scholarly journals Comparative Transcriptomic and Expression Profiles Between the Foot Muscle and Mantle Tissues in the Giant Triton Snail Charonia tritonis

2021 ◽  
Vol 12 ◽  
Author(s):  
Gege Zhang ◽  
Meng Xu ◽  
Chenglong Zhang ◽  
Huixia Jia ◽  
Hua Zhang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Dermatan Sulfate ◽  
Expression Profiles ◽  
Sulfur Metabolism ◽  
Illumina Hiseq ◽  
Sequencing Platform ◽  
Illumina Hiseq Sequencing ◽  
Coral Reef Ecosystems ◽  
Significant Divergence ◽  
Cellular Components

The giant triton snail (Charonia tritonis), an endangered gastropod species of ecological and economic importance, is widely distributed in coral reef ecosystems of the Indo-West Pacific region and the tropical waters of the South China Sea. Limited research on molecular mechanisms can be conducted because the complete genomic information on this species is unavailable. Hence, we performed transcriptome sequencing of the C. tritonis foot muscle and mantle using the Illumina HiSeq sequencing platform. In 109,722 unigenes, we detected 7,994 (3,196 up-regulated and 4,798 down-regulated) differentially expressed genes (DEGs) from the C. tritonis foot muscle and mantle transcriptomes. These DEGs will provide valuable resources to improve the understanding of molecular mechanisms involved in biomineralization of C. tritonis. In the Gene Ontology (GO) database, DEGs were clustered into three main categories (biological processes, molecular functions, and cellular components) and were involved in 50 functional subcategories. The top 20 GO terms in the molecular function category included sulfotransferase activity, transferring sulfur-containing groups, and calcium ion binding, which are terms considered to be related to biomineralization. In KEGG classifications, transcriptomic DEGs were mainly enriched in glycosaminoglycan biosynthesis-chondroitin sulfate/dermatan sulfate, and sulfur metabolism pathway, which may be related to biomineralization. The results of qPCR showed that three of the eight genes examined were significantly up-regulated in the mantle. The phylogenetic tree of BMP1 suggested a significant divergence between homologous genes in C. tritonis. Our results improve the understanding of biomineralization in C. tritonis and provide fundamental transcriptome information to study other molecular mechanisms such as reproduction.

Virus-Dependent and -Independent Responses of Sitobion avenae (Homoptera: Aphididae) Feeding on Wheat Infected by Transmitted and Nontransmitted Viruses at Transcriptomic Level

2019 ◽  
Vol 112 (5) ◽  
pp. 2067-2076
Author(s):  
Dandan Li ◽  
Dan Su ◽  
Zeqian Tong ◽  
Chi Zhang ◽  
Gaisheng Zhang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Barley Yellow Dwarf Virus ◽  
Plant Viruses ◽  
Sitobion Avenae ◽  
Differentially Expressed ◽  
Dwarf Virus ◽  
Illumina Hiseq ◽  
Sequencing Platform ◽  
Yellow Dwarf Virus ◽  
Transcriptomic Level

Abstract Most plant viruses maintain complex interactions with their vector or nonvector insects and can indirectly (via host plants) or directly affect the fitness of insects. However, little is known about the genes involved in the interactions between insects and transmitted or nontransmitted viruses, particularly nontransmitted viruses. Sitobion avenae (Fabricius) is a vector of barley yellow dwarf virus GAV strains (BYDV-GAV), but not a vector of wheat dwarf virus (WDV), which is transmitted by the leafhopper [Psammotettix alienus (Dahlbom)]. In this study, S. avenae was utilized to determine the transcriptomic responses after feeding on wheat infected by each of the two viruses, respectively, using an Illumina Hiseq sequencing platform. The transcriptomic data presented 61,508 genes, of which 854 differentially expressed. Moreover, in addition to sharing 208 genes, the number of differentially expressed genes (DEGs) in S. avenae exposed to BYDV was higher (800) than that when exposed to WDV (262). The DEGs related to the immune system and fitness of S. avenae in response to BYDV-/WDV-infected plants were identified and analyzed using Gene Ontologies (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG), and the number of related DEGs was lower as nonvector than as vector. This study provides the baseline information to further examine molecular mechanisms of how wheat viruses affect S. avenae fitness and immune response either as a vector for BYDV-GAV or as a nonvector for WDV.

scholarly journals Integrated analysis of sex-biased mRNA and miRNA expression profiles in the gonad of the discus fish (Symphysodon aequifasciatus)

2018 ◽  
Author(s):  
yuanshuai Fu ◽  
Zhe Xu ◽  
Zaizhong Chen ◽  
Bin Wen ◽  
Jianzhong Gao
Keyword(s):  
Molecular Mechanisms ◽  
Target Genes ◽  
High Efficiency ◽  
Expression Profiles ◽  
Gonad Development ◽  
Differentially Expressed ◽  
Cdna Libraries ◽  
Integrated Analysis ◽  
Illumina Hiseq ◽  
Differentially Expressed Mirnas

The discus fish (Symphysodon aequifasciatus) is an ornamental fish that is well-known around the world. Phenotype investigation indicated that there are no significant differences in appearance between males and females of the discus fish. To better understand the sexual development mechanisms and obtain a high efficiency sex identification method in the artificial reproduction process of the discus fish, we constructed six cDNA libraries from three adult testes and three adult ovaries, and perform RNA-sequencing for identifying sex-biased candidate genes, microRNA (miRNA), and metabolic pathway using the Illumina Hiseq 4000. A total of 50,082 non-redundant genes (unigenes) were identified, of which 18,570 unigenes were significantly overexpressed in testes, and 11,182 unigenes were significantly overexpressed in ovaries, and 8 differentially expressed unigenes were validated by quantitative Real-Time PCR (qPCR). A total of 551 miRNAs were identified, of which 47 miRNAs were differentially expressed between testes and ovaries, and 7 differentially expressed miRNAs and one non-differential miRNA were validated by qPCR. Twenty-four of these differentially expressed miRNAs and their 15 predicted target genes constituted 41 important miRNA-mRNA interaction pairs, which may be important candidates for sex-related miRNAs and sex-related genes in the discus fish. Some of vital sex-related metabolic pathways were also identified that may play key roles in regulating gonad development of the discus fish. These results can provide important insights to better understand molecular mechanisms for sexual dimorphism in gonads development.

scholarly journals RNA Sequencing Analysis to Capture the Transcriptome Landscape during Tenderization in Sea Cucumber Apostichopus japonicus

Molecules ◽  
2019 ◽  
Vol 24 (5) ◽  
pp. 998 ◽  
Author(s):  
Xiufang Dong ◽  
Hang Qi ◽  
Baoyu He ◽  
Di Jiang ◽  
Beiwei Zhu
Keyword(s):  
Gene Expression ◽  
Rna Sequencing ◽  
Sea Cucumber ◽  
Molecular Mechanisms ◽  
Apostichopus Japonicus ◽  
Expression Profiles ◽  
Textural Properties ◽  
Sequencing Analysis ◽  
Type Iv Collagenase ◽  
Illumina Hiseq

Sea cucumber (Apostichopus japonicus) is an economically significant species in China having great commercial value. It is challenging to maintain the textural properties during thermal processing due to the distinctive physiochemical structure of the A. japonicus body wall (AJBW). In this study, the gene expression profiles associated with tenderization in AJBW were determined at 0 h (CON), 1 h (T_1h), and 3 h (T_3h) after treatment at 37 °C using Illumina HiSeq™ 4000 platform. Seven-hundred-and-twenty-one and 806 differentially expressed genes (DEGs) were identified in comparisons of T_1h vs. CON and T_3h vs. CON, respectively. Among these DEGs, we found that two endogenous proteases—72 kDa type IV collagenase and matrix metalloproteinase 16 precursor—were significantly upregulated that could directly affect the tenderness of AJBW. In addition, 92 genes controlled four types of physiological and biochemical processes such as oxidative stress response (3), immune system process (55), apoptosis (4), and reorganization of the cytoskeleton and extracellular matrix (30). Further, the RT-qPCR results confirmed the accuracy of RNA-sequencing analysis. Our results showed the dynamic changes in global gene expression during tenderization and provided a series of candidate genes that contributed to tenderization in AJBW. This can help further studies on the genetics/molecular mechanisms associated with tenderization.

scholarly journals Transcriptome Analysis of Salt Stress Response in Roots of Halophyte Zoysia macrostachya

2021 ◽  
Vol 25 (03) ◽  
pp. 591-600
Author(s):  
Huaguang Hu
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Transcript Abundance ◽  
Nacl Stress ◽  
Ros Scavenging ◽  
Salt Stress Response ◽  
Sequencing Platform

Zoysia macrostachya Franch. et Sav. is a halophyte with very strong tolerance to salinity, which can serve as an alternative turfgrass for landscaping in saline-alkali land and provide the salt-tolerance genes for turfgrass breeding. To further illustrate the salt-tolerance mechanisms in this species at molecular level, the roots transcriptome of Z. macrostachya was investigated under salt stress using the Illumina sequencing platform. Altogether 47,325 unigenes were assembled, among which, 32,542 (68.76%) were annotated, and 87.61% clean reads were mapped to the unigenes. Specifically, 14,558 unigenes were shown to be the differentially expressed genes (DEGs) following exposure to 710 mM NaCl stress compared with control, including 7972 up-regulated and 6586 down-regulated DEGs. Among these DEGs, 24 were associated with the reactive oxygen species (ROS) scavenging system, 61 were found to be related to K+ and Na+ transportation, and 16 were related to the metabolism of osmotic adjustment substances. Additionally, 2327 DEGs that encoded the transcription factors (TFs) were also identified. The expression profiles for 10 DEGs examined through quantitative real-time PCR conformed to the individual alterations of transcript abundance verified through RNA-Seq. Taken together, results of transcriptome analysis in this study provided useful insights for salt-tolerance molecular mechanisms of Z. macrostachya. Furthermore, these DEGs under salt stress provided important clues for future salt-tolerance genes cloning of Z. macrostachya. © 2021 Friends Science Publishers

Nutritional status affects the microRNA profile of the hypothalamus of female sheep

2018 ◽  
Vol 30 (7) ◽  
pp. 946 ◽  
Author(s):  
Heng Yang ◽  
Shan Lin ◽  
Xiaoping Lei ◽  
Cong Yuan ◽  
Yaosheng Yu ◽  
...  
Keyword(s):  
Nutritional Status ◽  
Molecular Mechanisms ◽  
Reproductive Activity ◽  
Illumina Hiseq ◽  
Illumina Hiseq Sequencing ◽  
Photoperiodic Regulation ◽  
Micro Rnas ◽  
Microrna Profile ◽  
Polymerase Chain ◽  
The Brain

Recent studies on the seasonal regulation of the oestrous cycle in sheep have focussed mainly on the responses to photoperiod. However, the brain systems that control reproductive activity also respond to nutritional inputs, although the molecular mechanisms involved are not completely understood. One possibility is that small, non-coding RNAs, such as micro-RNAs (miRNAs), have significant influence. In the present study, the amounts and characteristics of miRNAs in hypothalamus from oestrous and anestrous ewes, fed low- or high-nutrient diets, were compared using Illumina HiSeq sequencing technology. In total, 398 miRNAs, including 261 novel miRNAs, were identified in ewes with an enhanced nutritional status (HEN), whereas 384 miRNAs, including 247 novel miRNAs, were identified in the ewes with a lesser nutritional status (HAN). There were eight conserved and 140 novel miRNAs expressed differentially between the two libraries. Based on quantitative real-time polymerase chain reaction, six miRNAs were assessed to verify the accuracy of the library database. Moreover, the correlation between the miRNA target and several upstream and downstream genes in the oestrus-related pathways were also verified in hypothalamus nerve cells. According to the results, nutritional status plays an important role in oestrous regulation in sheep, and the hypothalamic processes and pathways induced by nutritional signals (folic acid and tyrosine) are different from those induced by photoperiodic regulation of oestrus. We have expanded the repertoire of sheep miRNAs that could contribute to the molecular mechanisms that regulate the initiation of oestrous cycles in anestrous ewes in response to the influence of nutritional status.

scholarly journals Differential Gene Expression during Larval Metamorphic Development in the Pearl Oyster, Pinctada fucata, Based on Transcriptome Analysis

2016 ◽  
Vol 2016 ◽  
pp. 1-15 ◽  
Author(s):  
Haimei Li ◽  
Bo Zhang ◽  
Guiju Huang ◽  
Baosuo Liu ◽  
Sigang Fan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Principal Component ◽  
Pearl Oyster ◽  
Pinctada Fucata ◽  
Illumina Hiseq ◽  
Larval Stages ◽  
Metamorphic Development ◽  
Differential Gene

P. fucata experiences a series of transformations in appearance, from swimming larvae to sessile juveniles, during which significant changes in gene expression likely occur. Thus, P. fucata could be an ideal model in which to study the molecular mechanisms of larval metamorphosis during development in invertebrates. To study the molecular driving force behind metamorphic development in larvae of P. fucata, transcriptomes of five larval stages (trochophore, D-shape, umbonal, eyespots, and spats) were sequenced using an Illumina HiSeq™ 2000 system and assembled and characterized with the transcripts of six tissues. As a result, a total of 174,126 unique transcripts were assembled and 60,999 were annotated. The number of unigenes varied among the five larval stages. Expression profiles were distinctly different between trochophore, D-shape, umbonal, eyespots, and spats larvae. As a result, 29 expression trends were sorted, of which eight were significant. Among others, 80 development-related, differentially expressed unigenes (DEGs) were identified, of which the majority were homeobox-containing genes. Most DEGs occurred among trochophore, D-shaped, and UES (umbonal, eyespots, and spats) larvae as verified by qPCR. Principal component analysis (PCA) also revealed significant differences in expression among trochophore, D-shaped, and UES larvae with ten transcripts identified but no matching annotations.

scholarly journals Identification of biomarkers associated with metabolic cardiovascular disease using mRNA-SNP-miRNA regulatory network analysis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhiyuan Fan ◽  
Wenjuan Peng ◽  
Zhiwen Wang ◽  
Ling Zhang ◽  
Kuo Liu
Keyword(s):  
Cardiovascular Disease ◽  
Molecular Mechanisms ◽  
Early Stage ◽  
Expression Profiles ◽  
Interaction Network ◽  
Cell Receptor ◽  
Differentially Expressed ◽  
Eqtl Analysis ◽  
Nucleotide Polymorphisms ◽  
Illumina Hiseq

Abstract Background CVD is the leading cause of death in T2DM patients. However, few biomarkers have been identified to detect and diagnose CVD in the early stage of T2DM. The aim of our study was to identify the important mRNAs, micro (mi)RNAs and SNPs (single nucleotide polymorphisms) that are associated with metabolic cardiovascular disease. Materials and methods Expression profiles and GWAS data were obtained from Gene Expression Omnibus (GEO) database. MiRNA-sequencing was conducted by Illumina HiSeq 2000 platform in T2DM patients and T2DM with CVD patients. EQTL analysis and gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted. MRNA-miRNA co-expression network and mRNA-SNP-miRNA interaction network were established and visualized by Cytoscape 3.7.2. Results In our study, we identified 56 genes and 16 miRNAs that were significantly differentially expressed. KEGG analyses results indicated that B cell receptor signaling pathway and hematopoietic cell lineage were included in the biological functions of differentially expressed genes. MRNA-miRNA co-expression network and mRNA-SNP-miRNA interaction network illustrated that let-7i-5p, RASGRP3, KRT1 and CEP41 may be potential biomarkers for the early detection and diagnosis of CVD in T2DM patients. Conclusion Our results suggested that downregulated let-7i-5p, and upregulated RASGRP3, KRT1 and CEP41 may play crucial roles in molecular mechanisms underlying the initiation and development of CVD in T2DM patients.

scholarly journals Genome-Wide Identification of microRNAs in Response to Salt/Alkali Stress in Medicago truncatula through High-Throughput Sequencing

2018 ◽  
Vol 19 (12) ◽  
pp. 4076 ◽  
Author(s):  
Chunyu Cao ◽  
Ruicai Long ◽  
Tiejun Zhang ◽  
Junmei Kang ◽  
Zhen Wang ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Expression Patterns ◽  
Plant Stress ◽  
Alkaline Stress ◽  
Alkaline Soils ◽  
Illumina Hiseq ◽  
Sequencing Platform

Saline-alkaline stress is a universal abiotic stress that adversely affects plant growth and productivity. Saline-alkaline conditions results in plant abnormal transcriptome expression finally manifesting as defective phenotypes. Considerable research has revealed the active role of microRNA in various stress conditions. This study was aimed to identify novel miRNAs and the miRNA expression patterns in the leguminous model plant R108 (Medicago truncatula). The miRNA contained in the total RNA extracted from Medicago truncatula seedlings (72 h) that had been treated with solutions mimicking saline and alkaline soils was subjected to miRNA deep sequencing. The Illumina HiSeq sequencing platform was used to analyze nine small RNA libraries of three treatment groups: distilled water, 20 mM NaCl + Na2SO4 and 5 mM Na2CO3 + NaHCO3. Sequencing revealed that 876 miRNAs including 664 known miRNAs and 212 potential novel miRNAs were present in all the libraries. The miR159 family, miR156 family, miR2086-3p, miR396, miR166, miR319, miR167, miR5213-5p, miR1510 and miR2643 were among the most expressed miRNAs in all libraries. The results of miRNAs expression under treatments were validated by reverse-transcription quantitative PCR (RT-qPCR). Target gene prediction through computational analysis and pathway annotation analysis revealed that the primary pathways affected by stress were related to plant development, including metabolic processes, single-organism processes and response to the stimulus. Our results provide valuable information towards elucidating the molecular mechanisms of salt/alkali tolerance in Medicago truncatula and provide insight into the putative role of miRNAs in plant stress resistance.

Identification of biomarkers associated with metabolic cardiovascular disease using mRNA-SNP-miRNA regulatory network analysis

2021 ◽  
Author(s):  
Zhiyuan Fan ◽  
Wenjuan Peng ◽  
Zhiwen Wang ◽  
ling Zhang ◽  
Kuo Liu
Keyword(s):  
Cardiovascular Disease ◽  
Molecular Mechanisms ◽  
Early Stage ◽  
Expression Profiles ◽  
Interaction Network ◽  
Cell Receptor ◽  
Differentially Expressed ◽  
Eqtl Analysis ◽  
Nucleotide Polymorphisms ◽  
Illumina Hiseq

Abstract Background: CVD is the leading cause of death in T2DM patients. However, few biomarkers have been identified to detect and diagnose CVD in the early stage of T2DM. The aim of our study was to identify the important mRNAs, micro (mi)RNAs and SNPs (single nucleotide polymorphisms) that are associated with metabolic cardiovascular disease. Materials and methods: Expression profiles and GWAS data were obtained from Gene Expression Omnibus (GEO) database. MiRNA-sequencing was conducted by Illumina HiSeq 2000 platform in T2DM patients and T2DM with CVD patients. EQTL analysis and gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted. MRNA-miRNA co-expression network and mRNA-SNP-miRNA interaction network were established and visualized by Cytoscape 3.7.2.Results: In our study, we identified 56 genes and 16 miRNAs that were significantly differentially expressed. GO and KEGG analyses results indicated that B cell receptor signaling pathway and hematopoietic cell lineage were included in the biological functions of differentially expressed genes. MRNA-miRNA co-expression network and mRNA-SNP-miRNA interaction network illustrated that let-7i-5p, RASGRP3, KRT1 and CEP41 may be potential biomarkers for the early detection and diagnosis of CVD in T2DM patients.Conclusion: Our results suggested that downregulated let-7i-5p, and upregulated RASGRP3, KRT1 and CEP41 may play crucial roles in molecular mechanisms underlying the initiation and development of CVD in T2DM patients.

scholarly journals Exploring the genes involved in biosynthesis of dihydroquercetin and dihydromyricetin in Ampelopsis grossedentata

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zheng-Wen Yu ◽  
Ni Zhang ◽  
Chun-Yan Jiang ◽  
Shao-Xiong Wu ◽  
Xia-Yu Feng ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Differentially Expressed Gene ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Genetic Studies ◽  
Sequencing Platform ◽  
Protein Databases ◽  
Helix Loop Helix ◽  
Wd40 Domain ◽  
Ampelopsis Grossedentata

AbstractDihydroquercetin (DHQ), an extremely low content compound (less than 3%) in plants, is an important component of dietary supplements and used as functional food for its antioxidant activity. Moreover, as downstream metabolites of DHQ, an extremely high content of dihydromyricetin (DHM) is up to 38.5% in Ampelopsis grossedentata. However, the mechanisms involved in the biosynthesis and regulation from DHQ to DHM in A. grossedentata remain unclear. In this study, a comparative transcriptome analysis of A. grossedentata containing extreme amounts of DHM was performed on the Illumina HiSeq 2000 sequencing platform. A total of 167,415,597 high-quality clean reads were obtained and assembled into 100,584 unigenes having an N50 value of 1489. Among these contigs, 57,016 (56.68%) were successfully annotated in seven public protein databases. From the differentially expressed gene (DEG) analysis, 926 DEGs were identified between the B group (low DHM: 210.31 mg/g) and D group (high DHM: 359.12 mg/g) libraries, including 446 up-regulated genes and 480 down-regulated genes (B vs. D). Flavonoids (DHQ, DHM)-related DEGs of ten structural enzyme genes, three myeloblastosis transcription factors (MYB TFs), one basic helix–loop–helix (bHLH) TF, and one WD40 domain-containing protein were obtained. The enzyme genes comprised three PALs, two CLs, two CHSs, one F3’H, one F3’5’H (directly converts DHQ to DHM), and one ANS. The expression profiles of randomly selected genes were consistent with the RNA-seq results. Our findings thus provide comprehensive gene expression resources for revealing the molecular mechanism from DHQ to DHM in A. grossedentata. Importantly, this work will spur further genetic studies about A. grossedentata and may eventually lead to genetic improvements of the DHQ content in this plant.

Sign in / Sign up

Export Citation Format

Share Document