scholarly journals Genome-Wide Investigation of Spliceosomal SM/LSM Genes in Wheat (Triticum aestivum L.) and Its Progenitors

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1429
Author(s):  
Ruiting Gao ◽  
Ning Su ◽  
Wenqiu Pan ◽  
Qiaoyu Bao ◽  
Zhen Li ◽  
...  
Keyword(s):  
Rna Splicing ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Aegilops Tauschii ◽  
Enrichment Analysis ◽  
Wheat Chromosome ◽  
Triticum Aestivum L ◽  
Triticum Dicoccoides ◽  
Regulatory Elements ◽  
Salt Tolerance Gene

The SSM/SLSM (spliceosomal Smith (SM)/SM-like (LSM)) genes are the central components of the spliceosome in eukaryotes, which play an important role in regulating RNA splicing, participating in diverse biological processes. Although it has been detected in Arabidopsis and rice etc. plants, the members and significance of the SSM/SLSM gene family in wheat are still not reported. In this study, we identified the SSM/SLSM genes in wheat and its progenitors at genome-scale, where 57 SSM/SLSM genes were identified in wheat, together with 41, 17and 19 found in Triticum dicoccoides, Triticum urartu, and Aegilops tauschii. Furthermore, their phylogenetic relationship, gene structures, conserved motifs, and cis-regulatory elements were systematically analyzed. By synteny analysis, good collinearity of SSM/SLSM genes was found among bread wheat and its progenitors’ genomes, and the distribution of SMD2 genes in wheat chromosome 5A, 4B and 4D located in the 4AL-5AL-7BS chromosome model, due to the translocation. Then, the positively selected genes were further investigated based on the non-synonymous to synonymous (dN/dS) analysis of the orthologous pairs. Finally, the expression profiles of the SSM/SLSM genes were detected using RNA-seq datasets, and eight stress-responsive candidate genes were selected to validate their expression through qPCR (real-time quantitative polymerase chain reaction). According to the co-expression network analysis, the correlation between the LSM7-7A gene and related genes was illustrated through Gene Ontology (GO) enrichment analysis. Furthermore, the LSM7-7A gene was related to the Arabidopsis homologous salt tolerance gene RCY1. This investigation systematically identified the complete candidates of SSM/SLSM genes and their characters in wheat and its progenitors, and provided clues to a better understanding of their contribution during the wheat polyploidy process.

scholarly journals Genome-Wide Identification and Expression Profiling Analysis of WOX Family Proteins Encoded Genes in Triticeae Plant Species

2020 ◽  
Author(s):  
Lei Shi ◽  
Ke Wang ◽  
Lipu Du ◽  
Yuxia Song ◽  
Huihui Li ◽  
...  
Keyword(s):  
Plant Regeneration ◽  
Plant Species ◽  
Triticum Turgidum ◽  
Baby Boom ◽  
Expression Profiles ◽  
Aegilops Tauschii ◽  
Family Members ◽  
Triticum Dicoccoides ◽  
Substitution Lines ◽  
Specific Pcr

Abstract Background: Genotype dependence of plant regeneration is an important factor restricting the genetic improvement of Triticeae plant species. The WUSCHEL-related homeobox (WOX) is a group of plant specific transcription factor, which play an important role in plant growth and development, and cell division and differentiation. Recent studies revealed that the application of regeneration-related genes such as WOX and BABY BOOM (BBM) could improve plant regeneration. The application of WOX genes is one of the ways to improve the genetic transformation system of Triticeae and other species, but there are rare studies in this area.Results: From the available genome sequence database, in total 136 WOX transcripts were identified for the Triticeae plants, including 43 in Triticum aestivum, 30 in Triticum turgidum, 25 in Triticum dicoccoides, 17 in Hordeum vulgare, 13 in Aegilops tauschii, and 8 in Triticum urartu. All of the WOX family genes were distributed on the chromosomes of homologous groups 1 to 5 in the six Triticeae species, part of which were confirmed by their specific PCR markers using a set of T. durum-T. aestivum genome D substitution lines. All of the WOX proteins in the six Triticeae species could be grouped into three clades, similar to those in rice (Oryza sativa L.) and Arabidopsis. WOX family members were conserved among these Triticeae plants, all of them contained the conserved HOX DNA-binding homeodomain, and WUS clade members contained the characteristic WUS motif, while only TaWUS and TaWOX9 in all the six Triticeae plant species contained the ERF-associated amphiphilic repression (EAR) motif. The expression profiles of TaWOX genes by quantitative real-time PCR (qPCR) showed obvious difference among WOX family members.Conclusions: Totally 130 WOX genes were identified in the six Triticeae plant species. The WOX family genes were located on the chromosomes in the five homologous groups except groups 6 and 7 in the Triticeae species, and their expression profiles were different in different tissues, indicating that each of them had diverse function. The findings in this study could provide a basis for evolution and functional investigation and practical application of the WOX family genes in Triticeae plant species.

scholarly journals Identification of differentially expressed circulating exosomal lncRNAs in IgA nephropathy patients

2020 ◽  
Author(s):  
Na Guo ◽  
Qin Zhou ◽  
Xiang Huang ◽  
Jianwen Yu ◽  
Qianqian Han ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Immunoglobulin A ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Protein Coding ◽  
Non Invasive ◽  
First Degree Relatives ◽  
The Difference ◽  
Primary Glomerular Disease

Abstract Background: Immunoglobulin A nephropathy (IgAN) is one of the most prevalent primary glomerular disease. Non-invasive biomarkers are urgently needed for IgAN diagnosis. We investigate the difference in expression profiles of exosomal long non-coding-RNAs (lncRNAs) in plasma from IgAN patients compared with their healthy first-degree relatives, which may reveal novel non-invasive IgAN biomarkers. Methods: Exosomes were isolated from the plasma of IgAN patients and their healthy first-degree relatives. High-throughput RNA sequencing and real-time quantitative polymerase chain reaction (qRT-PCR) was used to validate lncRNA expression profiles. Pathway enrichment analysis was used to predict their nearest protein-coding genes. Results: lncRNA-G21551 was significantly down-regulated in IgAN patients. The nearest protein-coding gene was found to be encoding the low affinity receptor of the Fc segment of immunoglobulin G (FCGR3B). Conclusion: Exosomal lncRNA-G21551, with FCGR3B as the nearest protein-coding gene, was down-regulated in IgAN patients, indicating its potential to serve as a non-invasive biomarker for IgAN.

scholarly journals Construction of circRNA-miRNA-mRNA Network for Exploring Underlying Mechanisms of Lubrication Disorder

2021 ◽  
Vol 9 ◽  
Author(s):  
Shengnan Cong ◽  
Jinlong Li ◽  
Jingjing Zhang ◽  
Jingyi Feng ◽  
Aixia Zhang ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Differentially Expressed ◽  
Luciferase Reporter ◽  
Control Group ◽  
Sodium Reabsorption ◽  
Cerna Network ◽  
Reporter Assays

Lubrication disorder is a common health issue that manifests as insufficient sexual arousal at the beginning of sex. It often causes physical and psychological distress. However, there are few studies on lubrication disorder, and the complexity of circular RNA (circRNA) and the related competing endogenous RNA (ceRNA) network in lubrication disorder is still poorly known. Therefore, this study aims to build a regulatory circRNA-micro (mi)RNA-mRNA network and explore potential molecular markers of lubrication disorder. In the study, 12 subjects were recruited, including 6 in the lubrication disorder group and 6 in the normal control group. RNA sequencing was exploited to identify the expression profiles of circRNA, miRNA and mRNA between two groups, and then to construct the circRNA-miRNA-mRNA networks. The enrichment analyses of the differentially expressed (DE)-mRNAs were examined via Gene Set Enrichment Analysis (GSEA). Furthermore, the expression level and interactions among circRNA, miRNA, and mRNA were validated using real-time quantitative polymerase chain reaction (RT-qPCR) and dual-luciferase reporter assays. In the results, 73 circRNAs, 287 miRNAs, and 354 target mRNAs were differentially expressed between two groups when taking | Log2 (fold change)| > 1 and P-value < 0.05 as criteria, and then the results of GSEA revealed that DE-mRNAs were linked with “vascular smooth muscle contraction,” “aldosterone regulated sodium reabsorption,” “calcium signaling pathway,” etc. 19 target relationships among 5 circRNAs, 4 miRNAs, and 7 mRNAs were found and constructed the ceRNA network. Among them, hsa-miR-212-5p and hsa-miR-874-3p were demonstrated to be related to the occurrence of lubrication disorder. Eventually, consistent with sequencing, RT-qPCR showed that hsa_circ_0026782 and ASB2 were upregulated while hsa-miR-874-3p was downregulated, and dual-luciferase reporter assays confirmed the interactions among them. In summary, the findings indicate that the circRNA-miRNA-mRNA regulatory network is presented in lubrication disorder, and ulteriorly provide a deeper understanding of the specific regulatory mechanism of lubrication disorder from the perspective of the circRNA-miRNA-mRNA network.

scholarly journals Comprehensive Bioinformatics Identifies Key microRNA Players in ATG7-Deficient Lung Fibroblasts

2020 ◽  
Vol 21 (11) ◽  
pp. 4126 ◽  
Author(s):  
Stevan D. Stojanović ◽  
Maximilian Fuchs ◽  
Jan Fiedler ◽  
Ke Xiao ◽  
Anna Meinecke ◽  
...  
Keyword(s):  
Large Scale ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Human Fibroblasts ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Lung Fibroblasts ◽  
Specific Cell ◽  
Proteome Profiling

Background: Deficient autophagy has been recently implicated as a driver of pulmonary fibrosis, yet bioinformatics approaches to study this cellular process are lacking. Autophagy-related 5 and 7 (ATG5/ATG7) are critical elements of macro-autophagy. However, an alternative ATG5/ATG7-independent macro-autophagy pathway was recently discovered, its regulation being unknown. Using a bioinformatics proteome profiling analysis of ATG7-deficient human fibroblasts, we aimed to identify key microRNA (miR) regulators in autophagy. Method: We have generated ATG7-knockout MRC-5 fibroblasts and performed mass spectrometry to generate a large-scale proteomics dataset. We further quantified the interactions between various proteins combining bioinformatics molecular network reconstruction and functional enrichment analysis. The predicted key regulatory miRs were validated via quantitative polymerase chain reaction. Results: The functional enrichment analysis of the 26 deregulated proteins showed decreased cellular trafficking, increased mitophagy and senescence as the major overarching processes in ATG7-deficient lung fibroblasts. The 26 proteins reconstitute a protein interactome of 46 nodes and miR-regulated interactome of 834 nodes. The miR network shows three functional cluster modules around miR-16-5p, miR-17-5p and let-7a-5p related to multiple deregulated proteins. Confirming these results in a biological setting, serially passaged wild-type and autophagy-deficient fibroblasts displayed senescence-dependent expression profiles of miR-16-5p and miR-17-5p. Conclusions: We have developed a bioinformatics proteome profiling approach that successfully identifies biologically relevant miR regulators from a proteomics dataset of the ATG-7-deficient milieu in lung fibroblasts, and thus may be used to elucidate key molecular players in complex fibrotic pathological processes. The approach is not limited to a specific cell-type and disease, thus highlighting its high relevance in proteome and non-coding RNA research.

scholarly journals Phenylalanine Ammonia-Lyase (PAL) Genes Family in Wheat (Triticum aestivum L.): Genome-Wide Characterization and Expression Profiling

Agronomy ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 2511
Author(s):  
Fatima Rasool ◽  
Muhammad Uzair ◽  
Muhammad Kashif Naeem ◽  
Nazia Rehman ◽  
Amber Afroz ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Phenylalanine Ammonia Lyase ◽  
Chromosomal Rearrangements ◽  
Aegilops Tauschii ◽  
Triticum Aestivum L ◽  
Regulatory Elements ◽  
Phenylpropanoid Pathway ◽  
Evolutionary Analysis ◽  
Genome Wide ◽  
A Genome

Phenylalanine ammonia-lyase (PAL) is the first enzyme in the phenylpropanoid pathway and plays a vital role in adoption, growth, and development in plants but in wheat its characterization is still not very clear. Here, we report a genome-wide identification of TaPAL genes and analysis of their transcriptional expression, duplication, and phylogeny in wheat. A total of 37 TaPAL genes that cluster into three subfamilies have been identified based on phylogenetic analysis. These TaPAL genes are distributed on 1A, 1B, 1D, 2A, 2B, 2D, 4A, 5B, 6A, 6B, and 6D chromosomes. Gene structure, conserved domain analysis, and investigation of cis-regulatory elements were systematically carried out. Chromosomal rearrangements and gene loss were observed by evolutionary analysis of the orthologs among Triticum urartu, Aegilops tauschii, and Triticum aestivum during the origin of bread wheat. Gene ontology analysis revealed that PAL genes play a role in plant growth. We also identified 27 putative miRNAs targeting 37 TaPAL genes. The high expression level of PAL genes was detected in roots of drought-tolerant genotypes compared to drought-sensitive genotypes. However, very low expressions of TaPAL10, TaPAL30, TaPAL32, TaPAL3, and TaPAL28 were recorded in all wheat genotypes. Arogenate dehydratase interacts with TaPAL29 and has higher expression in roots. The analysis of all identified genes in RNA-seq data showed that they are expressed in roots and shoots under normal and abiotic stress. Our study offers valuable data on the functioning of PAL genes in wheat.

scholarly journals Genome-wide member identification, phylogeny and expression analysis of PEBP gene family in wheat and its progenitors

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10483
Author(s):  
Lei Dong ◽  
Yue Lu ◽  
Shubing Liu
Keyword(s):  
Seed Germination ◽  
Common Wheat ◽  
Expression Profiles ◽  
Aegilops Tauschii ◽  
Triticum Dicoccoides ◽  
Pcr Analysis ◽  
Specific Expression ◽  
Biotic Stresses ◽  
Organ Specific ◽  
Group 2

The phosphatidylethanolamine binding protein (PEBP) family comprises ancient proteins found throughout the biosphere that play an important role in plant growth and development, flowering, seed development and dormancy. However, not all PEBP genes have been identified or analyzed in common wheat (Triticum aestivum L.) and its progenitors. In this study, we identified the PEBP genes in common wheat, Triticum dicoccoides, Triticum urartu and Aegilops tauschii by searching whole genome sequences, and characterized these genes by phylogenetic and transcriptome analyses. A total of 76, 38, 16 and 22 PEBP genes were identified in common wheat, T. dicoccoides, T. urartu and Ae. tauschii, respectively. Phylogenetic analysis classified the PEBP genes into four subfamilies (PEBP-like, MFT-like, TFL-like and FT-like); the PEBP-like subfamily was identified as a new subfamily with genes in this subfamily were conserved in plants. Group 2, 3 and 5 chromosomes of common wheat and its progenitors contained more PEBP genes than other chromosomes. The PEBP genes were conserved in wheat during evolution, and tandem duplication played a more important role in the amplification of PEBP genes than segmental duplication. Furthermore, transcriptome analysis revealed that PEBP genes showed tissue/organ-specific expression profiles and some PEBP genes were induced to express by biotic stresses. Quantitative real-time PCR (qRT-PCR) analysis revealed that seven randomly selected PEBP genes expressed differently during seed germination under cold, drought, flood, heat and salt stress treatments, and five of these genes (TaPEBP1, TaPEBP5, TaPEBP9, TaPEBP66 and TaPEBP69) showed significantly higher expression under different stress treatments, indicating that these genes play important roles during seed germination under stress conditions.

scholarly journals Genome-level identification of cell wall invertase genes in wheat for the study of drought tolerance

2012 ◽  
Vol 39 (7) ◽  
pp. 569 ◽  
Author(s):  
Hollie Webster ◽  
Gabriel Keeble ◽  
Bernard Dell ◽  
John Fosu-Nyarko ◽  
Y. Mukai ◽  
...  
Keyword(s):  
Cell Wall ◽  
Drought Tolerance ◽  
Aegilops Tauschii ◽  
Sequence Divergence ◽  
Wheat Chromosome ◽  
Triticum Aestivum L ◽  
Pollen Sterility ◽  
Cell Wall Invertase ◽  
D Genome ◽  
Specific Expression

In wheat (Triticum aestivum L.) drought-induced pollen sterility is a major contributor to grain yield loss and is caused by the downregulation of the cell wall invertase gene IVR1. The IVR1 gene catalyses the irreversible hydrolysis of sucrose to glucose and fructose, the essential energy substrates which support pollen development. Downregulation of IVR1 in response to drought is isoform specific and shows variation in temporal and tissue-specific expression. IVR1 is now prompting interest as a candidate gene for molecular marker development to screen wheat germplasm for improved drought tolerance. The aim of this study was to define the family of IVR1 genes to enable: (1) individual isoforms to be assayed in gene expression studies; and (2) greater accuracy in IVR1 mapping to the wheat genetic map and drought tolerance QTL analysis. Using a cell wall invertase-specific motif as a probe, wheat genomics platforms were screened for the presence of unidentified IVR1 isoforms. Wheat genomics platforms screened included the IWGSC wheat survey sequence, the wheat D genome donor sequence from Aegilops tauschii Coss, and the CCG wheat chromosome 3B assembly: contig506. Chromosome-specific sequences homologous to the query motif were isolated and characterised. Sequence annotation results showed five previously unidentified IVR1 isoforms exist on multiple chromosome arms and on all three genomes (A, B and D): IVR1–3A, IVR1–4A, IVR1–5B, IVR1.2–3B and IVR1-5D. Including three previously characterised IVR1 isoforms (IVR1.1–1A, IVR1.2–1A and IVR1.1–3B), the total number of isoform gene family members is eight. The IVR1 isoforms contain two motifs common to cell wall invertase (NDPN and WECPDF) and a high degree of conservation in exon 4, suggesting conservation of functionality. Sequence divergence at a primary structure level in other regions of the gene was evident amongst the isoforms, which likely contributes to variation in gene regulation and expression in response to water deficit within this subfamily of IVR1 isoforms in wheat.

scholarly journals Comparing transcriptome profiles of human embryo cultured in closed and standard incubators

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9738
Author(s):  
Jingyu Li ◽  
Jiayu Huang ◽  
Wei Han ◽  
Xiaoli Shen ◽  
Ying Gao ◽  
...  
Keyword(s):  
Rna Splicing ◽  
Positive Impact ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Enrichment Analysis ◽  
Time Lapse ◽  
Human Embryos ◽  
Rna Seq ◽  
False Discovery ◽  
Time Lapse Imaging

It is necessary to compare the transcriptomic profiles of human embryos cultured in time-lapse imaging (TLI) incubators and standard incubators (SI) in order to determine whether a closed culture system has a positive impact on embryos. In this study, we used RNA-sequencing (RNA-Seq) to characterize and compare the gene expression profiles of eight-cell embryos of the same quality grade cultured in TLI and SI. We sequenced a total of 580,952,620 reads for zygotes, TLI-cultured, and SI-cultured eight-cell embryos. The global transcriptomic profiles of the TLI embryos were similar to those of the SI embryos and were highly distinct from the zygotes. We also detected 539 genes showing differential expression between the TLI and SI groups with a false discovery rate (FDR) < 0.05. Using gene ontology enrichment analysis, we found that the highly expressed SI genes tended to execute functions such as transcription, RNA splicing, and DNA repair, and that the highly expressed TLI genes were enriched in the cell differentiation and methyltransferase activity pathways. This study, the first to use transcriptome analysis to compare SI and TLI, will serve as a basis for assessing the safety of TLI application in assisted reproductive technology.

scholarly journals Genome-wide analysis of the polyamine oxidase gene family in wheat (Triticum aestivum L.) reveals involvement in temperature stress response

2020 ◽  
Author(s):  
Fatemeh Gholizadeh ◽  
Ghader Mirzaghaderi
Keyword(s):  
Triticum Aestivum ◽  
Abiotic Stresses ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Aegilops Tauschii ◽  
Triticum Aestivum L ◽  
Amine Oxidases ◽  
Oxidase Gene ◽  
Evolutionary Features ◽  
Heat And Cold Stress

AbstractAmine oxidases (AOs) including copper containing amine oxidases (CuAOs) and FAD-dependent polyamine oxidases (PAOs) are associated with polyamine catabolism in the peroxisome, apoplast and cytoplasm and play an essential role in growth and developmental processes and response to biotic and abiotic stresses. Here, we identified PAO genes in common wheat (Triticum aestivum), T. urartu and Aegilops tauschii and reported the genome organization, evolutionary features and expression profiles of the wheat PAO genes (TaPAO). Expression analysis using publicly available RNASeq data showed that TaPAO genes are expressed redundantly in various tissues and developmental stages. A large percentage of TaPAOs respond significantly to abiotic stresses, especially temperature (i.e. heat and cold stress). Some TaPAOs were also involved in response to other stresses such as powdery mildew, stripe rust and Fusarium infection. Overall, TaPAOs may have various functions in stress tolerances responses, and play vital roles in different tissues and developmental stages. Our results provided a reference for further functional investigation of TaPAO proteins.

scholarly journals Genome-wide Identification and Expression Profiling Analysis of WOX Family Proteins Encoded Genes in Triticeae Plant Species

2020 ◽  
Author(s):  
Lei Shi ◽  
Ke Wang ◽  
Lipu Du ◽  
Yuxia Song ◽  
Huihui Li ◽  
...  
Keyword(s):  
Plant Regeneration ◽  
Plant Species ◽  
Triticum Turgidum ◽  
Baby Boom ◽  
Expression Profiles ◽  
Aegilops Tauschii ◽  
Family Members ◽  
Triticum Dicoccoides ◽  
Substitution Lines ◽  
Specific Pcr

Abstract Background: Genotype dependence of plant regeneration is an important factor restricting the genetic improvement of Triticeae plant species. The WUSCHEL-related homeobox (WOX) is a group of plant specific transcription factor, which play an important role in plant growth and development, and cell division and differentiation. Recent studies revealed that the application of regeneration-related genes such as WOX and BABY BOOM (BBM) could improve plant regeneration. The application of WOX genes is one of the ways to improve the genetic transformation system of Triticeae and other species, but there are rare studies in this area.Results: From the available genome sequence database, in total 136 WOX transcripts were identified for the Triticeae plants, including 43 in Triticum aestivum, 30 in Triticum turgidum, 25 in Triticum dicoccoides, 17 in Hordeum vulgare, 13 in Aegilops tauschii, and 8 in Triticum urartu. All of the WOX family genes were distributed on the chromosomes of homologous groups 1 to 5 in the six Triticeae species, part of which were confirmed by their specific PCR markers using a set of T. durum-T. aestivum genome D substitution lines. All of the WOX proteins in the six Triticeae species could be grouped into three clades, similar to those in rice (Oryza sativa L.) and Arabidopsis. WOX family members were conserved among these Triticeae plants, all of them contained the conserved HOX DNA-binding homeodomain, and WUS clade members contained the characteristic WUS motif, while only TaWUS and TaWOX9 in all the six Triticeae plant species contained the ERF-associated amphiphilic repression (EAR) motif. The expression profiles of TaWOX genes by quantitative real-time PCR (qPCR) showed obvious difference among WOX family members.Conclusions: Totally 130 WOX genes were identified in the six Triticeae plant species. The WOX family genes were located on the chromosomes in the five homologous groups except groups 6 and 7 in the Triticeae species, and their expression profiles were different in different tissues, indicating that each of them had diverse function. The findings in this study could provide a basis for evolution and functional investigation and practical application of the WOX family genes in Triticeae plant species.

Sign in / Sign up

Export Citation Format

Share Document