Transcriptome-Wide Identification and Expression Profiling of SPX Domain-Containing Members in Responses to Phosphorus Deprivation of Pinus massoniana

The SPX domain-encoding proteins are believed to play important roles in phosphorus (Pi) homeostasis and signal transduction in plants. However, the overall information and responses of SPXs to phosphorus deficiency in pines, remain undefined. In this study, we screened the transcriptome data of Pinus massoniana in response to phosphorus deprivation. Ten SPX domain-containing genes were identified. Based on the conserved domains, the P. massoniana SPX genes were divided into four different subfamilies: SPX, SPX-MFS, SPX-EXS, and SPX-RING. RNA-seq analysis revealed that PmSPX genes were differentially expressed in response to phosphorus deprivation. Furthermore, real-time quantitative PCR (RT-qPCR) showed that PmSPX1 and PmSPX4 showed different expression patterns in different tissues under phosphorus stress. The promoter sequence of 2284 bp upstream of PmSPX1 was obtained by the genome walking method. A cis-element analysis indicated that there were several phosphorus stress response-related elements (e.g., two P1BS elements, a PHO element, and a W-box) in the promoter of PmSPX1. In addition, the previously obtained PmSPX2 promoter sequence contained a W-box, and it was shown that PmWRKY75 could directly bind to the PmSPX2 promoter using yeast one-hybrid analysis in this study. These results presented here revealed the foundational functions of PmSPXs in maintaining plant phosphorus homeostasis.

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Comprehensive Analysis of the TIFY Gene Family and Its Expression Profiles under Phytohormone Treatment and Abiotic Stresses in Roots of Populus trichocarpa

Forests ◽

10.3390/f11030315 ◽

2020 ◽

Vol 11 (3) ◽

pp. 315

Author(s):

Hanzeng Wang ◽

Xue Leng ◽

Xuemei Xu ◽

Chenghao Li

Keyword(s):

Gene Family ◽

Abiotic Stresses ◽

Expression Profiles ◽

Populus Trichocarpa ◽

Expression Patterns ◽

Interaction Network ◽

Pcr Analysis ◽

Phylogenetic Tree Analysis ◽

Element Analysis ◽

Cis Element

The TIFY gene family is specific to land plants, exerting immense influence on plant growth and development as well as responses to biotic and abiotic stresses. Here, we identify 25 TIFY genes in the poplar (Populus trichocarpa) genome. Phylogenetic tree analysis revealed these PtrTIFY genes were divided into four subfamilies within two groups. Promoter cis-element analysis indicated most PtrTIFY genes possess stress- and phytohormone-related cis-elements. Quantitative real-time reverse transcription polymerase chain reaction (qRT–PCR) analysis showed that PtrTIFY genes displayed different expression patterns in roots under abscisic acid, methyl jasmonate, and salicylic acid treatments, and drought, heat, and cold stresses. The protein interaction network indicated that members of the PtrTIFY family may interact with COI1, MYC2/3, and NINJA. Our results provide important information and new insights into the evolution and functions of TIFY genes in P. trichocarpa.

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Genome-Wide Identification of the LAC Gene Family and Its Expression Analysis Under Stress in Brassica napus

Molecules ◽

10.3390/molecules24101985 ◽

2019 ◽

Vol 24 (10) ◽

pp. 1985 ◽

Cited By ~ 3

Author(s):

Xiaoke Ping ◽

Tengyue Wang ◽

Na Lin ◽

Feifei Di ◽

Yangyang Li ◽

...

Keyword(s):

Brassica Napus ◽

Gene Family ◽

Vital Role ◽

Gene Family Evolution ◽

Rna Seq ◽

Chain Reaction ◽

Element Analysis ◽

Cis Element ◽

Genome Wide ◽

Polymerase Chain

Lignin is an important biological polymer in plants that is necessary for plant secondary cell wall ontogenesis. The laccase (LAC) gene family catalyzes lignification and has been suggested to play a vital role in the plant kingdom. In this study, we identified 45 LAC genes from the Brassica napus genome (BnLACs), 25 LAC genes from the Brassica rapa genome (BrLACs) and 8 LAC genes from the Brassica oleracea genome (BoLACs). These LAC genes could be divided into five groups in a cladogram and members in same group had similar structures and conserved motifs. All BnLACs contained hormone- and stress- related elements determined by cis-element analysis. The expression of BnLACs was relatively higher in the root, seed coat and stem than in other tissues. Furthermore, BnLAC4 and its predicted downstream genes showed earlier expression in the silique pericarps of short silique lines than long silique lines. Three miRNAs (miR397a, miR397b and miR6034) target 11 BnLACs were also predicted. The expression changes of BnLACs under series of stresses were further investigated by RNA sequencing (RNA-seq) and quantitative real-time polymerase chain reaction (qRT-PCR). The study will give a deeper understanding of the LAC gene family evolution and functions in B. napus.

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Characterization and expression analysis of the SPL gene family during floral development and abiotic stress in pecan (Carya illinoinensis)

PeerJ ◽

10.7717/peerj.12490 ◽

2021 ◽

Vol 9 ◽

pp. e12490

Author(s):

Min Wang ◽

Zhenghai Mo ◽

Ruozhu Lin ◽

Cancan Zhu

Keyword(s):

Fruit Development ◽

Expression Profiles ◽

Expression Patterns ◽

Element Analysis ◽

Systematic Analysis ◽

Cis Element ◽

Gene Pairs ◽

Spatiotemporal Expression ◽

Squamosa Promoter Binding Protein ◽

Flower And Fruit Development

SQUAMOSA promoter binding protein-like (SPL) genes are a type of plant-specific transcription factors that play crucial roles in the regulation of phase transition, floral transformation, fruit development, and various stresses. Although SPLs have been characterized in several model species, no systematic analysis has been studied in pecans, an important woody oil tree species. In this study, a total of 32 SPL genes (CiSPLs) were identified in the pecan genome. After conducting phylogenetic analysis of the conserved SBP proteins from Arabidopsis, rice, and poplar, the CiSPLs were separated into eight subgroups. The CiSPL genes within the same subgroup contained very similar exon-intron structures and conserved motifs. Nine segmentally duplicated gene pairs in the pecan genome and 16 collinear gene pairs between the CiSPL and AtSPL genes were identified. Cis-element analysis showed that CiSPL genes may regulate plant meristem differentiation and seed development, participate in various biological processes, and respond to plant hormones and environmental stresses. Therefore, we focused our study on the expression profiles of CiSPL genes during flower and fruit development. Most of the CiSPL genes were predominantly expressed in buds and/or female flowers. Additionally, quantitative real time PCR (qRT-PCR) analyses confirmed that CiSPL genes showed distinct spatiotemporal expression patterns in response to drought and salt treatments. The study provides foundation for the further exploration of the function and evolution of SPL genes in pecan.

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Genome-Wide Identification and Expression Analysis of Udp-Glucuronosyltransferases in the Whitefly Bemisia Tabaci (Gennadius) (HemipterA: Aleyrodidae)

International Journal of Molecular Sciences ◽

10.3390/ijms21228492 ◽

2020 ◽

Vol 21 (22) ◽

pp. 8492

Author(s):

Litao Guo ◽

Wen Xie ◽

Zezhong Yang ◽

Jianping Xu ◽

Youjun Zhang

Keyword(s):

Bemisia Tabaci ◽

Developmental Stages ◽

Expression Patterns ◽

Host Adaptation ◽

Reproductive Capacity ◽

Uridine Diphosphate ◽

Rna Seq ◽

Future Studies ◽

Real Time Quantitative Pcr ◽

Genome Wide

Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is an important agricultural pest worldwide. Uridine diphosphate (UDP)-glucuronosyltransferases (UGTs) are one of the largest and most ubiquitous groups of proteins. Because of their role in detoxification, insect UGTs are attracting increasing attention. In this study, we identified and analyzed UGT genes in B. tabaci MEAM1 to investigate their potential roles in host adaptation and reproductive capacity. Based on phylogenetic and structural analyses, we identified 76 UGT genes in the B. tabaci MEAM1 genome. RNA-seq and real-time quantitative PCR (RT-qPCR) revealed differential expression patterns of these genes at different developmental stages and in association with four host plants (cabbage, cucumber, cotton and tomato). RNA interference results of selected UGTs showed that, when UGT352A1, UGT352B1, and UGT354A1 were respectively silenced by feeding on dsRNA, the fecundity of B. tabaci MEAM1 was reduced, suggesting that the expressions of these three UGT genes in this species may be associated with host-related fecundity. Together, our results provide detailed UGTs data in B.tabaci and help guide future studies on the mechanisms of host adaptation by B.tabaci.

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Comprehensive Genomic Characterization and Expression Analysis of the Lipoxygenase Gene Family in Watermelon under Hormonal Treatments

Agriculture ◽

10.3390/agriculture10100429 ◽

2020 ◽

Vol 10 (10) ◽

pp. 429

Author(s):

Jianping Liu ◽

Yong Zhou ◽

Jingwen Li ◽

Feng Wang ◽

Youxin Yang

Keyword(s):

Gene Family ◽

Expression Patterns ◽

Protein Structures ◽

Promoter Regions ◽

Element Analysis ◽

Cis Element ◽

Genome Wide ◽

Genomic Characterization ◽

Gene Structures ◽

Lipoxygenase Gene Family

Lipoxygenases (LOXs) are non-haem iron-containing dioxygenases and play vital roles in a variety of plant biological processes. Here, we first carried out the genome-wide identification of LOX genes in watermelon. A total of 16 LOX genes were identified, which could be classified into two categories according to phylogenetic analysis: the 9-LOXs (ClLOX1–4, 12, and 15) and 13-LOXs (ClLOX5–11, 13, 14, and 16). Furthermore, the protein structures, intrachromosomal distributions, and gene structures were thoroughly analyzed. Cis-element analysis of the promoter regions indicated that the expression of ClLOX genes may be influenced by stress and plant hormones. Bioinformatic and expression analyses revealed that the expression of ClLOX genes is tissue-specific and hormone-responsive. The detected LOX genes exhibited distinctive expression patterns in various tissues. Different ClLOX genes showed different responses to methyl jasmonate (MeJA), salicylic acid (SA), and ethylene (ET) treatments, particularly ClLOX7, which exhibited the most active response to the above treatments. This study provides valuable information for a better understanding of the functions of LOX genes and further exploration of the LOX gene family in watermelon.

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Genome-wide identification and expression analysis of tomato ADK gene family during development and stress

10.21203/rs.3.rs-57426/v1 ◽

2020 ◽

Author(s):

Lu Yang ◽

Haohao Cao ◽

Xiaoping Zhang ◽

Liangxian Gui ◽

Qiang Chen ◽

...

Keyword(s):

Energy Homeostasis ◽

Functional Characterization ◽

Evolutionary Relationship ◽

Hormone Treatment ◽

Motif Analysis ◽

Element Analysis ◽

Real Time Quantitative Pcr ◽

Cis Element ◽

Genome Wide ◽

Relationship Of

Abstract Background: Adenylate kinase (ADK) is widely distributed in organisms and plays an important role in cellular energy homeostasis. In plants, ADK has important functions in plant growth and development regulation as well as adaptation to the environment. However, little information is available about the ADK genes in tomato (Solanum lycopersicum), an important economic crop.Results: To investigate the characteristics and functions of ADK genes in tomato, a total of 11 ADK genes were identified and named according to their chromosomal locations. The ADK family was divided into five groups and motif analysis revealed that each SlADK protein contained five to eight conserved motifs. Sequence analysis revealed 4-19 exons in all SlADKs and most members possessed four. The 11 SlADKs were randomly distributed on nine of the 12 tomato chromosomes. A cis-element analysis inferred that several stress response elements were found on the promoters of SlADKs. The online TomExpress platform prediction revealed that SlADKs were expressed in various tissues and organs, basically consistent with the data obtained from real-time quantitative PCR (qPCR). The qPCR verification was also used to determine the expression level of SlADKs and demonstrated that the genes responded to multiple abiotic stresses, such as drought, salt and cold. For example, almost all SlADKs contained two expression peaks at 9 and 48 h following salt treatment. The qPCR results showed that SlADK transcription was responsive to most of the applied hormone treatment: methyl jasmonate, ethylene, salicylic acid, indole 3-acetic acid and abscisic acid. Notably, SlADK2 and 4 exhibited significant changes under multiple stress treatments.Conclusions: These results provide valuable information for clarifying the evolutionary relationship of the tomato ADK family and in aiding functional characterization of SlADKs in further research.

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Differential expression analysis of genes in the root crown of alfalfa under low-temperature stress

10.21203/rs.2.17726/v1 ◽

2019 ◽

Author(s):

Xiaolong Wang ◽

Huiqing Jin ◽

Kai Meng ◽

Zhenyu Jia ◽

Shiyuan Yan ◽

...

Keyword(s):

Low Temperature ◽

Temperature Stress ◽

Expression Patterns ◽

Differential Expression Analysis ◽

Northern China ◽

Winter Hardiness ◽

Low Temperature Stress ◽

Rna Seq ◽

Real Time Quantitative Pcr ◽

Alfalfa Varieties

Abstract Background: Alfalfa ( Medicago sativa ) is a perennial forage crop widely cultivated in northern China. The root crown is an important storage organ of alfalfa, especially in the wintering process, as it is closely related to winter hardiness. However, the molecular mechanism underlying the winter hardiness of the alfalfa root crown remains unclear. To investigate these gaps in knowledge, the RNA sequencing (RNA-Seq) technology was used to identify critical genes related to winter hardiness. Results: In this study, the winter survival rate of the Lomgmu 806 variety was approximately 3.68-fold higher than that of the Sardi variety. We sequenced the transcriptomes of the root crown of the two alfalfa varieties. Among the 57,712 unigenes identified, 2,299 differentially expressed genes (DEGs) were upregulated, and 2,143 DEGs were downregulated. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotations showed that 1,159 unigenes were mainly annotated in 116 pathways. Seven DEGs belonging to the “plant hormone signalling transduction” pathway, the “peroxisome” pathway and transcription factor family (MYB, B3, AP2/ERF, and WRKY) and involved in alfalfa winter hardiness were identified. As a result, the expression patterns of seven DEGs were verified by real-time quantitative PCR (RT-qPCR) analyses, which verified the reliability of the RNA-Seq analyses. Conclusions: The RNA-Seq data revealed the gene regulation response of alfalfa to low-temperature stress, which provides a valuable resource for the further identification and functional analysis of candidate genes related to winter hardiness in alfalfa. Furthermore, these data provide references for future in-depth studies of winter hardiness mechanisms in alfalfa.

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Integration of transcriptomic data identifies key hallmark genes in hypertrophic cardiomyopathy

BMC Cardiovascular Disorders ◽

10.1186/s12872-021-02147-7 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Jing Xu ◽

Xiangdong Liu ◽

Qiming Dai

Keyword(s):

Machine Learning ◽

Hypertrophic Cardiomyopathy ◽

Heart Diseases ◽

Expression Patterns ◽

Support Vector ◽

Rna Seq ◽

Ppi Network ◽

Learning Methods ◽

Transcriptomic Data ◽

Machine Learning Methods

Abstract Background Hypertrophic cardiomyopathy (HCM) represents one of the most common inherited heart diseases. To identify key molecules involved in the development of HCM, gene expression patterns of the heart tissue samples in HCM patients from multiple microarray and RNA-seq platforms were investigated. Methods The significant genes were obtained through the intersection of two gene sets, corresponding to the identified differentially expressed genes (DEGs) within the microarray data and within the RNA-Seq data. Those genes were further ranked using minimum-Redundancy Maximum-Relevance feature selection algorithm. Moreover, the genes were assessed by three different machine learning methods for classification, including support vector machines, random forest and k-Nearest Neighbor. Results Outstanding results were achieved by taking exclusively the top eight genes of the ranking into consideration. Since the eight genes were identified as candidate HCM hallmark genes, the interactions between them and known HCM disease genes were explored through the protein–protein interaction (PPI) network. Most candidate HCM hallmark genes were found to have direct or indirect interactions with known HCM diseases genes in the PPI network, particularly the hub genes JAK2 and GADD45A. Conclusions This study highlights the transcriptomic data integration, in combination with machine learning methods, in providing insight into the key hallmark genes in the genetic etiology of HCM.

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Clustering Single-Cell RNA-Seq Data with Regularized Gaussian Graphical Model

Genes ◽

10.3390/genes12020311 ◽

2021 ◽

Vol 12 (2) ◽

pp. 311

Author(s):

Zhenqiu Liu

Keyword(s):

Single Cell ◽

Free Parameter ◽

Graphical Model ◽

Expression Patterns ◽

Information Criterion ◽

Log P ◽

Rna Seq ◽

Clustering Methods ◽

Wide Range ◽

Free Parameters

Single-cell RNA-seq (scRNA-seq) is a powerful tool to measure the expression patterns of individual cells and discover heterogeneity and functional diversity among cell populations. Due to variability, it is challenging to analyze such data efficiently. Many clustering methods have been developed using at least one free parameter. Different choices for free parameters may lead to substantially different visualizations and clusters. Tuning free parameters is also time consuming. Thus there is need for a simple, robust, and efficient clustering method. In this paper, we propose a new regularized Gaussian graphical clustering (RGGC) method for scRNA-seq data. RGGC is based on high-order (partial) correlations and subspace learning, and is robust over a wide-range of a regularized parameter λ. Therefore, we can simply set λ=2 or λ=log(p) for AIC (Akaike information criterion) or BIC (Bayesian information criterion) without cross-validation. Cell subpopulations are discovered by the Louvain community detection algorithm that determines the number of clusters automatically. There is no free parameter to be tuned with RGGC. When evaluated with simulated and benchmark scRNA-seq data sets against widely used methods, RGGC is computationally efficient and one of the top performers. It can detect inter-sample cell heterogeneity, when applied to glioblastoma scRNA-seq data.

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Transcriptome Analysis Reveals HgCl2 Induces Apoptotic Cell Death in Human Lung Carcinoma H1299 Cells through Caspase-3-Independent Pathway

International Journal of Molecular Sciences ◽

10.3390/ijms22042006 ◽

2021 ◽

Vol 22 (4) ◽

pp. 2006

Author(s):

Mi Jin Kim ◽

Jinhong Park ◽

Jinho Kim ◽

Ji-Young Kim ◽

Mi-Jin An ◽

...

Keyword(s):

Cell Cycle ◽

Cell Death ◽

Transcriptome Analysis ◽

Caspase 3 ◽

Apoptotic Cell ◽

Expression Patterns ◽

Nitrogen Compound ◽

Apoptotic Cell Death ◽

Mercury Chloride ◽

Rna Seq

Mercury is one of the detrimental toxicants that can be found in the environment and exists naturally in different forms; inorganic and organic. Human exposure to inorganic mercury, such as mercury chloride, occurs through air pollution, absorption of food or water, and personal care products. This study aimed to investigate the effect of HgCl2 on cell viability, cell cycle, apoptotic pathway, and alters of the transcriptome profiles in human non-small cell lung cancer cells, H1299. Our data show that HgCl2 treatment causes inhibition of cell growth via cell cycle arrest at G0/G1- and S-phase. In addition, HgCl2 induces apoptotic cell death through the caspase-3-independent pathway. Comprehensive transcriptome analysis using RNA-seq indicated that cellular nitrogen compound metabolic process, cellular metabolism, and translation for biological processes-related gene sets were significantly up- and downregulated by HgCl2 treatment. Interestingly, comparative gene expression patterns by RNA-seq indicated that mitochondrial ribosomal proteins were markedly altered by low-dose of HgCl2 treatment. Altogether, these data show that HgCl2 induces apoptotic cell death through the dysfunction of mitochondria.

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