scholarly journals Identification of Callose Synthases in Stinging Nettle and Analysis of Their Expression in Different Tissues

2020 ◽  
Vol 21 (11) ◽  
pp. 3853
Author(s):  
Gea Guerriero ◽  
Emilie Piasecki ◽  
Roberto Berni ◽  
Xuan Xu ◽  
Sylvain Legay ◽  
...  
Keyword(s):  
Developmental Stages ◽  
De Novo ◽  
Higher Plants ◽  
Expression Profiles ◽  
Model Organism ◽  
Differentially Expressed ◽  
Carbohydrate Active Enzymes ◽  
Stinging Nettle ◽  
Genes Encoding ◽  
External Stimuli

Callose is an important biopolymer of β-1,3-linked glucose units involved in different phases of plant development, reproduction and response to external stimuli. It is synthesized by glycosyltransferases (GTs) known as callose synthases (CalS) belonging to family 48 in the Carbohydrate-Active enZymes (CAZymes) database. These GTs are anchored to the plasma membrane via transmembrane domains. Several genes encoding CalS have been characterized in higher plants with 12 reported in the model organism Arabidopsis thaliana. Recently, the de novo transcriptome of a fibre-producing clone of stinging nettle (Urtica dioica L.) was published and here it is mined for CalS genes with the aim of identifying members differentially expressed in the core and cortical tissues of the stem. The goal is to understand whether specific CalS genes are associated with distinct developmental stages of the stem internodes (elongation, thickening). Nine genes, eight of which encoding full-length CalS, are identified in stinging nettle. The phylogenetic analysis with CalS proteins from other fibre crops, namely textile hemp and flax, reveals grouping into 6 clades. The expression profiles in nettle tissues (roots, leaves, stem internodes sampled at different heights) reveal differences that are most noteworthy in roots vs. leaves. Two CalS are differentially expressed in the internodes sampled at the top and middle of the stem. Implications of their role in nettle stem tissue development are discussed.

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 Transcriptomic analyses reveal molecular mechanisms underlying regulation of floral attributes in Lonicera japonica Thunb.

2021 ◽  
Author(s):  
Lei Shi ◽  
Yuan Shen ◽  
Yuhao Chi
Keyword(s):  
Flower Development ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
De Novo ◽  
Floral Scent ◽  
Expression Profiles ◽  
Lonicera Japonica ◽  
Biosynthesis Pathway ◽  
Terpenoid Biosynthesis ◽  
Genes Encoding

Abstract Background Lonicera Japonica Thunb. is a perennial, semi-evergreen and twining vine in the family of Caprifoliaceae, which is widely cultivated in Asia. Thus far, L. japonica is often used to treat some human diseases including COVID-19, H1N1 influenza and hand-foot-and-mouth diseases, however, the regulatory mechanism of intrinsic physiological processes during different floral developmental stages of L. japonica remain largely unknown. Results The complete transcriptome of L. japonica was de novo-assembled and annotated, generating a total of 195850 unigenes, of which 84657 could be functionally annotated. 70 candidate genes involved in flowering transition were identified and the flowering regulatory network of five pathways was constructed in L. japonica. The mRNA transcripts of AGL24 and SOC1 exhibited a downward trend during flowering transition and followed by a gradual increase during the flower development. The transcripts of AP1 was only detected during the floral development, whereas the transcript level of FLC was high during the vegetative stages. The expression profiles of AGL24, SOC1, AP1 and FLC genes indicate that these key integrators might play the essential and evolutionarily conserved roles in control of flowering switch across the plant kingdom. We also identified 54 L. japonica genes encoding enzymes involved in terpenoid biosynthesis pathway. Most highly expressed genes centered on the MEP pathway, suggesting that this plastid pathway might represent the major pathway for terpenoid biosynthesis in L. japonica. In addition, 33 and 31 key genes encoding enzymes involved in the carotenogenesis and anthocyanin biosynthesis pathway were identified, respectively. PSY transcripts gradually increased during the flower development, supporting its role as the first rate-limiting enzyme in carotenoid skeleton production. The expression level of most anthocyanin biosynthetic genes was dramatically decreased during the flower developmental stages, consistent with the decline in the contents of anthocyanin. Conclusion These results identified a large number of potential key regulators controlling flowering time, flower color and floral scent formation in L. japonica, which improves our understanding of the molecular mechanisms underlying the flower traits and flower metabolism, as well as sets the groundwork for quality improvement and molecular breeding of L. japonica.

scholarly journals Transcriptome analysis reveals the genetic basis underlying the development of skin appendages and immunity in hedgehog (Atelerix albiventris)

2020 ◽  
Author(s):  
Hui-Ming Li ◽  
Bi-Ze Yang ◽  
Xiu-Juan Zhang ◽  
Hai-Ying Jiang ◽  
Lin-Miao Li ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Developmental Stages ◽  
De Novo ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Immune Genes ◽  
Hair Type ◽  
Keratin Filament

AbstractThe expression of hair features is an evolutionary adaptation resulting from interactions between many organisms and their environment. Elucidation of the mechanisms that underlie the expression of such traits is a topic in evolutionary biology research. Therefore, we assessed the de novo transcriptome of Atelerix albiventris at three developmental stages and compared gene expression profiles between abdomen hair and dorsal spine tissues. We identified 328,576 unigenes in our transcriptome, among which 3,598 were differentially expressed between hair- and spine-type tissues. Dorsal and abdomen skin tissues 5 days after birth were compared and the resulting differentially expressed genes were mainly enriched in keratin filament, epithelium cell differentiation, and epidermis development based on GO enrichment analysis, and tight junction, p53, and cell cycle signaling pathways based on KEGG enrichment analysis. Expression variations of MBP8, SFN, Wnt10, KRT1, and KRT2 may be the main factors regulating hair and spine differentiation for the hedgehog. Strikingly, DEGs in hair-type tissues were also significantly enriched in immune-related terms and pathways with hair-type tissues exhibiting more upregulated immune genes than spine-type tissues. Thus, we propose that spine development was an adaptation that provided protection against injuries or stress and reduced hedgehog vulnerability to infection.

scholarly journals Comprehensive analysis of miRNA-mRNA/lncRNA during gonadal development of triploid female rainbow trout (Oncorhynchus mykiss)

2020 ◽  
Author(s):  
Tianqing Huang ◽  
Wei Gu ◽  
Enhui Liu ◽  
Xiulan Shi ◽  
Bingqian Wang ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Noncoding Rnas ◽  
Gonadal Development ◽  
Differentially Expressed ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
Oocyte Meiosis ◽  
Non Coding Rna

Abstract Background: Chromosomal ploidy manipulation is one of the means to create excellent germplasm. Triploid fish could provide an ideal sterile model for the mechanism research of abnormality in meiosis. The complete understanding of the coding and noncoding RNAs regulating sterility caused by meiosis abnormality is still not well understood.Results: By high-throughput sequencing, we compared the expression profiles of gonadal mRNA, long non-coding RNA (lncRNA), and microRNA (miRNA) at different developmental stages [65 days post fertilisation (dpf), 180 dpf, and 600 dpf] between the diploid (XX) and triploid (XXX) female rainbow trout. A majority of differentially expressed (DE) RNAs were identified, and 22 DE mRNAs related to oocyte meiosis and homologous recombination were characterized. The predicted miRNA-mRNA/lncRNA networks of 3 developmental stages were constructed based on the target pairs of DE lncRNA-miRNA and DE mRNA-miRNA. According to the networks, meiosis-related gene of ccne1 was targeted by dre-miR-15a-5p_R+1, and 6 targeted DE lncRNAs were identified. Also, RT-qPCR was performed to validate the credibility of the network.Conclusions: This study explored the potential interplay between coding and noncoding RNAs during the gonadal development of polyploid fish. It provides full insights into polyploidy-associated effects on fertility of fish. These differentially expressed coding and noncoding RNAs provide a novel resource for studying genome diversity of polyploid induction.

scholarly journals Altered miRNA and mRNA Expression in Sika Deer Skeletal Muscle with Age

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 172
Author(s):  
Boyin Jia ◽  
Yuan Liu ◽  
Qining Li ◽  
Jiali Zhang ◽  
Chenxia Ge ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Growth And Development ◽  
Molecular Mechanisms ◽  
Muscle Development ◽  
Sika Deer ◽  
De Novo ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Growth Development ◽  
Development And Aging

Studies of the gene and miRNA expression profiles associated with the postnatal late growth, development, and aging of skeletal muscle are lacking in sika deer. To understand the molecular mechanisms of the growth and development of sika deer skeletal muscle, we used de novo RNA sequencing (RNA-seq) and microRNA sequencing (miRNA-seq) analyses to determine the differentially expressed (DE) unigenes and miRNAs from skeletal muscle tissues at 1, 3, 5, and 10 years in sika deer. A total of 51,716 unigenes, 171 known miRNAs, and 60 novel miRNAs were identified based on four mRNA and small RNA libraries. A total of 2,044 unigenes and 11 miRNAs were differentially expressed between adolescence and juvenile sika deer, 1,946 unigenes and 4 miRNAs were differentially expressed between adult and adolescent sika deer, and 2,209 unigenes and 1 miRNAs were differentially expressed between aged and adult sika deer. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that DE unigenes and miRNA were mainly related to energy and substance metabolism, processes that are closely associate with the growth, development, and aging of skeletal muscle. We also constructed mRNA–mRNA and miRNA–mRNA interaction networks related to the growth, development, and aging of skeletal muscle. The results show that mRNA (Myh1, Myh2, Myh7, ACTN3, etc.) and miRNAs (miR-133a, miR-133c, miR-192, miR-151-3p, etc.) may play important roles in muscle growth and development, and mRNA (WWP1, DEK, UCP3, FUS, etc.) and miRNAs (miR-17-5p, miR-378b, miR-199a-5p, miR-7, etc.) may have key roles in muscle aging. In this study, we determined the dynamic miRNA and unigenes transcriptome in muscle tissue for the first time in sika deer. The age-dependent miRNAs and unigenes identified will offer insights into the molecular mechanism underlying muscle development, growth, and maintenance and will also provide valuable information for sika deer genetic breeding.

scholarly journals Characterization of Embryonic Skin Transcriptome in Anser cygnoides at Three Feather Follicles Developmental Stages

2019 ◽  
Vol 10 (2) ◽  
pp. 443-454
Author(s):  
Chang Liu ◽  
Cornelius Tlotliso Sello ◽  
Yujian Sui ◽  
Jingtao Hu ◽  
Shaokang Chen ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Developmental Stages ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Mitogen Activated Protein Kinase ◽  
Receptor Interaction ◽  
Keratinocyte Proliferation ◽  
Skin Development

In order to enrich the Anser cygnoides genome and identify the gene expression profiles of primary and secondary feather follicles development, de novo transcriptome assembly of skin tissues was established by analyzing three developmental stages at embryonic day 14, 18, and 28 (E14, E18, E28). Sequencing output generated 436,730,608 clean reads from nine libraries and de novo assembled into 56,301 unigenes. There were 2,298, 9,423 and 12,559 unigenes showing differential expression in three stages respectively. Furthermore, differentially expressed genes (DEGs) were functionally classified according to genes ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and series-cluster analysis. Relevant specific GO terms such as epithelium development, regulation of keratinocyte proliferation, morphogenesis of an epithelium were identified. In all, 15,144 DEGs were clustered into eight profiles with distinct expression patterns and 2,424 DEGs were assigned to 198 KEGG pathways. Skin development related pathways (mitogen-activated protein kinase signaling pathway, extra-cellular matrix -receptor interaction, Wingless-type signaling pathway) and genes (delta like canonical Notch ligand 1, fibroblast growth factor 2, Snail family transcriptional repressor 2, bone morphogenetic protein 6, polo like kinase 1) were identified, and eight DEGs were selected to verify the reliability of transcriptome results by real-time quantitative PCR. The findings of this study will provide the key insights into the complicated molecular mechanism and breeding techniques underlying the developmental characteristics of skin and feather follicles in Anser cygnoides.

scholarly journals HIV-1–infected dendritic cells show 2 phases of gene expression changes, with lysosomal enzyme activity decreased during the second phase

Blood ◽  
2009 ◽  
Vol 114 (1) ◽  
pp. 85-94 ◽  
Author(s):  
Andrew N. Harman ◽  
Marianne Kraus ◽  
Chris R. Bye ◽  
Karen Byth ◽  
Stuart G. Turville ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dendritic Cells ◽  
Antigen Processing ◽  
De Novo ◽  
Cathepsin L ◽  
Transcriptional Response ◽  
Differentially Expressed ◽  
Second Phase ◽  
Genes Encoding ◽  
Hiv 1

AbstractDendritic cells (DCs) play a key role in the pathogenesis of HIV infection. HIV interacts with these cells through 2 pathways in 2 temporal phases, initially via endocytosis and then via de novo replication. Here the transcriptional response of human DCs to HIV-1 was studied in these phases and at different stages of the virus replication cycle using purified HIV-1 envelope proteins, and inactivated and viable HIV-1. No differential gene expression was detected in response to envelope. However, more than 100 genes were differentially expressed in response to entry of viable and inactivated HIV-1 in the first phase. A completely different set of genes was differentially expressed in the second phase, predominantly in response to viable HIV-1, including up-regulation of immune regulation genes, whereas genes encoding lysosomal enzymes were down-regulated. Cathepsins B, C, S, and Z RNA and protein decreased, whereas cathepsin L was increased, probably reflecting a concomitant decrease in cystatin C. The net effect was markedly diminished cathepsin activity likely to result in enhanced HIV-1 survival and transfer to contacting T lymphocytes but decreased HIV-1 antigen processing and presentation to these T cells.

scholarly journals De novo characterization of the Lycium ruthenicum transcriptome and analysis of its digital gene expression profiles during fruit development and ripening

2017 ◽  
Vol 69 (1) ◽  
pp. 181-190 ◽  
Author(s):  
Yong Peng ◽  
Huiqin Ma ◽  
Shangwu Chen
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
De Novo ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Digital Gene Expression ◽  
Orthologous Group ◽  
Functional Studies ◽  
Lycium Ruthenicum

Lycium ruthenicum Murr., which belongs to the family Solanaceae, is a resource plant for Chinese traditional medicine and nutraceutical foods. In this study, RNA sequencing was applied to obtain raw reads of L. ruthenicum fruit at different stages of ripening, and a de novo assembly of its sequence was performed. Approximately 52.45 million 100-bp paired-end raw reads were generated from the samples by deep RNA-seq analysis. These short reads were assembled to obtain 164814 contigs, and the contigs were assembled into 84968 non-redundant unigenes using the Trinity method. Assembled sequences were annotated with gene descriptions, gene ontology, clusters of orthologous group and KEGG (Kyoto Encyclopedia of Genes and Genomes)pathway terms. Digital gene expression analysis was applied to compare gene-expression patterns at different fruit developmental stages. These results contribute to existing sequence resources for Lycium spp. during the fruit-ripening stages, which is valuable for further functional studies of genes involved in L. ruthenicum fruit nutraceutical quality.

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 Reduced Expression of Slc Genes in the VTA and NAcc of Male Mice with Positive Fighting Experience

2020 ◽  
Author(s):  
Dmitry A. Smagin ◽  
Vladimir N. Babenko ◽  
Irina L. Kovalenko ◽  
Anna G. Galyamina ◽  
Olga E. Redina ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Differentially Expressed ◽  
Male Mice ◽  
Agonistic Interactions ◽  
Specific Expression ◽  
Chronic Stimulation ◽  
Altered Expression ◽  
Slc Transporters ◽  
Genes Encoding ◽  
Complete Disruption

ABSTRACTThere are many psychiatric medications targeting the activity of SLC transporters. Therefore, further research is needed to elucidate the expression profiles of the Slc* genes, which may serve as markers of altered brain metabolic processes and neurotransmitter activities in psychoneurological disorders. We studied differentially expressed Slc genes using the transcriptomic profiles in the ventral tegmental area (VTA), nucleus accumbens (NAcc), and prefrontal cortex (PFC) of male mice with psychosis-like behavior induced by repeated aggression experience in daily agonistic interactions which are accompanied by wins. Most of differentially expressed Slc genes in the VTA and NAcc (12 of 17 and 25 of 26, respectively) were downregulated, which was not the case in the PFC (6 and 5, up- and down, respectively). Also, the majority of these genes were shown to have brain region-specific expression profiles. In the VTA and NAcc altered expression was observed for the genes encoding the transporters of neurotransmitters as well as inorganic and organic ions, amino acids, metals, glucose, etc. This means alteration in transport functions for many substrates, which results in complete disruption of all cellular and neurotransmitter processes. The neurotransmitter systems, especially, the dopaminergic one, in male mice with positive fighting experience in daily agonistic interactions undergo changes leading to profound genomic modifications which include downregulated expression of the majority of the Slc* genes at least in the VTA and NAcc, which is attributable to chronic stimulation of the reward systems.

Sign in / Sign up

Export Citation Format

Share Document