestinal microflora, where the relative abundance of Lactobacillus intestinalis had a positive correlation with ginsenosides content. Specifically, TP significantly increased the expression of low‑abundance microflora. Transcriptomic analysis results revealed 2,250, 3,432 and 261 DEGs in the GE, TG and TP groups compared with those in the Model group, respectively. In the expression analysis of DEGs, both TG and GE were found to markedly increase the expression levels of Klf4, Hhex, Pbx1, Kmt2a, Mecom, Zc3h12a, Zbtb16, Lilr4b, Flt3 and Klf13. Furthermore, TG inhibited the apoptosis of HSCs by increasing the expression levels of Bcl2 and Mcl1, whilst decreasing the expression of Bax. By contrast, GE inhibited the apoptosis of HSCs by reducing the expression of Bax and Bad. Regarding erythroid differentiation and blood cell parameters, GE was found to significantly increase the expression of TER‑119. In addition, GE and TG improved all blood cell parameters, including the count of white blood cells, neutrophils (NEUT), lymphocytes (LYMPH), red blood cells (RBC), hemoglobin (HGB) and reticulocyte and platelets (PLT), whereas TP could only improve the counts of LYMPH, RBC, HGB and PLT. The improvement effect of GE and TG on WBC, NEUT and Ret was superior to TP. In conclusion, TG may protect the hematopoiesis function of HSCs in a CY‑induced mouse model of HSC damage, followed by GE. However, TP did not appear to improve HSC damage. Ginsenosides may therefore be considered essential ingredients in GE when protecting HSCs against damage. GE and TG exerted their protective effects on HSCs by inhibiting the apoptosis of HSCs whilst improving the imbalance of intestinal microflora.

The storage quality and transcriptome analysis of fresh-cut taro by L-ascorbic acid combined with ultrasonic treatment

Fresh-cut taro, renowned for its high nutritional value and convenience, is prone to rapid browning post-cutting, which hinders its storage life. This study focused on the effects of L-ascorbic acid (AA) combined with ultrasound (US) treatment (AS) on the storage quality and transcriptome analysis of fresh-cut slices of Yongding June Red Taro. Compared to the control (CK) group, AS treatment effectively reduced the weight loss rate of taro slices, maintained higher hardness, delayed the increase of browning, and inhibited the accumulation of O2- and H2O2. Furthermore, the AS group showed increased glutathione levels and maintained higher activities of ascorbate peroxidase and glutathione reductase, yet decreased the contents of flavonoids and reducing sugars. Simultaneously, in the AS group, the activities of tyrosinase and lipoxygenase were lowered, thereby preserving the high sensory quality of fresh-cut taro slices. Transcriptome analysis revealed that differentially expressed genes (DEGs) between the AS and CK groups were annotated and categorized into 50 and 20 functional groups based on the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. Notably, both groups exhibited significant enrichment in processes related to photosynthesis, protein processing in the endoplasmic reticulum, and isoflavone biosynthesis. Therefore, we concluded that AS treatment could alleviate oxidative stress and maintain storage quality by regulating metabolic pathways. These findings provide insights into the physiological changes occurring in taro immediately after cutting and serve as an essential basis for developing effective storage and preservation techniques.

Endogenous cAMP elevation in Brassica napus causes changes in phytohormone levels

In higher plants, the regulatory roles of cAMP (cyclic adenosine 3',5'-monophosphate) signaling remain elusive until now. Cellular cAMP levels are generally much lower in higher plants than in animals and transiently elevated for triggering downstream signaling events. Moreover, plant adenylate cyclase (AC) activities are found in different moonlighting multifunctional proteins, which may pose additional complications in distinguishing a specific signaling role for cAMP. Here, we have developed rapeseed (Brassica napus L.) transgenic plants that overexpress an inducible plant-origin AC activity for generating high AC levels much like that in animal cells, which served the genetic model disturbing native cAMP signaling as a whole in plants. We found that overexpression of the soluble AC activity had significant impacts on the contents of indole-3-acetic acid (IAA) and stress phytohormones, i.e. jasmonic acid (JA), abscisic acid (ABA), and salicylic acid (SA) in the transgenic plants. Acute induction of the AC activity caused IAA overaccumulation, and upregulation of TAA1 and CYP83B1 in the IAA biosynthesis pathways, but also simultaneously the hyper-induction of PR4 and KIN2 expression indicating activation of JA and ABA signaling pathways. We observed typical overgrowth phenotypes related to IAA excess in the transgenic plants, including significant increases in plant height, internode length, width of leaf blade, petiole length, root length, and fresh shoot biomass, as well as the precocious seed development, as compared to wild-type plants. In addition, we identified a set of 1465 cAMP-responsive genes (CRGs), which are most significantly enriched in plant hormone signal transduction pathway, and function mainly in relevance to hormonal, abiotic and biotic stress responses, as well as growth and development. Collectively, our results support that cAMP elevation impacts phytohormone homeostasis and signaling, and modulates plant growth and development. We proposed that cAMP signaling may be critical in configuring the coordinated regulation of growth and development in higher plants.

Growth and physiological response of Yulu Hippophae rhamnoides to drought stress and its omics analysis

Hippophae rhamnoides (H. rhamnoides) is the primary tree species known for its ecological and economic benefits in arid and semi-arid regions. Understanding the response of H. rhamnoides roots to drought stress is essential for promoting the development of varieties. One-year-old Yulu H. rhamnoides was utilized as the experimental material, and three water gradients were established: control (CK), moderate (T1) and severe (T2), over a period of 120 days. The phenotypic traits and physiological indies were assessed and analyzed, while the roots were subjected by RNA-Seq transcriptome and Tandem Mass Tags (TMT) proteome analysis. Drought stress significantly reduced the plant height, ground diameter, root biomass and superoxide dismutase activity; however, the main root length increased. In comparison with CK, a total of 5789 and 5594 differential genes, as well as 63 and 1012 differential proteins, were identified in T1 and T2, respectively. The combined analysis of transcriptome and proteome showed that the number of differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) associated with T1, T2 and CK was 28 and 126, respectively, with 7 and 36 genes achieving effective KEGG annotation. In T1 and T2, the differential genes were significantly enriched in the plant hormone signal transduction pathway, but there was no significant enrichment in the protein expression profile. In T2, 38 plant hormone signal transduction function genes and 10 peroxisome related genes were identified. With the increase of drought stress, the combined expression of DEGs and DEPs increased. Yulu H. rhamnoides may allocate more resources toward CAT while simultaneously decreasing SOD and POD to mitigate the oxidative stress induced by drought. Furthermore, the molecular mechanisms underlying plant hormone signal transduction and peroxisome-related genes in the roots of H. rhamnoides were discussed in greater detail.

Unveiling molecular mechanisms of pigment synthesis in gardenia (Gardenia jasminoides) fruits through integrative transcriptomics and metabolomics analysis

This study conducted a combined transcriptomics and metabolomics analysis in premature and mature developmental stages of Gardenia jasminoides Ellis fruits to identify the molecular mechanisms of pigment synthesis. The transcriptomics data produced high-quality clean data amounting to 46.98 gigabytes, exhibiting a mapping ratio of 86.36% to 91.43%. Transcriptomics analysis successfully identified about 3,914 differentially expressed genes which are associated with pivotal biological processes, including photosynthesis, chlorophyll, biosynthetic processes, and protein-chromophore linkage pathways. Functional diversity was clarified by the Clusters of Orthologous Groups (COG) classification, which focused mainly on pigment synthesis functions. Pathways analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) revealed critical pathways affecting pigment development. Metabolomics studies were carried out utilizing Ultra Performance Liquid Chromatography and mass spectrometry (UPLC-MS). About 480 metabolites were detected via metabolomics investigation, the majority of that were significantly involved in pigment synthesis. Cluster and pathway analyses revealed the importance of pathways such as plant secondary metabolite biosynthesis, biosynthesis of phenylpropanoids and plant hormone signal transduction in pigment synthesis. Current research advances our comprehension of the underlying mechanisms at the molecular level governing pigment synthesis in gardenia fruits, furnishing valuable insights for subsequent investigations.

β-Nicotinamide Mononucleotide Reduces Oxidative Stress and Improves Steroidogenesis in Granulosa Cells Associated with Sheep Prolificacy via Activating AMPK Pathway

Oxidative stress is a significant factor in the death of granulosa cells (GCs), leading to follicular atresia and consequently limiting the number of dominant follicles that can mature and ovulate within each follicular wave. Follicular fluid contains a diverse array of metabolites that play crucial roles in regulating GCs' proliferation and oocyte maturation, which are essential for follicle development and female fertility. However, the mechanisms behind metabolite heterogeneity and its effects on GCs' function remain poorly understood. Here, we identified elevated nicotinamide levels in the follicular fluid of high-prolificacy sheep, correlated with oxidative stress in GCs, by an integrated analysis. In vitro experiments demonstrated that supplementation with β-nicotinamide mononucleotide (NMN) significantly increased the levels of nicotinamide adenine dinucleotide (NAD+) and adenosine triphosphate (ATP) in GCs. NMN treatment effectively reduced Lipopolysaccharide (LPS)-induced apoptosis and mitigated mitochondrial dysfunction, while also decreasing the production of reactive oxygen species (ROS), thereby enhancing the activity of the antioxidant defense system. Importantly, NMN treatment improved the impairments in steroid hormone levels induced by LPS. Mechanistically, the protective effects of NMN against GCs function were mediated via the AMPK/mTOR pathway. Collectively, our findings elucidate the metabolic characteristics associated with sheep prolificacy and demonstrate that NMN effectively protects GCs from LPS-induced dysfunction and enhances ovarian responsiveness via the AMPK/mTOR pathway. These findings also position NMN as a potential novel metabolic biomarker in enhancing ovarian function.

Transcriptomic comparison of corneal endothelial cells in young versus old corneas

Corneal endothelial cells, situated on the innermost layer of the cornea, are vital for maintaining its clarity and thickness by regulating fluid. In this study, we investigated the differences in the transcriptome between young and old corneal endothelial cells using next-generation sequencing (NGS). Cultured endothelial cells from both young and elderly donors were subjected to NGS to unravel the transcriptomic landscape. Subsequent analyses, facilitated by Metascape, allowed for the dissection of gene expression variances, unearthing pivotal biological pathways. A total of 568 genes showed differences, and were related to Endomembrane system organization, nuclear receptors meta pathway, efferocytosis, etc. Notably, a reduction in the expression of 260 genes was observed in the aged cells form old donors, and in the related analysis, eukaryotic translation initiation, integrator complex, and Hippo YAP signaling were significant. Conversely, 308 genes exhibited elevated expression levels in the elderly, correlating with processes including transition metal ion transport and glycoprotein biosynthesis. In conclusion, our investigation has revealed critical genes involved in the aging process of corneal endothelial cells and elucidated their underlying biological pathways. These insights are instrumental in selecting targets for therapeutic intervention, thereby facilitating the advancement of novel therapeutic approaches for the restoration and preservation of corneal endothelial cell function.

Dynamic transcriptomics unveils parallel transcriptional regulation in artemisinin and phenylpropanoid biosynthesis pathways under cold stress in Artemisia annua

Cold stress, a major abiotic factor, positively modulates the synthesis of artemisinin in Artemisia annua and influences the biosynthesis of other secondary metabolites. To elucidate the changes in the synthesis of secondary metabolites under low-temperature conditions, we conducted dynamic transcriptomic and metabolite quantification analyses of A. annua leaves. The accumulation of total organic carbon (TOC) in leaves under cold stress provided ample precursors for secondary metabolite synthesis. Short-term exposure to low temperature induced a transient increase in jasmonic acid synthesis, which positively regulates the artemisinin biosynthetic pathway, contributing to artemisinin accumulation. Additionally, transcripts of genes encoding key enzymes and transcription factors in both the phenylpropanoid and artemisinin biosynthetic pathways, including PAL, C4H, ADS, and DBR2, exhibited similar expression patterns, suggesting a coordinated effect between these pathways. Prolonged exposure to low temperature sustained high levels of phenylpropanoid synthesis, leading to significant increases in lignin, flavonoids, and anthocyanin. Conversely, the final stage of the artemisinin biosynthetic pathway is inhibited under these conditions, resulting in elevated levels of dihydroartemisinic acid and artemisinic acid. Collectively, our study provides insights into the parallel transcriptional regulation of artemisinin and phenylpropanoid biosynthetic pathways in A. annua under cold stress.

Transcriptome Analysis of the Harmful Dinoflagellate Heterocapsa bohaiensis Under Varied Nutrient Stress Conditions

The increasing prevalence of harmful algal blooms (HABs) driven by eutrophication, particularly in China's nearshore waters, is a growing concern. Dinoflagellate Heterocapsa bohaiensis blooms have caused significant ecological and economic damage, as well as mass mortality, in cultivated species. Nutrients are one of the primary inducers of H. bohaiensis blooms. However, the transcriptomic studies of H. bohaiensis remain sparse, and its metabolic pathways are unknown. This study analyzed the transcriptome of H. bohaiensis under varying nutrient conditions (nitrogen at 128, 512, and 880 μM; phosphate at 8, 6, and 32 μM), focusing on differential gene expression. The results indicated that deviations in nutrient conditions (higher or lower N:P ratios) led to a higher number of differentially expressed genes compared to the control (N:P ratios = 27.5), thereby underscoring their pivotal role in growth. Gene Ontology (GO) enrichment analyses showed that nutrient limitation upregulated the biosynthesis and catabolism processes while downregulating the cell cycle and division functions. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that, under nitrogen limitation, the proteasome pathways were upregulated, while photosynthesis and carbon fixation were downregulated; under phosphorus limitation, the proteasome pathways were upregulated and nitrogen metabolism was downregulated. These findings suggest that H. bohaiensis adapts to nutrient stress by adjusting its metabolic processes.

Transcriptomic analysis of male diamondback moth antennae: Response to female semiochemicals and allyl isothiocyanate

Female semiochemicals and allyl isothiocyanate (AITC) attract moths, and the moths use odorant-degrading enzymes (ODEs) to break down the excess odor. By identifying antennae-specific ODEs, researchers have established the molecular foundation for odorant degradation and signal inactivation in insects. This enables further exploration of new pest control methods. Currently, the degradation of female semiochemicals and AITC has received limited attention, inspiring this study to identify target ODEs in diamondback moths through transcriptome analysis. Sequencing of antennae from male adults (MA) exposed to female adults (FA) and AITC yielded a substantial 54.18 Gb of clean data, revealing 2276 differentially expressed genes (DEGs) between the MA and MA-FA treatments, and 629 DEGs between MA and MA-AITC treatments. The analysis of MAs exposed to FAs and AITC identified 29 and 17 ODEs, respectively, mainly involving aldehyde dehydrogenases (ALDHs), alcohol dehydrogenases (ADs), cytochrome P450s (CYPs), and UDP-glucuronosyltransferases (UGTs). Pathway analysis revealed primary enrichment in glycolysis/gluconeogenesis and fatty acid degradation in female adult treatments. In contrast, AITC treatments showed major enrichment in pathways related to pentose and glucuronate interconversions, retinol metabolism, and ascorbate and aldarate metabolism. Additionally, qRT-PCR analysis validated the expression patterns of 10 ODE genes in response to these treatments, with varying results observed among the genes. These findings indicate significant changes in ODE expression levels, providing a molecular foundation for identifying potential targets for behavioral inhibitors.

Cyclin-dependent kinases (CDKs) are key genes regulating early development of Neptunea arthritica cumingii: evidence from comparative transcriptome and proteome analyses

In this study, we applied comparative transcriptomics and proteomics techniques to systematically investigate the dynamic expression patterns of genes and proteins at various stages of early embryonic development of the gastropod Neptunea arthritica cumingii. Twelve cyclin-dependent kinase (CDKs) genes and five downstream proteins associated with these CDKs were identified. Through techniques such as qRT-PCR, our data elucidate for the first time the regulatory functions of CDK family genes and establish CDKs as a pivotal gene cluster in the early embryonic development of N. cumingii. These findings not only enhance the understanding of molecular developmental biology in N. cumingii and marine gastropods in general but also provide significant insights into the mechanisms involved in early embryonic development in N. cumingii. Furthermore, our results provide theoretical guidance for advancing artificial breeding technology for N. cumingii.

Mitochondrial dysfunction of Astrocyte induces cell activation under high salt condition

Excess dietary sodium can accumulate in brain and adversely affect human health. We have confirmed in previous studies that high salt can induce activation of astrocyte manifested by the secretion of various inflammatory factors. In order to further explore the effect of high salt on the internal cell metabolism of astrocytes, RNA sequencing was performed on astrocytes under high salt environment, which indicated the oxidative phosphorylation and glycolysis pathways of astrocytes were downregulated. Next, we found that high salt concentrations elicited astrocyte mitochondrial morphology change, as evidenced by swelling from a short rod to a round shape through a High Intelligent and Sensitive Structured Illumination Microscope (HIS-SIM). Furthermore, we found that high salt concentrations reduced astrocyte mitochondrial oxygen consumption and membrane potential. Treatment with 18-kDa translocator protein (TSPO) ligands FGIN-1-27 improved mitochondrial networks and reversed astrocyte activation under high-salt circumstances. Our study shows that high salt can directly disrupt astrocytic mitochondrial homeostasis and function. Targeting translocator protein signaling may have therapeutic potential against high-salt neurotoxicity.

Investigating the mechanism of auxin-mediated fulvic acid-regulated root growth in Oryza sativa through physiological and transcriptomic analyses

As rice is one of the most crucial staple food sources worldwide, enhancing rice yield is paramount for ensuring global food security. Fulvic acid (FA), serving as a plant growth promoter and organic fertilizer, holds significant practical importance in studying its impact on rice root growth for improving rice yield and quality. This study investigated the effects of different concentrations of FA on the growth of rice seedlings. The results indicated that 0.05 g/L FA could promote the growth of rice seedlings, while 0.5 g/L FA inhibited root growth, reduced cell activity and enzyme activity in the root tips, and accumulated reactive oxygen species in root cells. To further elucidate the molecular mechanisms underlying these effects, we performed transcriptomic analysis and found that auxin (Aux) may be involved in the growth process mediated by FA. Furthermore, transcriptome heatmap analysis revealed a significant upregulation of the Aux/indoleacetic acid (Aux/IAA) gene family after FA treatment, suggesting that this gene family plays a crucial role in the impact of FA on root growth. Additionally, by detecting endogenous Aux content and adding exogenous Aux inhibitors, we confirmed the involvement of FA in rice seedling root growth as well as in the synthesis and transduction pathway of Aux.

The RIG-I-like receptor signaling pathway triggered by Staphylococcus aureus promotes breast cancer metastasis

Host microbes are increasingly recognized as key components in various types of cancer, although their exact impact remains unclear. This study investigated the functional significance of Staphylococcus aureus (S. aureus) in breast cancer tumorigenesis and progression. We found that S. aureus invasion resulted in a compromised DNA damage response process, as evidenced by the absence of G1-phase arrest and apoptosis in breast cells in the background of double strand breaks production and the activation of the ataxia-telangiectasia mutated (ATM)-p53 signaling pathway. The high-throughput mRNA sequencing, bioinformatics analysis and pharmacological studies revealed that S. aureus facilitates breast cell metastasis through the innate immune pathway, particularly in cancer cells. During metastasis, S. aureus initially induced the expression of RIG-I-like receptors (RIG-I in normal breast cells, RIG-I and MDA5 in breast cancer cells), which in turn activated NF-κB p65 expression. We further showed that NF-κB p65 activated the CCL5-CCR5 pathway, contributing to breast cell metastasis. Our study provides novel evidence that the innate immune system, triggered by bacterial infection, plays a role in bacterial-driven cancer metastasis.

Use of Transcriptomics to Identify Candidate Genes for Hematopoietic Differences Between Wujin and Duroc Pigs

Hematopoiesis is a complex physiological process that ensures renewal of blood cells to maintain normal blood circulation and immune function. Wujin pigs exhibit distinct characteristics such as tender meat, high fat storage, strong resistance to roughage, robust disease resistance, and oxidation resistance. Therefore, using Wujin pigs as models may offer valuable insights for hematopoietic-related studies. In this study, twelve healthy 35-day-old piglets, including six Wujin and six Duroc piglets of similar weight, were selected from each of the Wujin and Duroc pig groups and housed in single cages. After 30 days of feeding, blood and bone marrow samples were collected. Routine blood indices and hematopoietic-related serum biochemical indexes of Wujin and Duroc pigs were determined, and bone marrow gene expression levels were analyzed using transcriptomics. (1) Hemoglobin (Hb) and Mean Corpuscular Hemoglobin Concentration (MCHC) levels in Wujin pigs were significantly higher than in Duroc pigs (p < 0.05), and platelet counts and serum Hb levels in Wujin pigs were significantly lower than in Duroc pigs (p < 0.05). (2) A total of 312 significantly differentially expressed genes were identified between the pigs. Their functions were mainly related to blood systems, inflammation, and oxidation. Six differentially expressed genes may be related to hematopoietic function. (3) By combining the differential genes screened through sequencing with Weighted Gene Co-expression Network Analysis results, 16 hematopoietic function differential genes were obtained, mainly focusing on immunity, inflammation, and induction of apoptosis functions. Differences were present in the immune and inflammatory responses between Wujin pigs and Duroc pigs, suggesting that differences in hematopoietic function between the two breeds were related to antioxidant capacity and disease resistance.

Tissue-specific transcriptome analyses unveils candidate genes for flavonoid biosynthesis, regulation and transport in the medicinal plant Ilex asprella

It is not clear that the genes involved with flavonoids synthesis, regulation and transport in Ilex asprella. Transcriptome analysis of leaf, stem and root has uncovered 28,478 differentially expressed genes (DEGs) that are involved in various biological processes. Among these, the expression of 31 candidate synthetase genes, 19 transcription factors, and 5 transporters associated with flavonoid biosynthesis varies across tissues, encompassing seven complete biosynthetic pathways (stilbene, aurone, flavone, isoflavone, flavonol, phlobaphene, and anthocyanin) and one partial pathway (proanthocyanidin). Tissue-specific expression patterns suggest that the stilbenes, aurones, flavones and anthocyanin branches are more prominent in roots, as indicated by key genes such as STS(Ilex_044726), CH4'GT(Ilex_047989), FNS(Ilex_043640) and UFGT(Ilex_014720). In leaves, the phlobaphenes and flavonols branches are dominant, determined by CHI(Ilex_005941), FNR(Ilex_039777) and FLS(Ilex_046424). The isoflavone pathway appears to be more active in stems due to the presence of IFS(Ilex_029360), mirroring the accumulation of the intermediate metabolite chalcone, which is regulated by CHS(Ilex_047537). The absence of LAR genes implies that gallocatechin, and catechin liked proanthocyanidins cannot be synthesized in I. asprella. Meanwhile, the general phenylpropanoid pathway is more active in roots, stems than in leaves, as evidenced by the expression of PAL(Ilex_042231, Ilex_014816), C4H(Ilex_017598), and 4CL(Ilex_042033). Flavanone, dihydroflavonol and leucoanthocyanidin, key intermediates, accumulate more rapidly in stem, stem and root, respectively, regulated by CHI(Ilex_005941), F3H(Ilex_004635) and DFR(Ilex_004771). Correlation and network analyses reveal that candidate regulators and transporters are closely associated with the synthesis genes. The study provides profound snoop into flavonoids metabolism in I. asprella and offers valuable refer for medicinal plant.

A hierarchical ubiquitination-mediated regulatory module controls bamboo lignin biosynthesis

The lignocellulosic feedstock of woody bamboo shows promising potential as an alternative to conventional wood, attributed to its excellent properties. The content and distribution of lignin serve as the foundation of these properties. While the regulation of lignin biosynthesis in bamboo has been extensively studied at the transcriptional level, its posttranslational control has remained poorly understood. This study provides a ubiquitinome dataset for moso bamboo (Phyllostachys edulis), identifying 13,015 ubiquitinated sites in 4,849 unique proteins. We further identified Kelch repeat F-box protein 9 (PeKFB9) that plays a negative role in lignin biosynthesis. Heterologous expression of PeKFB9 resulted in reduced accumulation of lignin and decreased phenylalanine ammonia lyase (PAL) activities. Both in vitro and in vivo assays identified interaction between PeKFB9 and PePAL10. Further examination revealed that SCFPeKFB9 mediated the ubiquitination and degradation of PePAL10 via the 26S proteasome pathway. Moreover, PebZIP28667 could bind to the PePAL10 promoter to significantly inhibit its transcription, and ubiquitination of PebZIP28667 weakened this inhibition. Collectively, our findings reveal a PeKFB9-PePAL10/PebZIP28667-PePAL10 module that acts as a negative regulator of lignin biosynthesis. This study advances our understanding of posttranslational regulation in plant lignification, which will facilitate the improvement of the properties of bamboo wood and the breeding of varieties.

Machine learning phenotyping and GWAS reveal genetic basis of Cd tolerance and absorption in jute

Cadmium (Cd) is a dangerous environmental contaminant. Jute (Corchorus sp.) is an important natural fiber crop with strong absorption and excellent adaptability to metal-stressed environments, used in the phytoextraction of heavy metals. Understanding the genetic and molecular mechanisms underlying Cd tolerance and accumulation in plants is essential for efficient phytoremediation strategies and breeding novel Cd-tolerant cultivars. Here, machine learning (ML) and hyperspectral imaging (HSI) combining genome-wide association studies (GWAS) and RNA-seq reveal the genetic basis of Cd resistance and absorption in jute. ML needs a small number of plant phenotypes for training and can complete the plant phenotyping of large-scale populations with efficiency and accuracy greater than 90%. In particular, a candidate gene for Cd resistance (COS02g_02406) and a candidate gene (COS06g_03984) associated with Cd absorption are identified in isoflavonoid biosynthesis and ethylene response signaling pathways. COS02g_02406 may enable plants to cope with metal stress by regulating isoflavonoid biosynthesis involved in antioxidant defense and metal chelation. COS06g_03984 promotes the binding of Cd2+ to ETR/ERS, resulting in Cd absorption and tolerance. The results confirm the feasibility of high-throughput phenotyping for studying plant Cd tolerance by combining HSI and ML approaches, facilitating future molecular breeding.

Effects of aflatoxin B1 on subacute exposure of hybrid groupers (Epinephelus fuscoguttatus♀ × Epinephelus lanceolatus♂): Growth, liver histology, and integrated liver transcriptome and metabolome analysis

With the increasing incorporation of plant-based ingredients into the grouper diet, the issue of aflatoxin B1 (AFB1) contamination in the diet has become a significant concern. In this study, the negative effects of AFB1 on the growth and liver health of hybrid groupers (Epinephelus fuscoguttatus♀ × Epinephelus lanceolatus♂) were investigated in the context of growth, liver histology, serum biochemical indices, and integrated transcriptomic and metabolomic data. A total of 540 healthy hybrid groupers, initially weighing 11.59 ± 0.03 g, were randomly divided into six groups (three replicates of 30 fish each): the control group was fed a basal diet, and the experimental groups were supplemented with 7 (AF7), 30 (AF30), 111 (AF111), 445 (AF445) and 2230 μg/kg AFB1 (AF2230) in the basal diet respectively, for 56 days. Groups control, AF445, and AF2230 were selected for subsequent histological, muscle fatty acid, and transcriptomic and metabolomic analyses based on the results of hybrid grouper growth and serum biochemical indices. Compared to the control group, both whole-body crude lipid and muscle crude lipid contents showed significant decreases in the AF2230 group (P < 0.05), while only muscle crude lipid content showed a significant decrease in the AF445 group (P = 0.001). Liver damage was seen in the histology of the liver of AF445 and AF2230 groups. Muscle fatty acid results showed that the addition of 445 and 2230 μg/kg AFB1 to the diets increased saturated fatty acids and monounsaturated fatty acids and decreased polyunsaturated fatty acids and highly unsaturated fatty acids in muscle (P < 0.05). Transcriptome analyses revealed multiple metabolic pathways associated with AFB1 metabolism, and metabolomics analyses further confirmed changes in the activity of these pathways. The results of the combined transcriptomic and metabolomic analyses indicated that AFB1 causes liver injury mainly by affecting liver retinol metabolism, metabolism of xenobiotics by cytochromes P450, drug metabolism-cytochromes P450 and biosynthesis of unsaturated fatty acids. In conclusion, dietary AFB1 levels above 445 μg/kg resulted in growth inhibition, liver injury, liver AFB1 accumulation, and reduced muscle polyunsaturated fatty acid content in groupers, thereby affecting muscle quality. This study provides novel insights into the detrimental effects of AFB1 on aquatic species and contributes to the scientific basis for the health and sustainability of aquaculture practices.

Comparative transcriptomic analysis revealed potential mechanisms regulating the hypertrophy of goose pectoral muscles

Pectoral muscle development is an important economic trait. According to the different essence, muscle development can be divided into 2 processes: embryonic muscle fiber generation and postnatal muscle fiber hypertrophy, and postnatal muscle fiber hypertrophy has a greater impact on muscle development than the number of muscle fibers formed during the embryonic phase in poultry. However, the underlying mechanisms regulating the hypertrophy of goose pectoral muscles have not been elucidated. Therefore, the purpose of the present study was to conduct transcriptome sequencing in pectoral muscles of both Landes (LD) and Sichuan White (SW) geese at 6, 10, and 30 weeks of age to reveal the molecular mechanisms regulating pectoral muscle hypertrophy through intra-breed and inter-breed bioinformatics analyses. Phenotypically, the pectoral muscle weight/index of LD and SW geese increased from 6 to 30 weeks of age, and except for the pectoral muscle index at 10 weeks of age (P = 0.962), at the same age, the pectoral muscle weight/index of LD geese were significantly higher than that of SW geese (P < 0.05). In transcriptional regulation, intra-breed bioinformatics analysis identified 3331 genes whose expression levels were opposite to the trend of pectoral muscle hypertrophy both in LD and SW geese, and the 3331 genes were mainly enriched into abundant KEGG pathways related to lipid metabolism, proliferation/apoptosis, and immune response. Moreover, 23 genes (including SLC2A10, TNFRSF1A, PRKAA1, SLC27A4, ITGB2, THY1, RHOA, MYL10, ACTB, PRKCB, PIK3R2, RAC2, DMD, LATS2, YAP1, WWTR1, SMAD7, CTGF, FGF1, AXIN2, GLI2, ID2, and CCND2) who were enriched in 6 crosstalk pathways named viral myocarditis, insulin resistance, sphingolipid signaling pathway, hippo signaling pathway, chemokine signaling pathway, and leukocyte transendothelial migration were identified as the key candidate genes regulating the hypertrophy of goose pectoral muscles. In inter-breed bioinformatics analysis, abundant different expression genes (DEGs) related to lipid metabolism, immune response, and proliferation/apoptosis were identified between LD and SW geese too, and compared with SW geese, the expression level of MYL10 in LD geese was lower, while the expression levels of GLI2/CTGF/SMAD7 in LD geese were higher. These results suggested that the hypertrophy of goose pectoral muscles might be achieved through more lipid deposition and less leukocyte infiltration to promote the proliferation of cells within the muscles, and the low expression of MYL10 and high expressions of GLI2/CTGF/SMAD7 might the keys to induce the pectoral muscle hypertrophy of LD geese from 6 to 30 weeks of age over that of SW geese. All data the present study obtained will provide new insights into the molecular mechanisms regulating the hypertrophy of goose pectoral muscles.

Genome-wide mapping of main histone modifications and coordination regulation of metabolic genes under salt stress in pea (Pisum sativum L)

Pea occupy a key position in modern biogenetics, playing multifaceted roles as food, vegetable, fodder, and green manure. However, due to the complex nature of its genome and the prolonged unveiling of high-quality genetic maps, research into the molecular mechanisms underlying pea development and stress responses has been significantly delayed. Furthermore, the exploration of its epigenetic modification profiles and associated regulatory mechanisms remains uncharted. This research conducted a comprehensive investigation of four specific histone marks, namely H3K4me3, H3K27me3, H3K9ac, and H3K9me2, and the transcriptome in pea under normal conditions, and established a global map of genome-wide regulatory elements, chromatin states, and dynamics based on these major modifications. Our analysis identified epigenomic signals across ~82.6% of the genome. Each modification exhibits distinct enrichment patterns: H3K4me3 is predominantly associated with the gibberellin response pathway, H3K27me3 is primarily associated with auxin and ethylene responses, and H3K9ac is primarily associated with negative regulatory stimulus responses. We also identified a novel bivalent chromatin state (H3K9ac-H3K27me3) in pea, which is related to their development and stress response. Additionally, we unveil that these histone modifications synergistically regulate metabolic-related genes, influencing metabolite production under salt stress conditions. Our findings offer a panoramic view of the major histone modifications in pea, elucidate their interplay, and highlight their transcriptional regulatory roles during salt stress.

Biocontrol potential of Bacillus velezensis HG-8-2 against postharvest anthracnose on chili pepper caused by Colletotrichum scovillei

Anthracnose caused by Colletotrichum scovillei is a significant disease of pepper, including in postharvest stage. Bacillus species represent a potential microbial resource for controlling postharvest plant diseases. Here, a strain HG-8-2 was obtained and identified as Bacillus velezensis through morphological, biochemical, physiological, and molecular analyses. The culture filtrate showed highly antifungal activity against C. scovillei both in vitro and on pepper fruit. Crude lipopeptide extracts, which had excellent stability, could effectively inhibit mycelial growth of C. scovillei with an EC50 value of 28.48 ± 1.45 μg mL-1 and inhibited conidial germination. Pretreatment with the extracts reduced the incidence and lesion size of postharvest anthracnose on pepper fruit. Analysis using propidium iodide staining, malondialdehyde content detection and scanning electron microscope observation suggested that the crude lipopeptide extracts harbored antifungal activity by damaging cell membranes and mycelial structures. The RNA-seq analysis conducted on C. scovillei samples treated with the extracts, as compared to untreated samples, revealed significant alterations in the expression of multiple genes involved in protein biosynthesis. Overall, these results demonstrated that B. velezensis HG-8-2 and its crude lipopeptide extracts exhibit highly antagonistic ability against C. scovillei, thereby offering an effective biological agent for the control of anthracnose in pepper fruit.

Transcriptomic analysis of the gonads of Locusta migratoria (Orthoptera: Acrididae) following infection with Paranosema locustae

Paranosema locustae is an environmentally friendly parasitic predator with promising applications in locust control. In this study, transcriptome sequencing was conducted on gonadal tissues of Locusta migratoria males and females infected and uninfected with P. locustae at different developmental stages. A total of 18,635 differentially expressed genes (DEGs) were identified in female ovary tissue transcriptomes, with the highest number of DEGs observed at 1 day post-eclosion (7141). In male testis tissue transcriptomes, a total of 32,954 DEGs were identified, with the highest number observed at 9 days post-eclosion (11,245). Venn analysis revealed 25 common DEGs among female groups and 205 common DEGs among male groups. Gene ontology and Kyoto Encyclopaedia of Genes and Genome analyses indicated that DEGs were mainly enriched in basic metabolism such as amino acid metabolism, carbohydrate metabolism, lipid metabolism, and immune response processes. Protein-protein interaction analysis results indicated that L. migratoria regulates the expression of immune- and reproductive-related genes to meet the body's demands in different developmental stages after P. locustae infection. Immune- and reproductive-related genes in L. migratoria gonadal tissue were screened based on database annotation information and relevant literature. Genes such as Tsf, Hex1, Apolp-III, Serpin, Defense, Hsp70, Hsp90, JHBP, JHE, JHEH1, JHAMT, and VgR play important roles in the balance between immune response and reproduction in gonadal tissues. For transcriptome validation, Tsf, Hex1, and ApoLp-III were selected and verified by quantitative real-time polymerase chain reaction (qRT-PCR). Correlation analysis revealed that the qRT-PCR expression patterns were consistent with the RNA-Seq results. These findings contribute to further understanding the interaction mechanisms between locusts and P. locustae.

Ovarian multi-omics analysis reveals key rate-limiting enzymes FASN, SCD5, FADS1, 3BHSD, and STAR as potential targets for regulating kidding traits in goats

The kidding traits of goats are an important index of production. However, the molecular regulatory mechanisms of kidding traits in goats have not been fully elucidated. This study aimed to investigate the molecular regulatory network of kidding traits in goats. Multi-omics revealed the enrichment of 10 signaling pathways, with fatty acid biosynthesis, biosynthesis of unsaturated fatty acids, and steroid hormone biosynthesis pathways being closely related to reproduction. Interestingly, the key rate-limiting enzymes, fatty acid synthase (FASN), stearoyl-CoA desaturase 5 (SCD5), fatty acid desaturase 1 (FADS1), 3β-hydroxysteroid dehydrogenase/isomerase (3BHSD), and steroidogenic acute regulatory protein (STAR) enriched in these pathways regulate changes in reproduction-related metabolites. In interference experiments, it was observed that suppressing these key rate-limiting enzymes inhibited the expression of CYP19A1, ESR2, and FSHR. Furthermore, interference inhibited granulosa cell proliferation, caused cell cycle arrest, and promoted apoptosis. Thus, these results suggest that the specific markers of nanny goats with multiple kids are the key rate-limiting enzymes FASN, SCD5, FADS1, 3BHSD, and STAR. These findings may greatly enhance the understanding of regulatory mechanisms that govern goat parturition.

PbAGL7-PbNAC47-PbMYB73 complex coordinately regulates PbC3H1 and PbHCT17 to promote the lignin biosynthesis in stone cells of pear fruit

Lignification of the cell wall in pear (Pyrus) fruit results in the formation of stone cells, which affects the texture and quality of the fruit. However, it is still unclear that how different transcription factors (TFs) work together to coordinate the synthesis and deposition of lignin. Here, we examined the transcriptome of pear varieties with different stone cell contents and found a key TF (PbAGL7) that can promote the increase of stone cell contents and secondary cell wall thicknesses. In addition, PbAGL7 can facilitate the expression level of lignin biosynthesis-related genes and accelerate the lignin biosynthesis in pear fruit and Arabidopsis. However, PbAGL7 did not directly bind to the promoters of PbC3H1 and PbHCT17 which are crucial genes involved in lignin biosynthesis. On the other hand, yeast two-hybrid (Y2H) library showed that PbNAC47 and PbMYB73 interacted with PbAGL7 in the nucleus. PbNAC47 and PbMYB73 also increased the stone cell and lignin contents, and upregulated the expressions of PbC3H1 and PbHCT17 by binding to the SNBE and AC elements, respectively. Moreover, PbNAC47 also interacted with PbMYB73 to form PbAGL7-PbNAC47-PbMYB73 complex. This complex significantly activated the expression levels of PbC3H1 and PbHCT17 and promoted lignin biosynthesis to form stone cells in pear fruit. Overall, our study provides new insights into the molecular mechanism of TFs that coordinately regulate the stone cell formation in pear fruit and extend our knowledge to understand cell wall lignification in plants.

Identification of Key Genes Correlated with Economic Trait Superiorities and Their SNP Screening Through Transcriptome Comparisons, WGCNA and Pearson Correlation Coefficient in the Sea Cucumber Apostichopus Japonicus

Variation in morphology-driven economic traits is a common issue hindering the development of the sea cucumber aquaculture industry. In this study, transcriptome comparisons, weighted gene correlation network analysis (WGCNA) and Pearson correlation coefficient (PCC) were first employed to identify key genes correlated with morphological variation in the sea cucumber Apostichopus japonicus, after which the relationship between identified key genes (relative expression and genotype) and economic trait phenotypes was investigated to screen potential biomarker targets for molecular-assisted breeding. The results showed that three genes (putative ficolin-2, fibrinogen c domain-containing protein 1, and angiopoietin-4) were closely associated with economic trait superiorities. Two single nucleotide polymorphisms (SNPs) were identified in the putative ficolin-2 gene as having a strong correlation with body weight and papilla number. The findings from this study will enrich breeding biomarker resources and benefit the development of molecular-assisted breeding techniques in sea cucumber aquaculture.

Circ_0001944 Targets the miR-1292-5p/FBLN2 Axis to Facilitate Sorafenib Resistance in Hepatocellular Carcinoma by Impeding Ferroptosis

BACKGROUND

Sorafenib, an orally active potent tyrosine kinase inhibitor (TKI), represented a primary treatment in patients with advanced hepatocellular carcinoma (HCC). Unfortunately, sorafenib resistance was regarded as a huge obstacle for HCC treatment.

METHODS

RNA-sequencing including circRNA Sequencing (circRNA-Seq) for circular RNAs (circRNAs), miRNA Sequencing (miRNA-Seq) for microRNAs (miRNAs), as well as mRNA Sequencing (mRNA-Seq) for mRNAs in sorafenib-resistant HCC cells vs sorafenib-sensitive HCC cells, were performed. Then, interaction correlation analysis between differentially expressed circRNAs and miRNAs and their target genes in Huh7/SOR and SMMC7721/SOR cells was exhibited. The "circRNA-miRNA-mRNA" network was constructed through the Cytoscape software application, Circular RNA Interactome and Targetscan prediction, RNA binding protein immunoprecipitation (RIP), RNA pull-down, and Dual luciferase reporter assay. Furthermore, mRNA-Seq, Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis for the downstream genes involved in the "circRNA-miRNA-mRNA" network was implemented. Iron detection assay, Lipid peroxidation quantification assay, ROS measurement assay, CCK-8 assay, and tumor challenge in vivo were used to determine the mechanisms promoting sorafenib resistance in HCC, where the "circRNA-miRNA-mRNA" network is clearly involved in.

RESULTS 

circ_0001944 and circ_0078607 with upregulation and 2 downregulated expressed circRNAs (circ_0002874 and circ_0069981), as well as 11 upregulated miRNAs including miR-193a-5p, miR-197-3p, miR-27a-5p, miR-551b-5p, miR-335-3p, miR-767-3p, miR-767-5p, miR-92a-1-5p, miR-92a-3p, miR-3940-3p, and miR-664b-3p and 3 downregulated expressed miRNAs (miR-1292-5p, let-7c-5p, and miR-99a-5p) in sorafenib-resistant HCC cells were determined. Among these non-coding RNAs (ncRNAs), circ_0001944 and miR-1292-5p should not be drop out of sight; circ_0001944 has been proved to target miR-1292-5p to inhibit its expression in HCC. Subsequent findings also raise that miR-1292-5p directly targeted the 3'-noncoding region (3'-UTR) of Fibulin 2 (FBLN2) mRNA. Furthermore, circ_0001944 targets the miR-1292-5p/FBLN2 axis to inhibit cell ferroptosis in which the indicated regulators associated with iron overload and lipid peroxidation were "rearranged". Most importantly, circ_0001944 advanced sorafenib resistance in HCC through mitigating ferroptosis, where the miR-1292-5p/FBLN2 axis cannot be left unrecognized.

CONCLUSION 

Circ_0001944 is a putative target for reversing sorafenib resistance in HCC. Our findings are expected to provide new targets and new directions for sorafenib sensitization in the treatment of HCC.

A Comprehensive Transcriptomic and Proteomics Analysis of Candidate Secretory Proteins in Rose Grain Aphid, Metopolophium dirhodum (Walker)

The Rose grain aphid, a notable agricultural pest, releases saliva while feeding. Yet, there is a need for a comprehensive understanding of the specific identity and role of secretory proteins released during probing and feeding. Therefore, a combined transcriptomic and proteomic approach was employed in this study to identify putative secretory proteins. The transcriptomic sequencing result led to the assembly of 18,030 unigenes out of 31,344 transcripts. Among these, 705 potential secretory proteins were predicted and functionally annotated against publicly accessible protein databases. Notably, a substantial proportion of secretory genes (71.5%, 69.08%, and 60.85%) were predicted to encode known proteins in Nr, Pfam, and Swiss-Prot databases, respectively. Conversely, 27.37% and 0.99% of gene transcripts were predicted to encode known proteins with unspecified functions in the Nr and Swiss-Prot databases, respectively. Meanwhile, the proteomic analysis result identified, 15 salivary proteins. Interestingly, most salivary proteins (i.e., 60% of the proteins) showed close similarity to A. craccivora, while 46.67% showed close similarity to A. glycines, M. sacchari and S. flava. However, to verify the expression of these secretory genes and characterize the biological function of salivary proteins further investigation should be geared towards gene expression and functional analysis.

TET3 regulates terminal cell differentiation at the metabolic level

TET-family members play a critical role in cell fate commitment. Indeed, TET3 is essential to postnatal development due to yet unknown reasons. To define TET3 function in cell differentiation, we have profiled the intestinal epithelium at single-cell level from wild-type and Tet3 knockout mice. We have found that Tet3 is mostly expressed in differentiated enterocytes. In the absence of TET3, enterocytes exhibit an aberrant differentiation trajectory and do not acquire a physiological cell identity due to an impairment in oxidative phosphorylation, specifically due to an ATP synthase assembly deficiency. Moreover, spatial metabolomics analysis has revealed that Tet3 knockout enterocytes exhibit an unphysiological metabolic profile when compared with their wild-type counterparts. In contrast, no metabolic differences have been observed between both genotypes in the stem cell compartment where Tet3 is mainly not expressed. Collectively, our findings suggest a mechanism by which TET3 regulates mitochondrial function and, thus, terminal cell differentiation at the metabolic level.

Blood mir-331-3p is a potential diagnostic marker for giant panda (Ailuropoda melanoleuca) testicular tumor

BACKGROUND

In recent years, several giant pandas have suffered from testicular tumor, which has seriously affected giant panda health. However, the pathogenesis of testicular tumor in giant panda is still unclear. Studies have shown that miRNAs are involved in the occurrence and development of a variety of cancers. However, the effect of miRNAs on giant panda testicular tumor has been little studied. Therefore, this study explored the pathogenesis of giant panda testicular tumor through miRNA and mRNA sequencing, and screened out diagnostic markers of testicular tumor.

RESULTS

Combined with phenotypic symptoms and pathological section results, three giant pandas were diagnosed with testicular tumor and divided into tumor group, and three other giant pandas were divided into normal group. A total of 29 differentially expressed miRNAs (DEmiRNAs) were screened by blood miRNA-seq, and 3149 target gene candidates were predicted. Functional enrichment analysis showed that the target genes were mainly involved in intermembrane lipid transfer and ATP-dependent chromatin remodeling. However, only 5 DEmiRNAs were screened by miRNA-seq of blood-derived exosomes and 364 target genes were predicted, which were mainly involved in antigen processing and presentation. In addition, 216 differentially expressed genes (DEGs) were screened by RNA-seq, and functional enrichment analysis showed that tumor-specific DEGs significantly enriched to protein phosphorylation. Spearman correlation analysis of miRNA-mRNA showed that the expressions of miR-331-3p and PKIG were significantly positively correlated (spearman = 0.943, p < 0.01), while the expressions of miR-331-3p and ENSAMEG00000013628 were significantly negatively correlated (spearman= -0.829, p < 0.05). RT-PCR showed that the expression of miR-331-3p was significantly decreased in giant panda with tumor (p < 0.01).

CONCLUSIONS

blood miRNAs and exosomal miRNAs exhibit distinct regulatory patterns concerning giant panda testicular tumor, potentially reflecting divergent biological processes in the disease's etiology. Meanwhile, miR-331-3p could be used as a potential diagnostic marker for giant panda testicular tumor. Our findings are conducive to the rapid clinical diagnosis of testicular tumor in giant pandas, and are also expected to provide scientific reference for further research on the pathogenesis of testicular tumor.

Transcriptomic Profiling Unravels the Disruption of Photosynthesis Apparatuses and Induction of Immune Responses by a Bipartite Begomovirus in Tomato Plants

Diseases caused by begomoviruses such as tomato yellow leaf curl disease (TYLCD) are major constraints in agriculture. While the interactions between plants and monopartite begomoviruses during TYLCD pathogenesis have been explored extensively, how bipartite begomoviruses interact with tomato plants are understudied. Here we first found that a bipartite begomovirus tomato yellow leaf curl Thailand virus (TYLCTHV) induced stunted growth, leaf curl and yellowing in tomato plants. We then profiled the tomato transcriptomic changes in response to TYLCTHV infection. In total, we identified 2322 upregulated and 1377 downregulated genes. KEGG enrichment analysis of the differentially expressed genes (DEGs) revealed that many KEGG pathways regulating plant photosynthesis processes and defenses were enriched. Specifically, TYLCTHV infection disrupted the expression of DEGs that function in the light-harvesting chlorophyll protein complex, photosystem I and II, cytochrome b6/f complex, photosynthetic electron transport and F-type ATPase. Additionally, the expression of many DEGs regulating plant defenses including pathogen-associated molecular pattern (PAMP)-triggered immunity, effector-triggered immunity and hypersensitive response was upregulated upon TYLCTHV infection. Taken together, we found that during the pathogenesis of TYLCD induced by TYLCTHV, the virus actively disrupts plant photosynthesis processes and induces defense responses. Our findings add to our knowledge of TYLCD pathogenesis and plant-virus interactions in general.

Role of DDR1 in Regulating MMPs in External Root Resorption

Human periodontal ligament cells (hPDLCs) express matrix metalloproteinases (MMPs), a group of enzymes responsible for the destruction of most extracellular matrix proteins in dental tissues, especially MMP-1, MMP-2, and MMP-13. Exploring the regulatory mechanism of MMPs is crucial for understanding external root resorption (ERR), one of the most severe complications, along with substantial loss of dental tissue, induced by trauma, pulpal infection, tooth bleaching, and orthodontic treatment, etc. Discoidin domain receptor 1 (DDR1), a cell surface receptor binding to collagen, has the potential to regulate the expression of MMP-1, MMP-2, and MMP-13, but the mechanism remains unclear. Thus, the present study aimed to investigate the connection and underlying mechanism between MMP-1, MMP-2, MMP-13, and DDR1 in hPDLCs. Our post-replantation ERR model revealed that Mmp-1, Mmp-2, Mmp-13, and Ddr1 all increased in the sites of ERR. hPDLCs with DDR1 knockdown exhibited a substantial reduction in MMP-1, MMP-2, and MMP-13 expression. To further confirm the underlying mechanism, we conducted further in vitro experiments, including RNA sequencing, RNA interference, RT-qPCR, Western blotting, and ELISA. Based on our results, MMP-1 was positively regulated by the Smad2/3 and MEK-ERK1/2 pathways and negatively regulated by the PI3K-Akt pathway through CCN2. MMP-2 and MMP-13 were positively regulated by the Smad2/3 pathway. MMP-13 was positively regulated by the MEK-ERK1/2 and PI3K/Akt signaling pathways. Collectively, DDR1 is a potent regulator of MMP-1, MMP-2, and MMP-13 expression through the Smad2/3, MEK-ERK1/2, and PI3K/Akt signaling pathways. Clarifying the significance and underlying mechanism by which DDR1 is involved in ERR might bring the chances to hinder the pathogenic process of ERR, hence reducing its incidence rate.

Investigation of cold adaptation mechanisms by transcriptome analysis in the liver of yellowtail kingfish (Seriola aureovittata)

Cold stress is an extreme environmental stressor that constrains the economic development of aquaculture. Yellowtail kingfish (Seriola aureovittata) is a commercially important fish species, but its molecular mechanisms in response to cold stress remain unknown. In this study, we investigated the transcriptional response of yellowtail kingfish liver to cold stress (10 °C) using RNA-sequencing analysis. We obtained 83.21 Gb of clean data from fish in the control group (0 h) and at 6, 12, and 24 h post-stimulation. A total of 2900 differentially expressed genes were identified from the comparison of the bioinformatic data from cold-stressed and control groups. Enrichment analysis suggested that protein processing, energy and lipid metabolism, signal transduction, and stress-induced cell cycle changes were highly involved during cold adaptation. Transport and utilization of fatty acids and cell cycle arrest were enhanced, whereas the rate of glycogen metabolism and protein biosynthesis were inhibited to maintain energy balance and normal fluidity of the cell membrane, thereby enhancing the tolerance of yellowtail kingfish to cold stress. Our study uncovered molecular pathways and key regulatory genes that are crucial for cold adaptation in yellowtail kingfish. These results provide new insights that could inform selective breeding programs aimed at enhancing cold resistance in aquaculture.

A comprehensive analysis of the defense responses of Odontotermes formosanus (Shiraki) provides insights into the changes during Serratia marcescens infection

BACKGROUND

Odontotermes formosanus (Shiraki) is a highly damaging agroforestry pest. Serratia marcescens is a broad-spectrum insecticidal pathogen and is highly lethal to O. formosanus. However, little is known about the mechanism between them. To improve the biological control of pests, a more in-depth analysis of the interactions between the pests and the pathogens is essential.

RESULTS

We used RNA-seq, enzyme activity assays and real-time fluorescent quantitative PCR (qPCR) to explore the defense responses of O. formosanus against SM1. RNA-seq results showed that 1,160, 2,531 and 4,536 genes were differentially expressed at 3, 6 and 12 h after SM1 infection, and Kyoto Encyclopedia of Genes and Genomes (KEGG) results indicated that immune response and energy metabolism were involved in the defense of O. formosanus against SM1. Reactive oxygen species (ROS) levels and ROS synthesis genes were significantly elevated, and the antioxidant system were induced in O. formosanus after SM1 infection. In addition, the cellular immune genes were affected, and the Toll, immune deficiency (Imd), Janus kinase/signal transducer and activator of transcription (JAK/STAT), c-Jun N-terminal Kinase (JNK) and melanization pathways were activated. In vitro, Oftermicin, an antimicrobial peptide, had a significantly inhibitory effect on SM1. Furthermore, the expression levels and enzyme activities of phosphofructokinase (PFK), lactate dehydrogenase (LDH), succinate dehydrogenase (SDH) and isocitrate dehydrogenase (IDH) in glycolysis and tricarboxylic acid (TCA) cycles were increased.

CONCLUSIONS

Our results clearly demonstrated that O. formosanus defended against SM1 by activating the antioxidant system, innate immunity and energy metabolism. This study would provide useful information for the development of biological controls of O. formosanus.

Transcriptional Profiling Analysis Providing Insights into the Harsh Environments Tolerance Mechanisms of Krascheninnikovia arborescens

Krascheninnikovia arborescens, an endemic shrub in China, thrives in desertification-prone environments due to its robust biomass, hairy leaves, and extensive root system. It is vital for ecological restoration and serves as a valuable forage plant. This study explored the molecular mechanisms underlying K. arborescens' adaptation to desert conditions, focusing on its physiological, biochemical, and transcriptomic responses to drought, salt, and alkali stresses. The results revealed that the three stresses have significant impacts on the photosynthetic, antioxidant, and ion balance systems of the plants, with the alkali stress inducing the most pronounced changes and differential gene expression. The clustering and functional enrichment analyses of differentially expressed genes (DEGs) highlighted the enrichment of the induced genes in pathways related to plant hormone signaling, phenylpropanoid biosynthesis, and transcription factors following stress treatments. In these pathways, the synthesis and signal transduction of abscisic acid (ABA) and ethylene, as well as the flavonoid and lignin synthesis pathways, and transcription factors such as MYB, AP2/ERF, bHLH, NAC, and WRKY responded actively to the stress and played pivotal roles. Through the WGCNA analysis, 10 key modules were identified, with the yellow module demonstrating a high correlation with the ABA and anthocyanin contents, while the turquoise module was enriched in the majority of genes related to hormone and phenylpropanoid pathways. The analysis of hub genes in these modules highlighted the significant roles of the bHLH and MYB transcription factors. These findings could offer new insights into the molecular mechanisms that enable the adaptation of K. arborescens to desert environments, enhancing our understanding of how other desert plants adapt to harsh conditions. These insights are crucial for exploring and utilizing high-quality forage plant germplasm resources and ecological development, with the identified candidate genes serving as valuable targets for further research on stress-resistant genes.

Integrative analysis of whole genome bisulfite and transcriptome sequencing reveals the effect of sodium butyrate on DNA methylation in the differentiation of bovine skeletal muscle satellite cells

Butyric acid as a short-chain fatty acid (SCFA) is one of the key microbial metabolites of ruminants. Numerous studies indicate that butyrate is crucial in muscle growth and development, and plays an important molecular regulatory role mainly by inhibiting histone deacetylation. DNA methylation, a major epigenetic modification, is involved in cell differentiation. Butyrate, in addition to its role in acetylation modifications, can alter the DNA methylation status of cells. However, the impact of butyrate on the DNA methylation of bovine skeletal muscle satellite cells (SMSCs) remains unclear. In this study, we developed a differentiation model of SMSCs and employed RNA sequencing (RNA-seq) alongside whole genome bisulfite sequencing (WGBS) to explore the effects of butyrate treatment on DNA methylation status and its relationship with gene expression. Treatment of SMSCs with sodium butyrate (NaB) at 1.0 mM for 2 days significantly inhibited the expression of DNA methyltransferases (DNMT1, DNMT2, DNMT3A) at the mRNA and protein levels while promoting the expression of demethylases (TET1, TET2, TET3) at mRNA levels. WGBS identified 4292 differentially methylated regions (DMRs), comprising 2294 hypermethylated and 1998 hypomethylated regions. These DMRs were significantly enriched in the MAPK, cAMP, and Wnt signaling pathways, all of which are implicated in myogenesis and development. Combining RNA-seq and WGBS data revealed a total of 130 overlapping genes, including MDFIC, CREBBP, DMD, LTBP2 and KLF4. These genes are predominantly involved in regulating the FoxO, MAPK, PI3K-Akt, and Wnt signaling pathways. This study provides new insights into the effects of butyrate-mediated DNA methylation on SMSC development and enhances our understanding of butyrate as an epigenetic modifier beyond its role in acetylation.

The poetry of nitrogen and carbon metabolic shifts: The role of C/N in pitaya phase change

Pitaya, a desert plant, has an underexplored flowering mechanism due to a lack of functional validation assays. This study reveals that the transition from vegetative to generative growth in pitaya is regulated by significant metabolic shift, underscoring the importance of understanding and address the challenging issue pitaya's phase change. Lateral buds from 6-years-old 'Guanhuahong' pitaya (Hylocereus monacanthus) plants were collected on April 8th, 18th, and 28th 2023, representing early, middle, and late stages of phase transition, respectively. Results showed diminished nitrogen levels concurrent with increased carbon levels and carbon-to-nitrogen (C/N) ratios during pitaya phase transition. Transcriptomic analysis identified batches of differentially expressed genes (DEGs) involved in downregulating nitrogen metabolism and upregulating carbon metabolism. These batches of genes play a central role in the metabolic shifts that predominantly regulate the transition to the generative phase in pitaya. This study unveils the intricate regulatory network involving 6 sugar synthesis and transport, 11 photoperiod (e.g., PHY, CRY, PIF) and 6 vernalization (e.g., VIN3) pathways, alongside 11 structural flowering genes (FCA, FLK, LFY, AGL) out of a vast array of potential candidates in pitaya phase change. These findings provide insights into the metabolic pathways involved in pitaya's phase transition, offering a theoretical framework for managing flowering, guiding breeding strategies to optimize flowering timing and improve crop yields under varied nitrogen conditions.

Proteomic analysis identified proteins that are differentially expressed in the flavonoid and carotenoid biosynthetic pathways of Camellia Nitidissima flowers

BACKGROUND

Camellia nitidissima Chi is a popular ornamental plant because of its golden flowers, which contain flavonoids and carotenoids. To understand the regulatory mechanism of golden color formation, the metabolites of C. nitidissima petals at five different developmental stages were detected, a proteome map of petals was first constructed via tandem mass tag (TMT) analysis, and the accuracy of the sequencing data was validated via parallel reaction monitoring (PRM).

RESULTS

Nineteen color components were detected, and most of these components were carotenoids that gradually accumulated, while some metabolites were flavonoids that were gradually depleted. A total of 97,647 spectra were obtained, and 6,789 quantifiable proteins were identified. Then, 1,319 differentially expressed proteins (DEPs) were found, 55 of which belong to the flavonoid and carotenoid pathways, as revealed by pairwise comparisons of protein expression levels across the five developmental stages. Notably, most DEPs involved in the synthesis of flavonoids, such as phenylalanine ammonium lyase and 4-coumarate-CoA ligase, were downregulated during petal development, whereas DEPs involved in carotenoid synthesis, such as phytoene synthase, 1-deoxy-D-xylulose-5-phosphate synthase, and β-cyclase, tended to be upregulated. Furthermore, protein‒protein interaction (PPI) network analysis revealed that these 55 DEPs formed two distinct PPI networks closely tied to the flavonoid and carotenoid synthesis pathways. Phytoene synthase and chalcone synthase exhibited extensive interactions with numerous other proteins and displayed high connectivity within the PPI networks, suggesting their pivotal biological functions in flavonoid and carotenoid biosynthesis.

CONCLUSION

Proteomic data on the flavonoid and carotenoid biosynthesis pathways were obtained, and the regulatory roles of the DEPs were analyzed, which provided a theoretical basis for further understanding the golden color formation mechanism of C. nitidissima.

Integrated Analysis of microRNAs and Transcription Factor Targets in Floral Transition of Pleioblastus pygmaeus

Bamboo plants have erratic flowering habits with a long vegetative growth and an uncertain flowering cycle. The process of floral transition has always been one of the hot and intriguing topics in bamboo developmental biology. As master modulators of gene expression at the post-transcriptional level, miRNAs play a crucial role in regulating reproductive growth, especially in floral transition of flowering plants. Pleioblastus pygmaeus is a kind of excellent ground cover ornamental bamboo species. In this study, we performed miRNA expression profiling of the shoot buds and flower buds from the bamboo species, to investigate flowering-related miRNAs in bamboo plants. A total of 179 mature miRNAs were identified from P. pygmaeus, including 120 known miRNAs and 59 novel miRNAs, of which 96 (61 known miRNAs and 35 novel miRNAs) were differentially expressed in the shoots at different growth stages. Based on target gene (TG) prediction, a total of 2099 transcription factors (TFs) were annotated to be TGs of the 96 differentially expressed miRNAs (DEMs), corresponding to 839 recordings of DEM-TF pairs. In addition, we identified 23 known DEMs involved in flowering and six known miRNAs related to floral organ development based on previous reports. Among these, there were 11 significantly differentially expressed miRNAs, with 124 TF targets corresponding to 132 DEM-TF pairs in P. pygmaeus. In particular, we focused on the identification of miR156a-SPL (SQUAMOSA Promoter-Binding protein-Like) modules in the age pathway, which are well-known to regulate the vegetative-to-reproductive phase transition in flowering plants. A total of 36 TF targets of miR156a were identified, among which there were 11 SPLs. The Dual-Luciferase transient expression assay indicated miR156a mediated the repression of the PpSPL targets in P. pygmaeus. The integrated analysis of miRNAs and TGs at genome scale in this study provides insight into the essential roles of individual miRNAs in modulating flowering transition through regulating TF targets in bamboo plants.