Diverse Upregulated Transcripts During Conidiation of the Aphid-Obligate Fungal Pathogen Conidiobolus Obscurus (Entomophthoromycotina)

Abstract Filamentous fungi in the order Entomophthorales are the main natural regulators of insect populations. Conidiation is crucial for entomopathogenic fungi to explore host resources due to the multifunction of conidia such as growth, infection, and stress resistance; however, the molecular mechanisms underlying the conidial functions in Entomophthorales is unknown. This study analyzed the differentially expressed transcriptomic patterns in three conidiation stages (pre-conidiation, emerging conidiation, and post-conidiation, respectively) of the aphid-obligate pathogen Conidiobolus obscurus (Entomophthoromycotina). The emerging conidiation stage vs. pre- or post- conidiation stage had 3,091 and 3,235 differentially expressed genes (DEGs), respectively, wherein 2,915 upregulated DEGs were putatively related to the conidial functions. A weighted gene co-expression network analysis showed that 772 hub genes in conidiation, which were related to cuticular component degradation, oxidative phosphorylation, ribosomal biogenesis, cell wall/membrane biosynthesis, MAPK signaling pathway, secondary metabolite biosynthesis, and other metabolic processes. This implied that the conidia of Entomophthorales have abundant transcripts with various functions to favor a quick response to the surrounding environment and effectively explore the host resources.

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Comparative transcriptome analyses of different Salvia miltiorrhiza varieties during the accumulation of tanshinones

PeerJ ◽

10.7717/peerj.12300 ◽

2021 ◽

Vol 9 ◽

pp. e12300

Author(s):

Jingwen Zhou ◽

Rui Liu ◽

Min Shuai ◽

Zhu-Yun Yan ◽

Xin Chen

Keyword(s):

Secondary Metabolite ◽

Intraspecific Variation ◽

Molecular Mechanisms ◽

Salvia Miltiorrhiza ◽

Differentially Expressed ◽

Pathway Enrichment Analysis ◽

Regulation Mechanism ◽

Dynamic Changes ◽

Secondary Metabolite Biosynthesis ◽

Diterpenoid Biosynthesis

Salvia miltiorrhiza (Labiatae) is an important medicinal plant in traditional Chinese medicine. Tanshinones are one of the main active components of S. miltiorrhiza. It has been found that the intraspecific variation of S. miltiorrhiza is relatively large and the content of tanshinones in its roots of different varieties is also relatively different. To investigate the molecular mechanisms that responsible for the differences among these varieties, the tanshinones content was determined and comparative transcriptomics analysis was carried out during the tanshinones accumulation stage. A total of 52,216 unigenes were obtained from the transcriptome by RNA sequencing among which 23,369 genes were differentially expressed among different varieties, and 2,016 genes including 18 diterpenoid biosynthesis-related genes were differentially expressed during the tanshinones accumulation stage. Functional categorization of the differentially expressed genes (DEGs) among these varieties revealed that the pathway related to photosynthesis, oxidative phosphorylation, secondary metabolite biosynthesis, diterpenoid biosynthesis, terpenoid backbone biosynthesis, sesquiterpenoid and triterpenoid biosynthesis are the most differentially regulated processes in these varieties. The six tanshinone components in these varieties showed different dynamic changes in tanshinone accumulation stage. In addition, combined with the analysis of the dynamic changes, 277 DEGs (including one dehydrogenase, three CYP450 and 24 transcription factors belonging to 12 transcription factor families) related to the accumulation of tanshinones components were obtained. Furthermore, the KEGG pathway enrichment analysis of these 277 DEGs suggested that there might be an interconnection between the primary metabolic processes, signaling processes and the accumulation of tanshinones components. This study expands the vision of intraspecific variation and gene regulation mechanism of secondary metabolite biosynthesis pathways in medicinal plants from the “omics” perspective.

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Genome-Wide Regulation of Acupuncture and Moxibustion on Ulcerative Colitis Rats

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2021/9945121 ◽

2021 ◽

Vol 2021 ◽

pp. 1-12

Author(s):

Zhaoqin Wang ◽

Yan Huang ◽

Di Wang ◽

Rumeng Wang ◽

Kunshan Li ◽

...

Keyword(s):

Ulcerative Colitis ◽

Signaling Pathway ◽

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Wnt Signaling Pathway ◽

Mapk Signaling ◽

Differentially Expressed ◽

Clinical Effects ◽

Sprague Dawley ◽

Acupuncture And Moxibustion

Acupuncture and moxibustion have definite clinical effects on treating ulcerative colitis (UC), but their mechanism is still unclear. To investigate the molecular mechanisms, we applied herb-partitioned moxibustion or electroacupuncture at the Tianshu (ST25) points on UC rats and used RNA sequencing to identify molecular consequences. Male Sprague Dawley (SD) rats were divided into 6 groups randomly: the normal control (NC) group, the control + herb-partitioned moxibustion (NCHM) group, the control + electroacupuncture (NCEA) group, the model (UC) group, the model + herb-partitioned moxibustion (UCHM) group, and the model + electroacupuncture (UCEA) group. Compared to the UC group, HE staining in the UCHM group and UCEA group indicated that colitis was relieved, the histopathological score and MPO were both significantly reduced, and the serum hs-CRP concentration was decreased significantly. The results of RNA-seq suggested that, compared to the NC group, 206 upregulated genes and 167 downregulated genes were identified in colon tissues from the UC group; compared to the UC group, the expression levels of some genes were both affected in the UCHM group and the UCEA group (684 differentially expressed genes were identified in the UCHM group, and 1182 differentially expressed genes were identified in the UCEA group). KEGG signal pathway analysis indicated that the differentially expressed genes in the UCHM group were associated with the JAK-STAT signaling pathway and cell adhesion molecule (CAM); the differentially expressed genes in the UCEA group were associated with the NF-κB signaling pathway, the toll-like receptor signaling pathways, the PI3K-Akt signaling pathway, the MAPK signaling pathway, and the Wnt signaling pathway. This is the first study to reveal the gene expression characteristics of the anti-inflammatory effect of UC rats from the perspective of acupuncture and moxibustion control, which provide a clue for further investigation into the molecular mechanisms of UC treatment by acupuncture and moxibustion.

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Comparative adipose transcriptome analysis digs out genes related to fat deposition in two pig breeds

Scientific Reports ◽

10.1038/s41598-019-49548-5 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 4

Author(s):

Kai Xing ◽

Kejun Wang ◽

Hong Ao ◽

Shaokang Chen ◽

Zhen Tan ◽

...

Keyword(s):

Candidate Genes ◽

Signaling Pathway ◽

Meat Quality ◽

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Mapk Signaling ◽

Fat Deposition ◽

Differentially Expressed ◽

Integrated Analysis ◽

Pig Breeds

Abstract Fatness traits are important in pigs because of their implications for fattening efficiency, meat quality, reproductive performance and immunity. Songliao black pigs and Landrace pigs show important differences in production and meat quality traits, including fatness and muscle growth. Therefore, we used a high-throughput massively parallel RNA-seq approach to identify genes differentially expressed in backfat tissue between these two breeds (six pigs in each). An average of 37.87 million reads were obtained from the 12 samples. After statistical analysis of gene expression data by edgeR, a total of 877 differentially expressed genes were detected between the two pig breeds, 205 with higher expression and 672 with lower expression in Songliao pigs. Candidate genes (LCN2, CES3, DGKB, OLR1, LEP, PGM1, PCK1, ACACB, FADS1, FADS2, MOGAT2, SREBF1, PPARGC1B) with known effects on fatness traits were included among the DEGs. A total of 1071 lncRNAs were identified, and 85 of these lncRNAs were differentially expressed, including 53 up-regulated and 32 down-regulated lncRNAs, respectively. The differentially expressed genes and lncRNAs involved in glucagon signaling pathway, glycolysis/gluconeogenesis, insulin signaling pathway, MAPK signaling pathway and so on. Integrated analysis potential trans-regulating or cis-regulating relation between DEGs and DE lncRNAs, suggested lncRNA MSTRG.2479.1 might regulate the expressed level of VLDLR affecting porcine fat metabolism. These results provide a number of candidate genes and lncRNAs potentially involved in porcine fat deposition and provide a basis for future research on the molecular mechanisms underlying in fat deposition.

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Transcriptome analysis of resistant and susceptible pepper (Capsicum annuum L.) in response to Xanthomonas campestris pv. Vesicatoria

10.1101/2020.09.24.311274 ◽

2020 ◽

Author(s):

Shenghua Gao ◽

Fei Wang ◽

Juntawong Niran ◽

Ning Li ◽

Yanxu Yin ◽

...

Keyword(s):

Transcriptome Analysis ◽

Xanthomonas Campestris ◽

Molecular Mechanisms ◽

Sugar Metabolism ◽

Amino Sugar ◽

Mapk Signaling ◽

Susceptible Variety ◽

Differentially Expressed ◽

Resistant Variety ◽

Sequencing Platform

AbstractBacterial spot (BS) disease of pepper, incited by Xanthomonas campestris pv. Vesicatoria (Xcv), is one of the most serious diseases. For a comparative analysis of defense response to Xcv infection, we performed a transcriptome analysis of BS -susceptible cultivar ECW and -resistant cultivar VI037601 using the HiSeq™ 2500 sequencing platform. Approximately 140.15 G clean data were generated from eighteen libraries. From the libraries generated, we identified 52,041 genes including 35,336 reference genes, 16,705 novel transcripts, and 4,794 differentially expressed genes (DEGs). There were 1,291, 2,956, 1,795 and 2,448 DEGs in ECW-24h-vs-ECW-0h, ECW-48h-vs-ECW-0h, VI037601-24h-vs-VI037601-0h and VI037601-48h-vs-VI037601-0h groups, respectively. Interestingly, DEGs involved in disease response in the resistant variety were induced at an earlier stage and at higher levels compared with the susceptible variety. Key enriched categories included amino sugar and nucleotide sugar metabolism, sesquiterpenoid and triterpenoid biosynthesis and MAPK signaling pathway. Moreover, 273 DEGs only differentially expressed in VI037601 and 436 overlapping DEGs in ECW and VI037601 post Xcv inoculation, including NBS-LRR genes, oxidoreductase gene, WRKY and NAC transcription factors were identified, which were mainly involved in metabolic process, response to stimulus and biological regulation pathways. Quantitative RT-PCR of sixteen selected DEGs further validated the RNA-seq differential gene expression analysis. Our results will provide a valuable resource for understanding the molecular mechanisms of pepper resistance to Xcv infection and improving pepper resistance cultivars against Xcv.

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Gene expression profiling analysis reveals fur development in rex rabbits (Oryctolagus cuniculus)

Genome ◽

10.1139/gen-2017-0003 ◽

2017 ◽

Vol 60 (12) ◽

pp. 1060-1067 ◽

Cited By ~ 3

Author(s):

BoHao Zhao ◽

Yang Chen ◽

XiaoRong Yan ◽

Ye Hao ◽

Jie Zhu ◽

...

Keyword(s):

Gene Expression ◽

Signaling Pathways ◽

Molecular Mechanisms ◽

Differentially Expressed Gene ◽

Mapk Signaling ◽

Gene Profiling ◽

Differentially Expressed ◽

Altered Expression ◽

Hair Follicle Development ◽

Fur Quality

Fur is an important economic trait in rabbits. The identification of genes that influence fur development and knowledge regarding the actions of these genes provides useful tools for improving fur quality. However, the mechanism of fur development is unclear. To obtain candidate genes related to fur development, the transcriptomes of tissues from backs and bellies of Chinchilla rex rabbits were compared. Of the genes analyzed, 336 showed altered expression in the two groups (285 upregulated and 51 downregulated, P ≤ 0.05, fold-change ≥2 or ≤0.5). Using GO and KEGG to obtain gene classes that were differentially enriched, we found several genes to be involved in many important biological processes. In addition, we identified several signaling pathways involved in fur development, including the Wnt and MAPK signaling pathways, revealing mechanisms of skin and hair follicle development, and epidermal cell and keratinocytes differentiation. The obtained rabbit transcriptome and differentially expressed gene profiling data provided comprehensive gene expression information for SFRP2, FRZB, CACNG1, SLC25A4, and SLC16A3. To validate the RNA-seq data, the expression levels of eight differentially expressed genes involved in fur development were confirmed by qRT-PCR. The results of rabbit transcriptomic profiling provide a basis for understanding the molecular mechanisms of fur development.

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Integrated mRNA-seq and miRNA-seq analysis of goat fibroblasts response to Brucella Melitensis strain M5-90

PeerJ ◽

10.7717/peerj.11679 ◽

2021 ◽

Vol 9 ◽

pp. e11679

Author(s):

Baobao Li ◽

Si Chen ◽

Chengqiang Wang ◽

Qiaoling Chen ◽

Churiga Man ◽

...

Keyword(s):

Signaling Pathway ◽

Molecular Mechanisms ◽

Defense Mechanism ◽

Brucella Melitensis ◽

Pearson Correlation ◽

Killer Cell ◽

Mapk Signaling ◽

Differentially Expressed ◽

Receptor Interaction ◽

Bacterial Disease

Brucellosis is a globally zoonotic bacterial disease of humans and various animals including goats, sheep, and cattle. Brucella melitensis M5-90, a live attenuated vaccine strain, has been widely used to prevent brucellosis in goats and sheep. However, the molecular mechanisms governing protective immunity response in non-professional phagocytes infected with B. melitensis M5-90 have not been fully investigated, especially in goats. In our research, goat fibroblasts were used as in vitro models to determine these mechanisms by transcriptome analysis. After incubating with B. melitensis M5-90 3 h, the infected goat fibroblasts were collected at 0 h, 4 h, 24 h, 48 h and 72 h for RNA-seq. The results indicated that there were totally 11,819 differentially expressed genes (DEGs) and 777 differentially expressed (DE) miRNAs found in experiment groups compared with the control groups (|log2(Foldchange)|≥1, FDR<0.05). GO and KEGG enrichment analyses revealed that down-regulated genes were involved in the riboflavin metabolism and positive regulation of IL-8 secretion pathway. The up-regulated genes were mainly involved in adaptive immunity, including TNF signaling pathway, MAPK signaling pathway and JAK/STAT pathway. Additionally, cytokine-cytokine receptor interaction, natural killer cell mediated cytotoxicity and toll-like receptor signaling pathway, which associated with innate immunity pathways, were also induced. Based on the Pearson correlation coefficients and prediction results of TargetScan and miRanda, the miRNA-mRNA networks of NFKB1, IFNAR2 and IL10RB were constructed and verified in goat fibroblasts by qPCR, which demonstrated that goat fibroblasts displayed immunomodulatory properties. Our findings provide a deeper insight into the host miRNA-driven B. melitensis defense mechanism and reveal the transcriptome changes involved in the innate and adaptive immune response of the goats to B. melitensis infection.

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Rootstock-Mediated Transcriptional Changes Associated with Cold Tolerance in Prunus mume Leaves

Horticulturae ◽

10.3390/horticulturae7120572 ◽

2021 ◽

Vol 7 (12) ◽

pp. 572

Author(s):

Faisal Hayat ◽

Chengdong Ma ◽

Shahid Iqbal ◽

Xiao Huang ◽

Ouma Kenneth Omondi ◽

...

Keyword(s):

Oxidative Damage ◽

Cold Stress ◽

Cold Tolerance ◽

Molecular Mechanisms ◽

Mapk Signaling ◽

Differentially Expressed ◽

Prunus Mume ◽

Japanese Apricot ◽

Cold Tolerant ◽

Cold Sensitive

Japanese apricot (Prunus mume) is remarkably valuable for its high ornamental and economic importance due to its distinctive features. Low temperature is a serious environmental constraint for this species, restricting its cultivation and dispersal in the north of China. To address this issue, breeding requires an understanding of the molecular mechanisms underlying responses to cold stress. We examined the leaf physiological and transcriptome profile by RNA sequencing in ‘Bungo’ scion cultivar grafted onto Prunus mume (cold-sensitive) and Prunus armeniaca (cold-tolerant) rootstocks at 4 °C for 0, 6, and 24 h. Our results revealed that the increased MDA concentration in the leaves of P. mume cultivar (cold-sensitive) suggests that cold stress might cause oxidative damage and increased sensitivity. Moreover, the cold-tolerant cultivar (P. armeniaca) considerably enhances the enzyme activities (i.e., SOD, POD, and CAT), as well as osmo-protectants (soluble sugars and proline) compared with sensitive cultivar, which helps plants to withstand oxidative damage caused by cold stress. Additionally, differentially expressed genes were shown to be enriched in plant hormone signal transduction, ribosome, MAPK signaling, and circadian rhythm pathway. After 24 h of cold stress, genes related to PYL4, histidine kinase 1, SAUR36, bHLH130, bHLH123, TIFY 6B-like, WRKY 40, WRKY 57, and 60S acidic ribosomal protein P1 were differentially expressed, implying that these DEGs involved in multiple pathways are involved in cold tolerance in Japanese apricot. This study improved our current understanding of the mechanism of cold tolerance in Japanese apricot, and the findings could be utilized for other related fruit species.

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Transcriptome analysis reveals defense-related genes and pathways against Xanthomonas campestris pv. vesicatoria in pepper (Capsicum annuum L.)

PLoS ONE ◽

10.1371/journal.pone.0240279 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0240279

Author(s):

Shenghua Gao ◽

Fei Wang ◽

Juntawong Niran ◽

Ning Li ◽

Yanxu Yin ◽

...

Keyword(s):

Transcription Factors ◽

Xanthomonas Campestris ◽

Molecular Mechanisms ◽

Enrichment Analysis ◽

Defense Responses ◽

Mapk Signaling ◽

Functional Enrichment ◽

Differentially Expressed ◽

Mitogen Activated Protein Kinase ◽

Sequencing Platform

Bacterial spot (BS), incited by Xanthomonas campestris pv. vesicatoria (Xcv), is one of the most serious diseases of pepper. For a comparative analysis of defense responses to Xcv infection, we performed a transcriptomic analysis of a susceptible cultivar, ECW, and a resistant cultivar, VI037601, using the HiSeqTM 2500 sequencing platform. Approximately 120.23 G clean bases were generated from 18 libraries. From the libraries generated, a total of 38,269 expressed genes containing 11,714 novel genes and 11,232 differentially expressed genes (DEGs) were identified. Functional enrichment analysis revealed that the most noticeable pathways were plant-pathogen interaction, MAPK signaling pathway—plant, plant hormone signal transduction and secondary metabolisms. 1,599 potentially defense-related genes linked to pattern recognition receptors (PRRs), mitogen-activated protein kinase (MAPK), calcium signaling, and transcription factors may regulate pepper resistance to Xcv. Moreover, after Xcv inoculation, 364 DEGs differentially expressed only in VI037601 and 852 genes in both ECW and VI037601. Many of those genes were classified as NBS-LRR genes, oxidoreductase gene, WRKY and NAC transcription factors, and they were mainly involved in metabolic process, response to stimulus and biological regulation pathways. Quantitative RT-PCR of sixteen selected DEGs further validated the RNA-seq differential gene expression analysis. Our results will provide a valuable resource for understanding the molecular mechanisms of pepper resistance to Xcv infection and improving pepper resistance cultivars against Xcv.

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Comparative Transcriptome Analysis Identifies Candidate Genes Related to Black-Spotted Pattern Formation in Spotted Scat (Scatophagus argus)

Animals ◽

10.3390/ani11030765 ◽

2021 ◽

Vol 11 (3) ◽

pp. 765

Author(s):

Xiaozhan Lin ◽

Changxu Tian ◽

Yang Huang ◽

Hongjuan Shi ◽

Guangli Li

Keyword(s):

Signaling Pathway ◽

Fish Species ◽

Molecular Mechanisms ◽

Skin Pigmentation ◽

Wnt Signaling Pathway ◽

Mapk Signaling ◽

Differentially Expressed ◽

Marine Aquaculture ◽

Pigment Synthesis ◽

Scatophagus Argus

Spotted scat (Scatophagus argus) is an economically important marine aquaculture and ornamental fish species in Asia, especially in southeast China. In this study, skin transcriptomes of S. argus were obtained for three types of skin, including black-spotted skin (A), non-spotted skin (B) and caudal fin (C). A total of nine complementary DNA (cDNA) libraries were obtained by Illumina sequencing. Bioinformatics analysis revealed that 1358, 2086 and 487 genes were differentially expressed between A and B, A and C, and B and C, respectively. The results revealed that there were 134 common significantly differentially expressed genes (DEGs) and several key genes related to pigment synthesis and pigmentation, including tyrp1, mitf, pmel, slc7a2, tjp1, hsp70 and mart-1. Of these, some DEGs were associated with pigmentation-related Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, such as tyrosine metabolism, melanogenesis, the Wnt signaling pathway and the mitogen-activated protein kinase (MAPK) signaling pathway. The results will facilitate understanding the molecular mechanisms of skin pigmentation differentiation in S. argus and provide valuable information for skin coloration, especially the formation of spotted patterns on other marine fish species.

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The Anti-Atherogenic Properties of Sesamin are Mediated via Improved Macrophage Cholesterol Efflux Through PPARγ1-LXRα and MAPK Signaling

International Journal for Vitamin and Nutrition Research ◽

10.1024/0300-9831/a000195 ◽

2014 ◽

Vol 84 (1-2) ◽

pp. 79-91 ◽

Cited By ~ 7

Author(s):

Amin F. Majdalawieh ◽

Hyo-Sung Ro

Keyword(s):

Cholesterol Efflux ◽

Transcriptional Activity ◽

Molecular Mechanisms ◽

Foam Cell ◽

Mapk Signaling ◽

Luciferase Reporter ◽

Foam Cell Formation ◽

Dependent Manner ◽

Concentration Dependent Manner ◽

Macrophage Cholesterol Efflux

Background: Foam cell formation resulting from disrupted macrophage cholesterol efflux, which is triggered by PPARγ1 and LXRα, is a hallmark of atherosclerosis. Sesamin and sesame oil exert anti-atherogenic effects in vivo. However, the exact molecular mechanisms underlying such effects are not fully understood. Aim: This study examines the potential effects of sesamin (0, 25, 50, 75, 100 μM) on PPARγ1 and LXRα expression and transcriptional activity as well as macrophage cholesterol efflux. Methods: PPARγ1 and LXRα expression and transcriptional activity are assessed by luciferase reporter assays. Macrophage cholesterol efflux is evaluated by ApoAI-specific cholesterol efflux assays. Results: The 50 μM, 75 μM, and 100 μM concentrations of sesamin up-regulated the expression of PPARγ1 (p< 0.001, p < 0.001, p < 0.001, respectively) and LXRα (p = 0.002, p < 0.001, p < 0.001, respectively) in a concentration-dependent manner. Moreover, 75 μM and 100 μM concentrations of sesamin led to 5.2-fold (p < 0.001) and 6.0-fold (p<0.001) increases in PPAR transcriptional activity and 3.9-fold (p< 0.001) and 4.2-fold (p < 0.001) increases in LXR transcriptional activity, respectively, in a concentration- and time-dependent manner via MAPK signaling. Consistently, 50 μM, 75 μM, and 100 μM concentrations of sesamin improved macrophage cholesterol efflux by 2.7-fold (p < 0.001), 4.2-fold (p < 0.001), and 4.2-fold (p < 0.001), respectively, via MAPK signaling. Conclusion: Our findings shed light on the molecular mechanism(s) underlying sesamins anti-atherogenic effects, which seem to be due, at least in part, to its ability to up-regulate PPARγ1 and LXRα expression and transcriptional activity, improving macrophage cholesterol efflux. We anticipate that sesamin may be used as a therapeutic agent for treating atherosclerosis.

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