scholarly journals Phosphate transporter genes: genome-wide identification and characterization in Camelina sativa

2021 ◽  
Author(s):  
Soosan Hasanzadeh ◽  
Sahar Faraji ◽  
Abdullah ◽  
Parviz Heidari
Keyword(s):  
Phosphate Transporter ◽  
Rna Seq ◽  
Specific Expression ◽  
Cis Acting ◽  
Genome Wide ◽  
Sodium Dependent ◽  
Intron Number ◽  
Response To Stress ◽  
Growth Energy ◽  
Root Tissues

Phosphorus is known as a key element associated with growth, energy, and cell signaling. In plants, phosphate transporters (PHTs) are responsible for moving and distributing phosphorus in cells and organs. PHT genes have been genome-wide identified and characterized in various plant species, however, these genes have not been widely identified based on available genomic data in Camellia sativa, which is an important oil seed plant. In the present study, we found 66 PHT genes involved in phosphate transporter/translocate in C. sativa. The recognized genes belonged to PHTs1, PHTs2, PHTs4, PHOs1, PHO1 homologs, glycerol-3-PHTs, sodium dependent PHTs, inorganic PHTs, xylulose 5-PHTs, glucose-6-phosphate translocators, and phosphoenolpyruvate translocators. Our finding revealed that PHT proteins are divers based on their physicochemical properties such as Isoelectric point (pI), molecular weight, GRAVY value, and exon-intron number(s). Besides, the expression profile of PHT genes in C. sativa based on RNA-seq data indicate that PHTs are involved in response to abiotic stresses such as cold, drought, salt, and cadmium. The tissue specific expression high expression of PHO1 genes in root tissues of C. sativa. In additions, four PHTs, including a PHT4;5 gene, a sodium dependent PHT gene, and two PHO1 homolog 3 genes were found with an upregulation in response to aforementioned studied stresses. In the current study, we found that PHO1 proteins and their homologs have high potential to post-translation modifications such as N-glycosylation and phosphorylation. Besides, different cis-acting elements associated with response to stress and phytohormone were found in the promoter region of PHT genes. Overall, our results show that PHT genes play various functions in C. Sativa and regulate Camellia responses to external and intracellular stimuli. The results can be used in future studies related to the functional genomics of C. sativa.

scholarly journals Genome-Wide Identification and Analysis of Cell Cycle Genes in Birch

Forests ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 120
Author(s):  
Yijie Li ◽  
Song Chen ◽  
Yuhang Liu ◽  
Haijiao Huang
Keyword(s):  
Cell Cycle ◽  
Growth And Development ◽  
Betula Pendula ◽  
Cell Cycle Gene ◽  
Expression Data ◽  
Rna Seq ◽  
Specific Expression ◽  
Cell Cycles ◽  
Cell Cycle Genes ◽  
Genome Wide

Research Highlights: This study identified the cell cycle genes in birch that likely play important roles during the plant’s growth and development. This analysis provides a basis for understanding the regulatory mechanism of various cell cycles in Betula pendula Roth. Background and Objectives: The cell cycle factors not only influence cell cycles progression together, but also regulate accretion, division, and differentiation of cells, and then regulate growth and development of the plant. In this study, we identified the putative cell cycle genes in the B. pendula genome, based on the annotated cell cycle genes in Arabidopsis thaliana (L.) Heynh. It can be used as a basis for further functional research. Materials and Methods: RNA-seq technology was used to determine the transcription abundance of all cell cycle genes in xylem, roots, leaves, and floral tissues. Results: We identified 59 cell cycle gene models in the genome of B. pendula, with 17 highly expression genes among them. These genes were BpCDKA.1, BpCDKB1.1, BpCDKB2.1, BpCKS1.2, BpCYCB1.1, BpCYCB1.2, BpCYCB2.1, BpCYCD3.1, BpCYCD3.5, BpDEL1, BpDpa2, BpE2Fa, BpE2Fb, BpKRP1, BpKRP2, BpRb1, and BpWEE1. Conclusions: By combining phylogenetic analysis and tissue-specific expression data, we identified 17 core cell cycle genes in the Betulapendula genome.

scholarly journals Genome-wide identification, characterization, and expression analysis of tea plant autophagy-related genes (CsARGs) demonstrates that they play diverse roles during development and under abiotic stress

2020 ◽  
Author(s):  
Huan Wang ◽  
ZhaoTang Ding ◽  
Mengjie Gou ◽  
Jianhui Hu ◽  
Yu Wang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Expression Analysis ◽  
Molecular Mechanisms ◽  
Tea Plant ◽  
Future Research ◽  
Specific Expression ◽  
Genome Wide ◽  
Physiological Analysis ◽  
Response To Stress ◽  
Tea Plants

Abstract Background: Autophagy, meaning ‘self-eating’, is required for the degradation and recycling of cytoplasmic constituents under stressful and non-stressful conditions, which helps to maintain cellular homeostasis and delay aging and longevity in eukaryotes. To date, the functions of autophagy have been heavily studied in yeast, mammals and model plants, but few studies have focused on economically important crops, especially tea plants (Camellia sinensis). The roles played by autophagy in coping with various environmental stimuli have not been fully elucidated to date. Therefore, investigating the functions of autophagy-related genes in tea plants may help to elucidate the mechanism governing autophagy in response to stresses in woody plants.Results: In this study, we identified 35 C. sinensis autophagy-related genes (CsARGs). Each CsARG is highly conserved with its homologues from other plant species, except for CsATG14. Tissue-specific expression analysis demonstrated that the abundances of CsARGs varied across different tissues, but CsATG8c/i showed a degree of tissue specificity. Under hormone and abiotic stress conditions, most CsARGs were upregulated at different time points during the treatment. In addition, the expression levels of 10 CsARGs were higher in the cold-resistant cultivar ‘Longjing43’ than in the cold-susceptible cultivar ‘Damianbai’ during the CA period; however, the expression of CsATG101 showed the opposite tendency.Conclusions: We performed a comprehensive bioinformatic and physiological analysis of CsARGs in tea plants, and these results may help to establish a foundation for further research investigating the molecular mechanisms governing autophagy in tea plant growth, development and response to stress. Meanwhile, some CsARGs could serve as putative molecular markers for the breeding of cold-resistant tea plants in future research.

scholarly journals Cell-specific expression buffering promotes cell survival and cancer robustness

2021 ◽  
Author(s):  
Hao-Kuen Lin ◽  
Jen-Hao Cheng ◽  
Chia-Chou Wu ◽  
Feng-Shu Hsieh ◽  
Carolyn A Dunlap ◽  
...  
Keyword(s):  
Cell Survival ◽  
Rna Seq ◽  
Specific Expression ◽  
Tissue Specific ◽  
Gene Pairs ◽  
Genome Wide ◽  
A Cell ◽  
Physiological Homeostasis ◽  
Multicellular Organisms ◽  
Score Index

Functional buffering ensures biological robustness critical for cell survival and physiological homeostasis in response to environmental challenges. However, in multicellular organisms, the mechanism underlying cell- and tissue-specific buffering and its implications for cancer development remain elusive. Here, we propose a Cell-specific Expression-BUffering (CEBU) mechanism, whereby a gene's function is buffered by cell-specific expression of a buffering gene, to describe functional buffering in humans. The likelihood of CEBU between gene pairs is quantified using a C-score index. By computing C-scores using genome-wide CRISPR screens and transcriptomic RNA-seq of 684 human cell lines, we report that C-score-identified putative buffering gene pairs are enriched for members of the same pathway, protein complex and duplicated gene family. Furthermore, these buffering gene pairs contribute to cell-specific genetic interactions and are indicative of tissue-specific robustness. C-score derived buffering capacities can help predict patient survival in multiple cancers. Our results reveal CEBU as a critical mechanism of functional buffering contributing to cell survival and cancer robustness in humans.

scholarly journals Defining the function of SUMO system in pod development and abiotic stresses in Peanut

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Yiyang Liu ◽  
Jiao Zhu ◽  
Sheng Sun ◽  
Feng Cui ◽  
Yan Han ◽  
...  
Keyword(s):  
Abiotic Stresses ◽  
Developmental Process ◽  
Expression Patterns ◽  
Rna Seq ◽  
Specific Expression ◽  
Genome Wide ◽  
Pod Development ◽  
Core Components ◽  
Arachis Duranensis ◽  
New Strategies

Abstract Background Posttranslational modification of proteins by small ubiquitin like modifier (SUMO) proteins play an important role during the developmental process and in response to abiotic stresses in plants. However, little is known about SUMOylation in peanut (Arachis hypogaea L.), one of the world’s major food legume crops. In this study, we characterized the SUMOylation system from the diploid progenitor genomes of peanut, Arachis duranensis (AA) and Arachis ipaensis (BB). Results Genome-wide analysis revealed the presence of 40 SUMO system genes in A. duranensis and A. ipaensis. Our results showed that peanut also encodes a novel class II isotype of the SCE1, which was previously reported to be uniquely present in cereals. RNA-seq data showed that the core components of the SUMOylation cascade SUMO1/2 and SCE1 genes exhibited pod-specific expression patterns, implying coordinated regulation during pod development. Furthermore, both transcripts and conjugate profiles revealed that SUMOylation has significant roles during the pod development. Moreover, dynamic changes in the SUMO conjugates were observed in response to abiotic stresses. Conclusions The identification and organization of peanut SUMO system revealed SUMOylation has important roles during stress defense and pod development. The present study will serve as a resource for providing new strategies to enhance agronomic yield and reveal the mechanism of peanut pod development.

scholarly journals Network analysis links genome-wide phenotypic and transcriptional stress responses in a bacterial pathogen with a large pan-genome

2016 ◽  
Author(s):  
Paul A. Jensen ◽  
Zeyu Zhu ◽  
Tim van Opijnen
Keyword(s):  
Gene Expression ◽  
Stress Responses ◽  
Meta Analysis ◽  
Bacterial Pathogen ◽  
Metabolic Model ◽  
Genetic Network ◽  
Rna Seq ◽  
Genome Wide ◽  
A Genome ◽  
Response To Stress

ABSTRACTBackgroundBacteria modulate subcellular processes to handle stressful environments. Genome-wide profiling of gene expression (RNA-Seq) and fitness (Tn-Seq) allows two views of the same genetic network underlying these responses. However, it remains unclear how they combine, enabling a bacterium to overcome a perturbation.ResultsHere we generate RNA-Seq and Tn-Seq profiles in three strains of S. pneumoniae in response to stress defined by different levels of nutrient depletion. These profiles show that genes that change their expression and/or become phenotypically important come from a diverse set of functional categories, and genes that are phenotypically important tend to be highly expressed. Surprisingly, we find that expression and fitness changes rarely occur on the same gene, which we confirmed by over 140 validation experiments. To rationalize these unexpected results we built the first genome-scale metabolic model of S. pneumoniae showing that differential expression and phenotypic importance actually correlate between nearest neighbors, although they are distinctly partitioned into small subnetworks. Moreover, a meta-analysis of 234 S. pneumoniae gene expression studies reveals that essential genes and phenotypically important subnetworks rarely change expression, indicating that they are shielded from transcriptional fluctuations and that a clear distinction exists between transcriptional and phenotypic response networks.ConclusionsWe present a genome-wide computational/experimental approach that contextualizes changes that occur on transcriptomic and phenomic levels in response to stress. Importantly, this highlights the need to connect disparate response networks, for instance in antibiotic target identification, where preferred targets are phenotypically important genes that would be overlooked by transcriptomic analyses alone.

scholarly journals Sex-specific expression and DNA methylation in a species with extreme sexual dimorphism and paternal genome elimination

2020 ◽  
Author(s):  
Stevie A. Bain ◽  
Hollie Marshall ◽  
Laura Ross
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Alternative Splicing ◽  
Sexual Dimorphism ◽  
Planococcus Citri ◽  
Specific Gene ◽  
Paternal Genome ◽  
Specific Expression ◽  
Cis Acting ◽  
Genome Wide

AbstractSexual dimorphism is exhibited in many species across the tree of life with many phenotypic differences mediated by differential expression and alternative splicing of genes present in both sexes. However, the mechanisms that regulate these sex-specific expression and splicing patterns remain poorly understood. The mealybug, Planococcus citri, displays extreme sexual dimorphism and exhibits an unusual instance of sex-specific genomic imprinting, Paternal Genome Elimination (PGE), in which the paternal chromosomes in males are highly condensed and eliminated from the sperm. P. citri also has no sex chromosomes and as such both sexual dimorphism and PGE are predicted to be under epigenetic control. We recently showed that P. citri females display a highly unusual DNA methylation profile for an insect species, with the presence of promoter methylation associated with lower levels of gene expression. In this study we therefore decided to explore genome-wide differences in DNA methylation between male and female P. citri using whole genome bisulfite sequencing. We have identified extreme differences in genome-wide levels and patterns between the sexes. Males display overall higher levels of DNA methylation which manifests as more uniform low-levels across the genome. Whereas females display more targeted high levels of methylation. We suggest these unique sex-specific differences are due to chromosomal differences caused by PGE and may be linked to possible ploidy compensation. Using RNA-Seq we identified extensive sex-specific gene expression and alternative splicing. We found cis-acting DNA methylation is not directly associated with differentially expressed or differentially spliced genes, indicating a broader role for chromosome-wide trans-acting DNA methylation in this species.

scholarly journals Genome-wide identification and expression analysis of the xyloglucan endotransglucosylase/hydrolase gene family in poplar

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zihan Cheng ◽  
Xuemei Zhang ◽  
Wenjing Yao ◽  
Yuan Gao ◽  
Kai Zhao ◽  
...  
Keyword(s):  
Salt Stress ◽  
Stress Responses ◽  
Tissue Specificity ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Rna Seq ◽  
Salt Stress Response ◽  
Populus Simonii ◽  
Cis Acting ◽  
Genome Wide

Abstract Background Xyloglucan endotransglucosylase/hydrolase (XTH) family plays an important role in cell wall reconstruction and stress resistance in plants. However, the detailed characteristics of XTH family genes and their expression pattern under salt stress have not been reported in poplar. Results In this study, a total of 43 PtrXTH genes were identified from Populus simonii × Populus nigra, and most of them contain two conserved structures (Glyco_hydro_16 and XET_C domain). The promoters of the PtrXTH genes contain mutiple cis-acting elements related to growth and development and stress responses. Collinearity analysis revealed that the XTH genes from poplar has an evolutionary relationship with other six species, including Eucalyptus robusta, Solanum lycopersicum, Glycine max, Arabidopsis, Zea mays and Oryza sativa. Based on RNA-Seq analysis, the PtrXTH genes have different expression patterns in the roots, stems and leaves, and many of them are highly expressed in the roots. In addition, there are11 differentially expressed PtrXTH genes in the roots, 9 in the stems, and 7 in the leaves under salt stress. In addition, the accuracy of RNA-Seq results was verified by RT-qPCR. Conclusion All the results indicated that XTH family genes may play an important role in tissue specificity and salt stress response. This study will lay a theoretical foundation for further study on molecular function of XTH genes in poplar.

scholarly journals Genome-wide Identification and Expression Analysis of the Eyloglucan Endotransglucosylase/hydrolase Gene Family in Poplar

2021 ◽  
Author(s):  
Zihan Cheng ◽  
Xuemei Zhang ◽  
Wenjing Yao ◽  
Yuan Gao ◽  
Kai Zhao ◽  
...  
Keyword(s):  
Salt Stress ◽  
Plant Cell Wall ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Rna Seq ◽  
Promoter Regions ◽  
Salt Stress Response ◽  
Populus Simonii ◽  
Cis Acting ◽  
Genome Wide

Abstract Background: Xyloglucan endotransglucosylase/hydrolase (XTH) plays an important role in the process of plant cell wall reconstruction, and also involved in plants stress resistance. However, its characteristics of XTH family genes have not been reported in poplar. Results: In this study, we found 43 PtrXTH genes from Populus simonii × Populus nigra, and most of them contain two conserved structures (Glyco_hydro_16 and XET_C domain). The promoter regions of the PtrXTH genes contain many cis-acting elements related to growth and development and adverse stresses responses. Collinearity analysis revealed that the XTH family from poplarhave an evolutionary relationship with other five species, including Eucalyptus robusta, Solanum lycopersicum, Glycine max, Arabidopsis, Zea mays and Oryza sativa. Through RNA-Seq analysis, we found that the PtrXTH genes have different expression patterns in the roots, stems and leaves, and many of them are highly expressed in the roots. In addition, we found 11 differentially expressed PtrXTH genes in the roots, 9 in the stems, and 7 in the leaves under salt stress, and verified the accuracy of RNA-Seq analysis by RT-qPCR.Conclusion: All the results indicated that XTH family genes may play an important role in tissue specificity and salt stress response. This study laid a theoretical foundation for further study on the functions of XTH genes in poplar.

scholarly journals Genome-wide identification and characterization of the OFP gene family in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10934
Author(s):  
Ruihua Wang ◽  
Taili Han ◽  
Jifeng Sun ◽  
Ligong Xu ◽  
Jingjing Fan ◽  
...  
Keyword(s):  
Gene Family ◽  
Brassica Rapa ◽  
Expression Patterns ◽  
Structural Evolution ◽  
Amino Acid Residues ◽  
Rna Seq ◽  
Cis Acting ◽  
Genome Wide ◽  
Genome Triplication

Ovate family proteins (OFPs) are a class of proteins with a conserved OVATE domain that contains approximately 70 amino acid residues. OFP proteins are plant-specific transcription factors that participate in regulating plant growth and development and are widely distributed in many plants. Little is known about OFPs in Brassica rapa to date. We identified 29 OFP genes in Brassica rapa and found that they were unevenly distributed on 10 chromosomes. Intron gain events may have occurred during the structural evolution of BraOFP paralogues. Syntenic analysis verified Brassica genome triplication, and whole genome duplication likely contributed to the expansion of the OFP gene family. All BraOFP genes had light responsive- and phytohormone-related cis-acting elements. Expression analysis from RNA-Seq data indicated that there were obvious changes in the expression levels of six OFP genes in the Brassica rapa hybrid, which may contribute to the formation of heterosis. Finally, we found that the paralogous genes had different expression patterns among the hybrid and its parents. These results provide the theoretical basis for the further analysis of the biological functions of OFP genes across the Brassica species.

scholarly journals Novel lincRNA Discovery and Tissue-Specific Gene Expression across 30 Normal Human Tissues

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 614
Author(s):  
Xianfeng Chen ◽  
Zhifu Sun
Keyword(s):  
Brain Regions ◽  
Tissue Type ◽  
Specific Gene ◽  
The Novel ◽  
Rna Seq ◽  
Specific Expression ◽  
Tissue Specific ◽  
Genome Wide ◽  
Gene Transcripts ◽  
Normal Human

Long non-coding RNAs (lncRNAs) are a large class of gene transcripts that do not code proteins; however, their functions are largely unknown and many new lncRNAs are yet to be discovered. Taking advantage of our previously developed, super-fast, novel lncRNA discovery pipeline, UClncR, and rich resources of GTEx RNA-seq data, we performed systematic novel lincRNA discovery for over 8000 samples across 30 tissue types. We conducted novel detection for each major tissue type first and then consolidated the novel discoveries from all tissue types. These novel lincRNs were profiled and analyzed along with known genes to identify tissue-specific genes in 30 major human tissue types. Thirteen sub-brain regions were also analyzed in a similar manner. Our analysis revealed thousands to tens of thousands of novel lincRNAs for each tissue type. These lincRNAs could define each tissue type’s identity and demonstrated their reliability and tissue-specific expression. Tissue-specific genes were identified for each major tissue type and sub-brain region. The tissue-specific genes clearly defined each respective tissue’s unique function and could be used to expand the interpretation of non-coding SNPs from genome-wide association (GWAS) studies.

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