scholarly journals Transcriptome Analysis Reveals Dynamic Fat Accumulation in the Walnut Kernel

2018 ◽  
Vol 2018 ◽  
pp. 1-13 ◽  
Author(s):  
Shuang Zhao ◽  
Xuemei Zhang ◽  
Yanping Su ◽  
Yilan Chen ◽  
Yang Liu ◽  
...  
Keyword(s):  
High Throughput ◽  
Developmental Stages ◽  
Juglans Regia ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Functional Categories ◽  
Sequencing Technology ◽  
Gene Enrichment ◽  
Three Stages ◽  
Fat Synthesis

Walnut (Juglans regia L.) is an important woody oilseed species cultivated throughout the world. In this study, comparative transcript profiling was performed using high-throughput RNA sequencing technology at the following three stages of walnut fat synthesis in the “Lvling” walnut cultivar: the initial developmental stage (L1), the fast developing stage (L2), and the last developing stage (L3). A total of 68.18 GB of data were obtained on the three developmental stages, and 92% to 94% of clean data were able to be located to the reference genome. Further comparisons of the transcripts in the three libraries revealed that 724, 2027, and 4817 genes were differentially expressed between the L2 and L1 (L2vsL1), L3 and L2 (L3vsL2), and L3 and L1 (L3vsL1) samples, respectively. Through the GO gene enrichment analysis, differentially expressed genes (DEGs) in L2vsL1, L3vsL2, and L3vsL1 were enriched into 3, 0, and 2 functional categories, respectively. According to the KEGG enrichment analysis, DEGs in L2vsL1, L3vsL2, and L3vsL1 were annotated into 77, 110, and 3717 taxonomic metabolic pathways in the KEGG database, respectively. Next, we analyzed expression levels of genes related to fat synthesis. Our results indicated that ACCase, LACS, and FAD7 were the key genes related to fat synthesis. The high-throughput transcriptome sequencing of walnut in different developmental stages has greatly enriched the current genomic available resources. The comparison of DEGs under different developmental stages identified a wealth of candidate genes involved in fat synthesis, which will facilitate further genetic improvement and molecular studies of the walnut.

Transcriptional identification of differentially expressed genes during the prepupal–pupal transition in the oriental armyworm, Mythimna separata (Walker) (Lepidoptera: Noctuidae)

2021 ◽  
pp. 1-14
Author(s):  
Peirong Li ◽  
Xinru Li ◽  
Wei Wang ◽  
Xiaoling Tan ◽  
Xiaoqi Wang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Metabolic Pathways ◽  
Developmental Stages ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Mythimna Separata ◽  
Kegg Pathway Analysis ◽  
Oriental Armyworm ◽  
Lepidoptera Noctuidae

Abstract The oriental armyworm, Mythimna separata (Walker) is a serious pest of agriculture that does particular damage to Gramineae crops in Asia, Europe, and Oceania. Metamorphosis is a key developmental stage in insects, although the genes underlying the metamorphic transition in M. separata remain largely unknown. Here, we sequenced the transcriptomes of five stages; mature larvae (ML), wandering (W), and pupation (1, 5, and 10 days after pupation, designated P1, P5, and P10) to identify transition-associated genes. Four libraries were generated, with 22,884, 23,534, 26,643, and 33,238 differentially expressed genes (DEGs) for the ML-vs-W, W-vs-P1, P1-vs-P5, and P5-vs-P10, respectively. Gene ontology enrichment analysis of DEGs showed that genes regulating the biosynthesis of the membrane and integral components of the membrane, which includes the cuticular protein (CP), 20-hydroxyecdysone (20E), and juvenile hormone (JH) biosynthesis, were enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that DEGs were enriched in the metabolic pathways. Of these DEGs, thirty CP, seventeen 20E, and seven JH genes were differentially expressed across the developmental stages. For transcriptome validation, ten CP, 20E, and JH-related genes were selected and verified by real-time PCR quantitative. Collectively, our results provided a basis for further studies of the molecular mechanism of metamorphosis in M. separata.

scholarly journals Transcriptome and Gene Expression Analysis of Cylas formicarius (Coleoptera: Brentidae) During Different Development Stages

2016 ◽  
Vol 16 (1) ◽  
Author(s):  
Juan Ma ◽  
Rongyan Wang ◽  
Xiuhua Li ◽  
Bo Gao ◽  
Shulong Chen
Keyword(s):  
Sweet Potato ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
De Novo ◽  
Average Length ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Cylas Formicarius ◽  
Important Pest

Abstract The sweet potato weevil, Cylas formicarius (F.) (Coleoptera: Brentidae), is an important pest of sweet potato worldwide. However, there is limited knowledge on the molecular mechanisms underlying growth and differentiation of C. formicarius. The transcriptomes of the eggs, second instar larvae, third instar larvae (L3), pupae, females, and males of C. formicarius were sequenced using Illumina sequencing technology for obtaining global insights into developing transcriptome characteristics and elucidating the relative functional genes. A total of 54,255,544 high-quality reads were produced, trimmed, and de novo assembled into 115,281 contigs. 61,686 unigenes were obtained, with an average length of 1,009 nt. Among these unigenes, 17,348 were annotated into 59 Gene Ontology (GO) terms and 12,660 were assigned to 25 Cluster of Orthologous Groups classes, whereas 24,796 unigenes were mapped to 258 pathways. Differentially expressed unigenes between various developmental stages of C. formicarius were detected. Higher numbers of differentially expressed genes (DEGs) were recorded in the eggs versus L3 and eggs versus male samples (2,141 and 2,058 unigenes, respectively) than the others. Genes preferentially expressed in each stage were also identified. GO and pathway-based enrichment analysis were used to further investigate the functions of the DEGs. In addition, the expression profiles of ten DEGs were validated by quantitative real-time PCR. The transcriptome profiles presented in this study and these DEGs detected by comparative analysis of different developed stages of C. formicarius will facilitate the understanding of the molecular mechanism of various living process and will contribute to further genome-wide research.

scholarly journals Identification of mRNA and Long Non-Coding RNA Expression Profiles in Developing Yorkshire Pig Spleens

2021 ◽  
Author(s):  
Xinjian Li ◽  
Xuelei Han ◽  
Caixia Sun ◽  
Gaiying Li ◽  
Kejun Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Economic Loss ◽  
Differentially Expressed ◽  
Farm Animals ◽  
Lncrna Expression ◽  
Lncrna Transcript

Abstract Background: Epidemic diseases cause great economic loss in pig farms each year, some of which are characterized mainly in spleen. Yorkshire pig is the most popular used first dam in the commercial pork production system. But the mRNA and lncRNA expression networks in developing Yorkshire pig spleens remain obscure. Results: Here, we profiled the systematic characters of mRNA and lncRNA repertoires in three groups of spleens from nine Yorkshire pigs, each three aged at 7 days, 90 days and 180 days. By using a precise mRNA and lncRNA identification pipeline, we identified 19,647 genes and 219 known and 3,219 putative lncRNA transcripts, 1,729 genes and 64 lncRNAs therein were found to express differentially in three groups. Gene expression characteristics of genes and lncRNAs were found to be basically fixed before 90 days after birth. Enrichment analysis of differentially expressed genes and potential target genes of differentially expressed lncRNAs both displayed crucial roles of up-regulation in immune activation and hematopoiesis and down-regulation in cell replication and division in 90 and 180 days compared to 7 days. The unregulated terms and their significance levels in 90 and 180 days both showed an extremely high degree of consistency. ENSSSCT00000001325 was the only lncRNA transcript that existed in three groups. CDK1, PCNA and PLK were detected to be hub genes that varied with age. BNIP3L, IL5, CD38 and TGFβ1 were found to be common top regulators from 7 to 90 and 180 days while ERAP1, NLRC5 and IL2RG were top regulators from 90 to 180 days.Conclusions: This study provided the first mRNA and lncRNA expression profiles in Yorkshire spleens at three developmental stages. We established gene expression modules and networks in the spleen of pigs from immune system initiation to adulthood. Our results are helpful for the study of transcriptome and functional genomics of spleen tissue in farm animals.

scholarly journals Early Response of Radish to Heat Stress by Strand-Specific Transcriptome and miRNA Analysis

2019 ◽  
Vol 20 (13) ◽  
pp. 3321 ◽  
Author(s):  
Zhuang Yang ◽  
Wen Li ◽  
Xiao Su ◽  
Pingfei Ge ◽  
Yan Zhou ◽  
...  
Keyword(s):  
Heat Stress ◽  
Heat Shock ◽  
Rna Sequencing ◽  
Carbon Fixation ◽  
Enrichment Analysis ◽  
Early Response ◽  
Differentially Expressed ◽  
Physiological Parameter ◽  
Small Rna Sequencing ◽  
Sequencing Technology

Radish is a crucial vegetable crop of the Brassicaceae family with many varieties and large cultivated area in China. Radish is a cool season crop, and there are only a few heat tolerant radish varieties in practical production with little information concerning the related genes in response to heat stress. In this work, some physiological parameter changes of young leaves under short-term heat stress were detected. Furthermore, we acquired 1802 differentially expressed mRNAs (including encoding some heat shock proteins, heat shock factor and heat shock-related transcription factors), 169 differentially expressed lncRNAs and three differentially expressed circRNAs (novel_circ_0000265, novel_circ_0000325 and novel_circ_0000315) through strand-specific RNA sequencing technology. We also found 10 differentially expressed miRNAs (ath-miR159b-3p, athmiR159c, ath-miR398a-3p, athmiR398b-3p, ath-miR165a-5p, ath-miR169g-3p, novel_86, novel_107, novel_21 and ath-miR171b-3p) by small RNA sequencing technology. Through function prediction and enrichment analysis, our results suggested that the significantly possible pathways/complexes related to heat stress in radish leaves were circadian rhythm-plant, photosynthesis—antenna proteins, photosynthesis, carbon fixation in photosynthetic organisms, arginine and proline metabolism, oxidative phosphorylation, peroxisome and plant hormone signal transduction. Besides, we identified one lncRNA–miRNA–mRNAs combination responsive to heat stress. These results will be helpful for further illustration of molecular regulation networks of how radish responds to heat stress.

scholarly journals Comparative RNA-Seq Analysis of High- and Low-Oil Yellow Horn During Embryonic Development

2018 ◽  
Vol 19 (10) ◽  
pp. 3071 ◽  
Author(s):  
Li Wang ◽  
Chengjiang Ruan ◽  
Lingyue Liu ◽  
Wei Du ◽  
Aomin Bao
Keyword(s):  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Acyl Carrier Protein ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Oil Accumulation ◽  
Carboxylase Activity

Yellow horn (Xanthoceras sorbifolium Bunge) is an endemic oil-rich shrub that has been widely cultivated in northern China for bioactive oil production. However, little is known regarding the molecular mechanisms that contribute to oil content in yellow horn. Herein, we measured the oil contents of high- and low-oil yellow horn embryo tissues at four developmental stages and investigated the global gene expression profiles through RNA-seq. The results found that at 40, 54, 68, and 81 days after anthesis, a total of 762, 664, 599, and 124 genes, respectively, were significantly differentially expressed between the high- and low-oil lines. Gene ontology (GO) enrichment analysis revealed some critical GO terms related to oil accumulation, including acyl-[acyl-carrier-protein] desaturase activity, pyruvate kinase activity, acetyl-CoA carboxylase activity, and seed oil body biogenesis. The identified differentially expressed genes also included several transcription factors, such as, AP2-EREBP family members, B3 domain proteins and C2C2-Dof proteins. Several genes involved in fatty acid (FA) biosynthesis, glycolysis/gluconeogenesis, and pyruvate metabolism were also up-regulated in the high-oil line at different developmental stages. Our findings indicate that the higher oil accumulation in high-oil yellow horn could be mostly driven by increased FA biosynthesis and carbon supply, i.e. a source effect.

scholarly journals Transcriptional Analysis of the Early Ripening of ‘Kyoho’ Grape in Response to the Treatment of Riboflavin

Genes ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 514 ◽  
Author(s):  
Zhen-Guang Wang ◽  
Li-Li Guo ◽  
Xiao-Ru Ji ◽  
Yi-He Yu ◽  
Guo-Hai Zhang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Grape Berry ◽  
Differentially Expressed ◽  
Transcriptional Analysis ◽  
Regulation Mechanism ◽  
Chlorophyll Metabolism ◽  
Early Ripening

Previous study has demonstrated that the riboflavin treatment promoted the early ripening of the ‘Kyoho’ grape berry. However, the molecular mechanism causing this was unclear. In order to reveal the regulation mechanism of riboflavin treatment on grape berry development and ripening, the different berry developmental stages of the ‘Kyoho’ berry treated with 0.5 mmol/L of riboflavin was sampled for transcriptome profiling. RNA-seq revealed that 1526 and 430 genes were up-regulated and down-regulated, respectively, for the comparisons of the treatment to the control. TCseq analysis showed that the expression patterns of most of the genes were similar between the treatment and the control, except for some genes that were related to the chlorophyll metabolism, photosynthesis–antenna proteins, and photosynthesis, which were revealed by the enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The differentially expressed genes and weighted gene co-expression network analysis (WGCNA) analysis identified some significantly differentially expressed genes and some hub genes, including up-regulation of the photosynthesis-related ELIP1 and growth and development-related GDSL; and down-regulation of the oxidative stress-related ATHSP22 and berry softening-related XTH32 and GH9B15. The results suggested that the riboflavin treatment resulted in the variations of the expression levels of these genes, and then led to the early ripening of the ‘Kyoho’ berry.

scholarly journals Joint analysis of lncRNA m6A methylome and lncRNA/mRNA expression profiles in gastric cancer

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Zhi Lv ◽  
Liping Sun ◽  
Qian Xu ◽  
Chengzhong Xing ◽  
Yuan Yuan
Keyword(s):  
Gastric Cancer ◽  
Mrna Expression ◽  
Expression Analysis ◽  
Target Genes ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Joint Analysis ◽  
Gene Enrichment Analysis ◽  
Gene Enrichment

Abstract Background N6-methyladenosine (m6A) modification might be closely associated with the genesis and development of gastric cancer (GC). Currently, the evidence established by high-throughput assay for GC-related m6A patterns based on long non-coding RNAs (lncRNAs) remains limited. Here, a joint analysis of lncRNA m6A methylome and lncRNA/mRNA expression profiles in GC was performed to explore the regulatory roles of m6A modification in lncRNAs. Methods Three subjects with primary GC were enrolled in our study and paired sample was randomly selected from GC tissue and adjacent normal tissue for each case. Methylated RNA Immunoprecipitation NextGeneration Sequencing (MeRIP-Seq) and Microarray Gene Expression Profiling was subsequently performed. Then co-expression analysis and gene enrichment analysis were successively conducted. Results After data analysis, we identified 191 differentially m6A-methylated lncRNAs, 240 differentially expressed lncRNAs and 229 differentially expressed mRNAs in GC. Furthermore, four differentially m6A-methylated and expressed lncRNAs (dme-lncRNAs) were discovered including RASAL2-AS1, LINC00910, SNHG7 and LINC01105. Their potential target genes were explored by co-expression analysis. And gene enrichment analysis suggested that they might influence the cellular processes and biological behaviors involved in mitosis and cell cycle. The potential impacts of these targets on GC cells were further validated by CCLE database and literature review. Conclusions Four novel dme-lncRNAs were identified in GC, which might exert regulatory roles on GC cell proliferation. The present study would provide clues for the lncRNA m6A methylation-based research on GC epigenetic etiology and pathogenesis.

scholarly journals Bioinformatics Analysis Predicts ceRNA Regulatory Axes Related to Melanoma Pathogenesis

2021 ◽  
Author(s):  
Lina Liu ◽  
Feng Yang ◽  
Saiyun Lei
Keyword(s):  
Cutaneous Melanoma ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Cerna Network ◽  
Gene Enrichment Analysis ◽  
Gene Enrichment ◽  
Incidence And Mortality ◽  
Malignant Skin ◽  
Clinical Verification ◽  
Geo Database

Abstract Background Melanoma is a highly malignant skin tumour, with an incidence and mortality rates accounting for approximately 5% and >75% of all tumours, respectively. In the present study, we aimed to screen mRNAs, microRNAs, and circRNAs related to the pathogenesis of melanoma via bioinformatics methods. Materials and methods The microarray data correlating with melanoma were obtained from the GEO database, and the differentially expressed genes between melanomatissues and non-melanoma tissues were screened using GEO2R. Moreover, the Hub genes were screened using the STRING database, Cytoscape software, and GEPIA database. The DAVID database was used for gene enrichment analysis. Thereafter, the ceRNA network diagram was constructed using the starBase database and was analysed for survival in order to predict the molecular markers for diagnosis and treatment of skin cutaneous melanoma; the most probable ceRNA mechanism was screened via pan-cancer analysis. Furthermore, the ceRNA network was verified using the GEPIA and UALCAN databases. Results In total, 266, 20, and 10 differentially expressed mRNAs, microRNAs, and circRNA10 were screened. Using Cytoscape software, 59 Hub and 31 key genes were screened, followed by construction of the ceRNA and ceRNA-gene enrichment analysis networks. Conclusion Clinical verification revealed that SIPA1L1 could regulate the expression of DSC3 by sponge adsorption of has-miR-106b and has-miR-20b, and thereby affect the pathogenesis and progression of skin cutaneous melanoma.

scholarly journals Differentially Expressed Circular Non-coding RNAs in Atherosclerotic Aortic Vessels and Their Potential Functions in Endothelial Injury

2021 ◽  
Vol 8 ◽  
Author(s):  
Houwei Li ◽  
Xue Liu ◽  
Na Sun ◽  
Tianshuo Wang ◽  
Jia Zhu ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Enrichment Analysis ◽  
Potential Functions ◽  
Endothelial Injury ◽  
Differentially Expressed ◽  
Vascular Endothelial ◽  
Rt Pcr ◽  
Potential Target ◽  
Gene Enrichment Analysis ◽  
Gene Enrichment

Background: Circular non-coding RNA (circRNA) has a variety of biological functions. However, the expression profile and potential effects of circRNA on atherosclerosis (AS) and vascular endothelial injury have not been fully elucidated. This study aims to identify the differentially expressed circRNAs in atherosclerotic aortic vessels and predict their potential functions in endothelial injury.Method: ApoE-/- mice were fed with high-fat diet for 12 weeks to induce AS. Atherosclerotic plaques were evaluated by H&E and Masson staining and immunohistochemistry; differentially expressed circRNAs were detected by Arraystar Circular RNA Microarray and verified by RT-PCR; the potential target mircoRNAs of circRNAs were predicted by miRanda, Tarbase, Targetscan and their expression changes were verified by RT-PCR; the potential target genes of mircoRNAs were predicted by Targetscan and verified by Western blot; the signaling pathways that they might annotate or regulate and their potential functions in vascular endothelial injury were predicted by gene enrichment analysis.Results: Fifty two circRNAs were up-regulated more than twice and 47 circRNAs were down-regulated more than 1.5 times in AS aortic vessels. Mmmu_circRNA_36781 and 37699 were up-regulated both in AS aortic vessels and H2O2-treated mouse aortic endothelial cells (MAECs). The expression of miR-30d-3p and miR-140-3p, the target microRNA of circRNA_37699 and circRNA_36781, were downregulated both in AS vessels and H2O2-treated MAECs. On the contrary, MKK6 and TP53RK, the potential target gene of miR-140-3p and miR-30d-3p, were upregulated both in AS aortic roots and H2O2-treated MAECs. Besides, gene enrichment analysis showed that MAPK and PI3K-AKT signaling pathway were the most potential signaling pathways regulated by the differentially expressed circRNAs in atherosclerosis.Conclusions: Mmu_circRNA_36781 (circRNA ABCA1) and 37699 (circRNA KHDRBS1) were significantly up-regulated in AS aortic vessels and H2O2-treated MAECs. They have potential regulatory effects on atherosclerosis and vascular endothelial injury by targeting miR-30d-3p-TP53RK and miR-140-3p-MKK6 axis and their downstream signaling pathways.

scholarly journals Genome-Wide Identification of CircRNAs of Infective Larvae and Adult Worms of Parasitic Nematode, Haemonchus contortus

2021 ◽  
Vol 11 ◽  
Author(s):  
Caixian Zhou ◽  
Yao Zhang ◽  
Simin Wu ◽  
Zhiheng Wang ◽  
Waresi Tuersong ◽  
...  
Keyword(s):  
Haemonchus Contortus ◽  
Parasitic Nematode ◽  
Developmental Stages ◽  
Enrichment Analysis ◽  
Mapk Signaling ◽  
Differentially Expressed ◽  
Parasitic Nematodes ◽  
Transcriptional Level ◽  
Blood Sucking ◽  
Third Stage

CircRNAs, a novel class of ncRNA family, are endogenous transcriptional products involved in various biological and physiological processes in plants and animals. However, almost no information is available for circRNAs of parasitic helminths. In the present study, the circRNAs repertoire was comprehensively explored in Haemonchus contortus, a blood-sucking parasitic nematode of ruminants. In total, 20073 circRNAs were identified and annotated from three key developmental stages/genders of H. contortus including the free-living infective third-stage larvae (L3, 18883), parasitic adult female (Af, 3491), and male worms (Am, 2550) via deep-sequencing technology and bioinformatic analysis. Among these identified circRNAs, 71% were derived from exonic regions of protein-coding genes. The number of circRNAs transcribed from the X chromosome (4704) was higher than that from Chromosome I-V (3143, 3273, 3041, 3030, 2882). The amount of highly expressed circRNAs in third-stage larvae was significantly more abundant than that in adult stage. 15948 and 16847 circRNAs were differentially expressed between Af and L3s and between Am and L3, respectively. Among them, 13409 circRNAs existed in both comparisons. Furthermore, 1119 circRNAs were differentially expressed between Af_and_Am. GO enrichment analysis indicated that source genes of circRNAs differentially expressed between Am and L3 as well as between Af and L3 were significantly enriched in many biological processes, primarily including signaling, signal transduction and cell communication terms. KEGG analysis revealed that parental genes of differentially expressed circRNAs were mainly related to metabolism (pyruvate metabolism, glycerophospholipid metabolism, and carbon metabolism), MAPK signaling pathway, and phosphatidylinositol signaling system. Moreover, many circRNAs contained one or more miRNA potential binding sites, suggesting that they could regulate gene expression at the post-transcriptional level. Furthermore, the correctness of head-to-tail back splicing site and alternative circularization events were verified by Sanger sequencing using both divergent and convergent primers. Finally, the reliability of RNA-Seq data and the resistance of circRNAs to RNase R digestion were confirmed by quantitative RT-PCR. Taken together, our findings provide a foundation for elucidating the regulatory mechanisms of circRNAs in H. contortus, which will advance the understanding of circRNAs in parasitic nematodes.

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