scholarly journals Transcriptome atlas of Phalaenopsis equestris

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12600
Author(s):  
Anna V. Klepikova ◽  
Artem S. Kasianov ◽  
Margarita A. Ezhova ◽  
Aleksey A. Penin ◽  
Maria D. Logacheva
Keyword(s):  
Gene Expression ◽  
Apical Meristem ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Rna Seq ◽  
Orphan Genes ◽  
Functional Studies ◽  
Reproductive Structures ◽  
Transcriptome Variation

The vast diversity of Orchidaceae together with sophisticated adaptations to pollinators and other unique features make this family an attractive model for evolutionary and functional studies. The sequenced genome of Phalaenopsis equestris facilitates Orchidaceae research. Here, we present an RNA-seq-based transcriptome map of P. equestris that covers 19 organs of the plant, including leaves, roots, floral organs and the shoot apical meristem. We demonstrated the high quality of the data and showed the similarity of the P. equestris transcriptome map with the gene expression atlases of other plants. The transcriptome map can be easily accessed through our database Transcriptome Variation Analysis (TraVA) for visualizing gene expression profiles. As an example of the application, we analyzed the expression of Phalaenopsis “orphan” genes–those that do not have recognizable similarity with the genes of other plants. We found that approximately half of these genes were not expressed; the ones that were expressed were predominantly expressed in reproductive structures.

scholarly journals Transcriptome atlas of Phalaenopsis equestris

2020 ◽  
Author(s):  
Anna V. Klepikova ◽  
Artem S. Kasianov ◽  
Margarita A. Ezhova ◽  
Aleksey A. Penin ◽  
Maria D. Logacheva
Keyword(s):  
Gene Expression ◽  
Apical Meristem ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Rna Seq ◽  
Orphan Genes ◽  
Functional Studies ◽  
Transcriptome Variation ◽  
Predominant Expression

AbstractThe vast diversity of Orchidaceae together with sophisticated adaptations to pollinators and other unique features make this family an attractive model for evolutionary and functional studies. The sequenced genome of Phalaenopsis equestris facilitates Orchidaceae research. Here we present an RNA-seq based transcriptome map of P. equestris which covers 19 organs of the plant including leaves, roots, floral organs and shoot apical meristem. We demonstrated the high quality of the data and showed the similarity of P. equestris transcriptome map with gene expression atlases of other plants. The transcriptome map can be easily accessed through our database Transcriptome Variation Analysis (TraVA) visualizing gene expression profiles. As an example of the application we analyzed the expression of Phalaenopsis “orphan” genes – the ones that do not have recognizable similarity with genes of other plants. We found that about a half of them are not expressed; the ones that are expressed have a predominant expression pattern in reproductive structures.

scholarly journals A tensor decomposition-based integrated analysis applicable to multiple gene expression profiles without sample matching

2021 ◽  
Author(s):  
Taguchi Y-h. ◽  
Turki Turki
Keyword(s):  
Gene Expression ◽  
Learning Strategies ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Tensor Decomposition ◽  
Integrated Analysis ◽  
Rna Seq ◽  
Prior Learning ◽  
Multiple Gene ◽  
Machine Learning Applications

Abstract The integrated analysis of multiple gene expression profiles measured in distinct studies is always problematic. Especially, missing sample matching and missing common labeling between distinct studies prevent the integration of multiple studies in fully data-driven and unsupervised manner. In this study, we propose a strategy enabling the integration of multiple gene expression profiles among multiple independent studies without either labeling or sample matching, using tensor decomposition-based unsupervised feature extraction. As an example, we applied this strategy to Alzheimer’s disease (AD)-related gene expression profiles that lack exact correspondence among samples as well as AD single-cell RNA-seq (scRNA-seq) data. We found that we could select biologically reasonable genes with integrated analysis. Overall, integrated gene expression profiles can function analogously to prior learning and/or transfer learning strategies in other machine learning applications. For scRNA-seq, the proposed approach was able to drastically reduce the required computational memory.

The characteristics of mesenteric adipose tissue attached to different intestinal segments and their roles in immune regulation

2022 ◽  
Author(s):  
Haowei Zhang ◽  
Yujin Ding ◽  
Qin Zeng ◽  
Dandan Wang ◽  
Ganglei Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Adipose Tissue ◽  
Immune Regulation ◽  
Expression Profiles ◽  
Critical Role ◽  
Gene Expression Profiles ◽  
Rna Seq ◽  
Mesenteric Adipose Tissue ◽  
Cell Components ◽  
Subsequent Effect

Background: Mesenteric adipose tissue (MAT) plays a critical role in the intestinal physiological ecosystems. Small and large intestines have evidently intrinsic and distinct characteristics. However, whether there exist any mesenteric differences adjacent to the small and large intestines (SMAT and LMAT) has not been properly characterized. We studied the important facets of these differences, such as morphology, gene expression, cell components and immune regulation of MATs, to characterize the mesenteric differences. Methods: The SMAT and LMAT of mice were utilized for comparison of tissue morphology. Paired mesenteric samples were analyzed by RNA-seq to clarify gene expression profiles. MAT partial excision models were constructed to illustrate the immune regulation roles of MATs, and 16S-seq was applied to detect the subsequent effect on microbiota. Results: Our data show that different segments of mesenteries have different morphological structures. SMAT not only has smaller adipocytes but also contains more fat-associated lymphoid clusters than LMAT. The gene expression profile is also discrepant between these two MATs in mice. B-cell markers were abundantly expressed in SMAT, while development-related genes were highly expressed in LMAT. Adipose-derived stem cells of LMAT exhibited higher adipogenic potential and lower proliferation rates than those of SMAT. In addition, SMAT and LMAT play different roles in immune regulation and subsequently affect microbiota components. Finally, our data clarified the described differences between SMAT and LMAT in humans. Conclusions: There were significant differences in cell morphology, gene expression profiles, cell components, biological characteristics, and immune and microbiota regulation roles between regional MATs.

scholarly journals Comparative Transcriptome Analysis of Different Dendrobium Species Reveals Active Ingredients-Related Genes and Pathways

2020 ◽  
Vol 21 (3) ◽  
pp. 861 ◽  
Author(s):  
Yingdan Yuan ◽  
Bo Zhang ◽  
Xinggang Tang ◽  
Jinchi Zhang ◽  
Jie Lin
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Rna Seq ◽  
Active Ingredients ◽  
Hub Genes ◽  
Transcriptome Database ◽  
Gene Modules ◽  
Functional Investigation ◽  
First Time

Dendrobium is widely used in traditional Chinese medicine, which contains many kinds of active ingredients. In recent years, many Dendrobium transcriptomes have been sequenced. Hence, weighted gene co-expression network analysis (WGCNA) was used with the gene expression profiles of active ingredients to identify the modules and genes that may associate with particular species and tissues. Three kinds of Dendrobium species and three tissues were sampled for RNA-seq to generate a high-quality, full-length transcriptome database. Based on significant changes in gene expression, we constructed co-expression networks and revealed 19 gene modules. Among them, four modules with properties correlating to active ingredients regulation and biosynthesis, and several hub genes were selected for further functional investigation. This is the first time the WGCNA method has been used to analyze Dendrobium transcriptome data. Further excavation of the gene module information will help us to further study the role and significance of key genes, key signaling pathways, and regulatory mechanisms between genes on the occurrence and development of medicinal components of Dendrobium.

scholarly journals Interferon-regulated genetic programs and JAK/STAT pathway activate the intronic promoter of the short ACE2 isoform in renal proximal tubules

2021 ◽  
Author(s):  
Jakub Jankowski ◽  
Hye Kyung Lee ◽  
Julia Wilflingseder ◽  
Lothar Hennighausen
Keyword(s):  
Gene Expression ◽  
Proximal Tubule ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Regulatory Elements ◽  
Rna Seq ◽  
Angiotensin Converting Enzyme 2 ◽  
Genome Wide ◽  
Cytokine Stimulation

SummaryRecently, a short, interferon-inducible isoform of Angiotensin-Converting Enzyme 2 (ACE2), dACE2 was identified. ACE2 is a SARS-Cov-2 receptor and changes in its renal expression have been linked to several human nephropathies. These changes were never analyzed in context of dACE2, as its expression was not investigated in the kidney. We used Human Primary Proximal Tubule (HPPT) cells to show genome-wide gene expression patterns after cytokine stimulation, with emphasis on the ACE2/dACE2 locus. Putative regulatory elements controlling dACE2 expression were identified using ChIP-seq and RNA-seq. qRT-PCR differentiating between ACE2 and dACE2 revealed 300- and 600-fold upregulation of dACE2 by IFNα and IFNβ, respectively, while full length ACE2 expression was almost unchanged. JAK inhibitor ruxolitinib ablated STAT1 and dACE2 expression after interferon treatment. Finally, with RNA-seq, we identified a set of genes, largely immune-related, induced by cytokine treatment. These gene expression profiles provide new insights into cytokine response of proximal tubule 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 Transcriptome Analysis of the Gene Expression Profiles Associated with Fungal Keratitis in Mice Based on RNA-Seq

2020 ◽  
Vol 61 (6) ◽  
pp. 32
Author(s):  
Qing Zhang ◽  
Jian Zhang ◽  
Mengting Gong ◽  
Ruolan Pan ◽  
Yanchang Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptome Analysis ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Fungal Keratitis ◽  
Rna Seq

scholarly journals Analysis of theIn VivoTranscriptome ofBordetella pertussisduring Infection of Mice

mSphere ◽  
2019 ◽  
Vol 4 (2) ◽  
Author(s):  
Ting Y. Wong ◽  
Jesse M. Hall ◽  
Evan S. Nowak ◽  
Dylan T. Boehm ◽  
Laura A. Gonyar ◽  
...  
Keyword(s):  
Gene Expression ◽  
Iron Acquisition ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Growth Conditions ◽  
Rna Seq ◽  
Content Type ◽  
Murine Lung

ABSTRACTBordetella pertussiscauses the disease whooping cough through coordinated control of virulence factors by theBordetellavirulence gene system. Microarrays and, more recently, RNA sequencing (RNA-seq) have been used to describein vitrogene expression profiles ofB. pertussisand other pathogens. In previous studies, we have analyzed thein vitrogene expression profiles ofB. pertussis, and we hypothesize that the infection transcriptome profilein vivois significantly different from that under laboratory growth conditions. To study the infection transcriptome ofB. pertussis, we developed a simple filtration technique for isolation of bacteria from infected lungs. The work flow involves filtering the bacteria out of the lung homogenate using a 5-μm-pore-size syringe filter. The captured bacteria are then lysed to isolate RNA for Illumina library preparation and RNA-seq analysis. Upon comparing thein vitroandin vivogene expression profiles, we identified 351 and 255 genes as activated and repressed, respectively, during murine lung infection. As expected, numerous genes associated with virulent-phase growth were activated in the murine host, including pertussis toxin (PT), the PT secretion apparatus, and the type III secretion system. A significant number of genes encoding iron acquisition and heme uptake proteins were highly expressed during infection, supporting iron acquisition as critical forB. pertussissurvivalin vivo. Numerous metabolic genes were repressed during infection. Overall, these data shed light on the gene expression profile ofB. pertussisduring infection, and this method will facilitate efforts to understand how this pathogen causes infection.IMPORTANCEIn vitrogrowth conditions for bacteria do not fully recapitulate the host environment. RNA sequencing transcriptome analysis allows for the characterization of the infection gene expression profiles of pathogens in complex environments. Isolation of the pathogen from infected tissues is critical because of the large amounts of host RNA present in crude lysates of infected organs. A filtration method was developed that enabled enrichment of the pathogen RNA for RNA-seq analysis. The resulting data describe the “infection transcriptome” ofB. pertussisin the murine lung. This strategy can be utilized for pathogens in other hosts and, thus, expand our knowledge of what bacteria express during infection.

Sign in / Sign up

Export Citation Format

Share Document