Genome-wide analysis of PRR gene family uncovers their roles in circadian rhythmic changes and response to drought stress in Gossypium hirsutum L.

Background The circadian clock not only participates in regulating various stages of plant growth, development and metabolism, but confers plant environmental adaptability to stress such as drought. Pseudo-Response Regulators (PRRs) are important component of the central oscillator (the core of circadian clock) and play a significant role in plant photoperiod pathway. However, no systematical study about this gene family has been performed in cotton. Methods PRR genes were identified in diploid and tetraploid cotton using bioinformatics methods to investigate their homology, duplication and evolution relationship. Differential gene expression, KEGG enrichment analysis and qRT-PCR were conducted to analyze PRR gene expression patterns under diurnal changes and their response to drought stress. Results A total of 44 PRR family members were identified in four Gossypium species, with 16 in G. hirsutum, 10 in G. raimondii, and nine in G. barbadense as well as in G. arboreum. Phylogenetic analysis indicated that PRR proteins were divided into five subfamilies and whole genome duplication or segmental duplication contributed to the expansion of Gossypium PRR gene family. Gene structure analysis revealed that members in the same clade are similar, and multiple cis-elements related to light and drought stress response were enriched in the promoters of GhPRR genes. qRT-PCR results showed that GhPRR genes transcripts presented four expression peaks (6 h, 9 h, 12 h, 15 h) during 24 h and form obvious rhythmic expression trend. Transcriptome data with PEG treatment, along with qRT-PCR verification suggested that members of clade III (GhPRR5a, b, d) and clade V (GhPRR3a and GhPRR3c) may be involved in drought response. This study provides an insight into understanding the function of PRR genes in circadian rhythm and in response to drought stress in cotton.

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Evolution of Acyl-CoA-binding protein gene family in plants provides insights into potential functions of grapevine (Vitis vinifera L.)

Journal of Berry Research ◽

10.3233/jbr-200528 ◽

2020 ◽

Vol 10 (4) ◽

pp. 677-696

Author(s):

Zhi-Gang Dong ◽

Hui Liu ◽

Xiao-Long Wang ◽

Jun Tang ◽

Kai-Kai Zhu ◽

...

Keyword(s):

Drought Stress ◽

Gene Family ◽

Microarray Data ◽

Expression Profiles ◽

Functional Divergence ◽

Expression Patterns ◽

Potential Functions ◽

Physiological Data ◽

Structural Annotation ◽

Qrt Pcr

BACKGROUND: Grapevine was one of the most important perennial fruit crops worldwide. Acyl-CoA-binding proteins (ACBPs) in eudicots and monocots show conservation in an acyl-CoA-binding domain (ACB domain) which binds acyl-CoA esters. OBJECTIVE: The information and data provided in the present study contributes to understand the evolutionary processes and potential functions of this gene family in grapevine growth and development, and responses to abiotic stress. METHODS: Using the complete grapevine genome sequences, we investigated the number grapevine ACBP genes, the exon-intron structure, phylogenetic relationships and synteny with the Arabidopsis ACBP gene family. Furthermore, the expression profiles of VvACBP genes based on public microarray data in different tissues, and the expression patterns responding to different exogenous hormones as well as abiotic and biotic stresses were presented. The qRT-PCR was used to verify the microarray data under drought stress treatments. Finally, the leaf relative water content (RWC), leaf chlorophyll content, and enzymatic activities were measured to further examine the tolerance to drought stress in grapevine. RESULTS: The six grapevine ACBPs were identified. Their distribution into various groups differed from Arabidopsis and rice. Synteny analysis demonstrated that several VvACBP genes were found in corresponding syntenic blocks of Arabidopsis, suggesting that these genes arose before the divergence of the respective lineages. Sequence alignment and structural annotation provided an overview of variations that might contribute to functional divergence from Arabidopsis ACBPs. Expressional analyses suggested that both conserved and variant biological functions exist in ACBPs across different species. The expression pattern of these genes were similar in the microarray and qRT-PCR analyses. Gene structure organization and expression characteristics of VvACBPs resembled those of their Arabidopsis orthologous, although species-specific differences also exist. Differential regulation of genes suggested functional diversification among isoforms. The biochemical and physiological data showed the tolerance to drought stress of grapevine. CONCLUSIONS: These findings provided insight into evolution of ACBP gene family in plants and a solid foundation for a deeper understanding of the complex molecular responses of grapevine to stress.

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Genome-wide analysis of BpDof genes and the tolerance to drought stress in birch (Betula platyphylla)

PeerJ ◽

10.7717/peerj.11938 ◽

2021 ◽

Vol 9 ◽

pp. e11938

Author(s):

Shilin Sun ◽

Bo Wang ◽

Qi Jiang ◽

Zhuoran Li ◽

Site Jia ◽

...

Keyword(s):

Drought Stress ◽

Gene Family ◽

Expression Patterns ◽

Structure Evolution ◽

Gene Gain ◽

Betula Platyphylla ◽

Ros Scavenging ◽

Promoter Regions ◽

Chromosomal Distribution ◽

Qrt Pcr

Background DNA binding with one finger (Dof) proteins are plant-specific transcription factors playing vital roles in developmental processes and stress responses in plants. Nevertheless, the characterizations, expression patterns, and functions of the Dof family under drought stress (a key determinant of plant physiology and metabolic homeostasis) in woody plants remain unclear. Methods The birch (Betula platyphylla var. mandshuric) genome and plant TFDB database were used to identify Dof gene family members in birch plants. ClustalW2 of BioEdit v7.2.1, MEGA v7.0, ExPASy ProtParam tool, Subloc, TMHMM v2.0, GSDS v2.0, MEME, TBtools, KaKs Calculator v2.0, and PlantCARE were respectively used to align the BpDof sequences, build a phylogenetic tree, identify the physicochemical properties, analyze the chromosomal distribution and synteny, and identify the cis-elements in the promoter regions of the 26 BpDof genes. Additionally, the birch seedlings were exposed to PEG6000-simulated drought stress, and the expression patterns of the BpDof genes in different tissues were analyzed by qRT-PCR. The histochemical staining and the evaluation of physiological indexes were performed to assess the plant tolerance to drought with transient overexpression of BpDof4, BpDof11, and BpDof17 genes. SPSS software and ANOVA were used to conduct all statistical analyses and determine statistically significant differences between results. Results A total of 26 BpDof genes were identified in birch via whole-genome analysis. The conserved Dof domain with a C(x)2C(x)21C(x)2C zinc finger motif was present in all BpDof proteins. These birch BpDofs were classified into four groups (A to D) according to the phylogenetic analysis of Arabidopsis thaliana Dof genes. BpDof proteins within the same group mostly possessed similar motifs, as detected by conserved motif analysis. The exon–intron analysis revealed that the structures of BpDof genes differed, indicating probable gene gain and lose during the BpDof evolution. The chromosomal distribution and synteny analysis showed that the 26 BpDofs were unevenly distributed on 14 chromosomes, and seven duplication events among six chromosomes were found. Cis-acting elements were abundant in the promoter regions of the 26 BpDof genes. qRT-PCR revealed that the expression of the 26 BpDof genes was differentially regulated by drought stress among roots, stems, and leaves. Most BpDof genes responded to drought stress, and BpDof4, BpDof11, and BpDof17 were significantly up-regulated. Therefore, plants overexpressing these three genes were generated to investigate drought stress tolerance. The BpDof4-, BpDof11-, and BpDof17-overexpressing plants showed promoted reactive oxygen species (ROS) scavenging capabilities and less severe cell damage, suggesting that they conferred enhanced drought tolerance in birch. This study provided an in-depth insight into the structure, evolution, expression, and function of the Dof gene family in plants.

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Analysis of Transcriptional Changes in Different Brassica napus Synthetic Allopolyploids

Genes ◽

10.3390/genes12010082 ◽

2021 ◽

Vol 12 (1) ◽

pp. 82

Author(s):

Yunxiao Wei ◽

Guoliang Li ◽

Shujiang Zhang ◽

Shifan Zhang ◽

Hui Zhang ◽

...

Keyword(s):

Gene Expression ◽

Brassica Napus ◽

Differentially Expressed Genes ◽

Expression Patterns ◽

Female Parent ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Transcriptional Changes ◽

Aa Genome ◽

High Degree

Allopolyploidy is an evolutionary and mechanistically intriguing process involving the reconciliation of two or more sets of diverged genomes and regulatory interactions, resulting in new phenotypes. In this study, we explored the gene expression patterns of eight F2 synthetic Brassica napus using RNA sequencing. We found that B. napus allopolyploid formation was accompanied by extensive changes in gene expression. A comparison between F2 and the parent shows a certain proportion of differentially expressed genes (DEG) and activation\silent gene, and the two genomes (female parent (AA)\male parent (CC) genomes) showed significant differences in response to whole-genome duplication (WGD); non-additively expressed genes represented a small portion, while Gene Ontology (GO) enrichment analysis showed that it played an important role in responding to WGD. Besides, genome-wide expression level dominance (ELD) was biased toward the AA genome, and the parental expression pattern of most genes showed a high degree of conservation. Moreover, gene expression showed differences among eight individuals and was consistent with the results of a cluster analysis of traits. Furthermore, the differential expression of waxy synthetic pathways and flowering pathway genes could explain the performance of traits. Collectively, gene expression of the newly formed allopolyploid changed dramatically, and this was different among the selfing offspring, which could be a prominent cause of the trait separation. Our data provide novel insights into the relationship between the expression of differentially expressed genes and trait segregation and provide clues into the evolution of allopolyploids.

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GENECFE-ANFIS: A NEURO-FUZZY INFERENCE SYSTEM TO INFER GENE-GENE INTERACTIONS BASED ON RECOGNITION OF MICROARRAY GENE EXPRESSION PATTERNS

Biomedical Engineering Applications Basis and Communications ◽

10.4015/s1016237207000112 ◽

2007 ◽

Vol 19 (02) ◽

pp. 71-78 ◽

Cited By ~ 1

Author(s):

Cheng-Long Chuang ◽

Chung-Ming Chen ◽

Grace S. Shieh ◽

Joe-Air Jiang

Keyword(s):

Gene Expression ◽

Fuzzy Inference System ◽

Fuzzy Inference ◽

Expression Patterns ◽

Gene Interactions ◽

Microarray Gene Expression ◽

Inference System ◽

Qrt Pcr ◽

Neuro Fuzzy ◽

Microarray Gene

A neuro-fuzzy inference system that recognizes the expression patterns of genes in microarray gene expression (MGE) data, called GeneCFE-ANFIS, is proposed to infer gene interactions. In this study, three primary features are utilized to extract genes' expression patterns and used as inputs to the neuro-fuzzy inference system. The proposed algorithm learns expression patterns from the known genetic interactions, such as the interactions confirmed by qRT-PCR experiments or collected through text-mining technique by surveying previously published literatures, and then predicts other gene interactions according to the learned patterns. The proposed neuro-fuzzy inference system was applied to a public yeast MGE dataset. Two simulations were conducted and checked against 112 pairs of qRT-PCR confirmed gene interactions and 77 TFs (Transcriptional Factors) pairs collected from literature respectively to evaluate the performance of the proposed algorithm.

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Stability of the Synechococcus elongatus PCC 7942 circadian clock under directed anti-phase expression of the kai genes

Microbiology ◽

10.1099/mic.0.28030-0 ◽

2005 ◽

Vol 151 (8) ◽

pp. 2605-2613 ◽

Cited By ~ 33

Author(s):

Jayna L. Ditty ◽

Shannon R. Canales ◽

Breanne E. Anderson ◽

Stanly B. Williams ◽

Susan S. Golden

Keyword(s):

Circadian Clock ◽

Expression Patterns ◽

Phase Relationship ◽

Synechococcus Elongatus ◽

Cycle Period ◽

Rhythmic Expression ◽

Core Components ◽

Synechococcus Elongatus Pcc 7942 ◽

Time Required ◽

Pcc 7942

The kaiA, kaiB and kaiC genes encode the core components of the cyanobacterial circadian clock in Synechococcus elongatus PCC 7942. Rhythmic expression patterns of kaiA and of the kaiBC operon normally peak in synchrony. In some mutants the relative timing of peaks (phase relationship) between these transcription units is altered, but circadian rhythms persist robustly. In this study, the importance of the transcriptional timing of kai genes was examined. Expressing either kaiA or kaiBC from a heterologous promoter whose peak expression occurs 12 h out of phase from the norm, and thus 12 h out of phase from the other kai locus, did not affect the time required for one cycle (period) or phase of the circadian rhythm, as measured by bioluminescence reporters. Furthermore, the data confirm that specific cis elements within the promoters of the kai genes are not necessary to sustain clock function.

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Genome-Wide Gene Expression Profiles Analysis Reveal Novel Insights into Drought Stress in Foxtail Millet (Setaria italica L.)

International Journal of Molecular Sciences ◽

10.3390/ijms21228520 ◽

2020 ◽

Vol 21 (22) ◽

pp. 8520

Author(s):

Ling Qin ◽

Erying Chen ◽

Feifei Li ◽

Xiao Yu ◽

Zhenyu Liu ◽

...

Keyword(s):

Gene Expression ◽

Signal Transduction ◽

Drought Stress ◽

Expression Profiles ◽

Expression Patterns ◽

Foxtail Millet ◽

Gene Expression Profiles ◽

Sugar Metabolism ◽

Setaria Italica ◽

Phenylpropanoid Biosynthesis

Foxtail millet (Setaria italica (L.) P. Beauv) is an important food and forage crop because of its health benefits and adaptation to drought stress; however, reports of transcriptomic analysis of genes responding to re-watering after drought stress in foxtail millet are rare. The present study evaluated physiological parameters, such as proline content, p5cs enzyme activity, anti-oxidation enzyme activities, and investigated gene expression patterns using RNA sequencing of the drought-tolerant foxtail millet variety (Jigu 16) treated with drought stress and rehydration. The results indicated that drought stress-responsive genes were related to many multiple metabolic processes, such as photosynthesis, signal transduction, phenylpropanoid biosynthesis, starch and sucrose metabolism, and osmotic adjustment. Furthermore, the Δ1-pyrroline-5-carboxylate synthetase genes, SiP5CS1 and SiP5CS2, were remarkably upregulated in foxtail millet under drought stress conditions. Foxtail millet can also recover well on rehydration after drought stress through gene regulation. Our data demonstrate that recovery on rehydration primarily involves proline metabolism, sugar metabolism, hormone signal transduction, water transport, and detoxification, plus reversal of the expression direction of most drought-responsive genes. Our results provided a detailed description of the comparative transcriptome response of foxtail millet variety Jigu 16 under drought and rehydration environments. Furthermore, we identify SiP5CS2 as an important gene likely involved in the drought tolerance of foxtail millet.

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The Circadian NAD+Metabolism: Impact on Chromatin Remodeling and Aging

BioMed Research International ◽

10.1155/2016/3208429 ◽

2016 ◽

Vol 2016 ◽

pp. 1-7 ◽

Cited By ~ 11

Author(s):

Yasukazu Nakahata ◽

Yasumasa Bessho

Keyword(s):

Gene Expression ◽

Circadian Clock ◽

Cell Fate ◽

Chromatin Remodeling ◽

Expression Patterns ◽

Fine Tuning ◽

Cellular Functions ◽

Nad Metabolism ◽

Structure Changes ◽

Age Related

Gene expression is known to be a stochastic phenomenon. The stochastic gene expression rate is thought to be altered by topological change of chromosome and/or by chromatin modifications such as acetylation and methylation. Changes in mechanical properties of chromosome/chromatin by soluble factors, mechanical stresses from the environment, or metabolites determine cell fate, regulate cellular functions, or maintain cellular homeostasis. Circadian clock, which drives the expression of thousands of genes with 24-hour rhythmicity, has been known to be indispensable for maintaining cellular functions/homeostasis. During the last decade, it has been demonstrated that chromatin also undergoes modifications with 24-hour rhythmicity and facilitates the fine-tuning of circadian gene expression patterns. In this review, we cover data which suggests that chromatin structure changes in a circadian manner and that NAD+is the key metabolite for circadian chromatin remodeling. Furthermore, we discuss the relationship among circadian clock, NAD+metabolism, and aging/age-related diseases. In addition, the interventions of NAD+metabolism for the prevention and treatment of aging and age-related diseases are also discussed.

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Identification and Expression Analysis of the PIN and AUX/LAX Gene Families in Ramie (Boehmeria nivea L. Gaud)

Agronomy ◽

10.3390/agronomy9080435 ◽

2019 ◽

Vol 9 (8) ◽

pp. 435 ◽

Cited By ~ 2

Author(s):

Yaning Bao ◽

Xing Huang ◽

Muzammal Rehman ◽

Yunhe Wang ◽

Bo Wang ◽

...

Keyword(s):

Drought Stress ◽

Auxin Transport ◽

Expression Patterns ◽

Gene Families ◽

Ramie Fiber ◽

Biological Functions ◽

Qrt Pcr ◽

Boehmeria Nivea ◽

Auxin Distribution ◽

Indole 3 Acetic Acid

Auxin regulates diverse aspects of growth and development. Furthermore, polar auxin transport, which is mediated by the PIN-FORMED (PIN) and AUXIN1/LIKE-AUX (AUX/LAX) proteins, plays a crucial role in auxin distribution. In this study, six PIN and four AUX/LAX genes were identified in ramie (Boehmeria nivea L.). We used qRT-PCR to characterize and analyze the two gene families, including phylogenetic relationships, intron/exon structures, cis-elements, subcellular localization, and the expression patterns in different tissues. The expression of these genes in response to indole-3-acetic acid (IAA) treatment and drought stress was also assessed; the results indicate that most of the BnAUX/LAX and BnPIN genes were regulated as a result of IAA treatment and drought stress. Our study provides insights into ramie auxin transporters and lays the foundation for further analysis of their biological functions in ramie fiber development and adaptation to environmental stresses.

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Genome-wide characterization and expression analysis of the Dof gene family related to abiotic stress in watermelon

10.7287/peerj.preprints.27819 ◽

2019 ◽

Author(s):

Yong Zhou ◽

Yuan Cheng ◽

Chunpeng Wan ◽

Youxin Yang ◽

Jinyin Chen

Keyword(s):

Phylogenetic Analysis ◽

Gene Family ◽

Expression Patterns ◽

Future Research ◽

Biological Processes ◽

Biological Functions ◽

Specific Expression ◽

Qrt Pcr ◽

Genome Wide ◽

Intron Structure

The plant DNA-binding with one finger (Dof) gene family is a class of plant-specific transcription factors that play vital roles in many biological processes and response to stresses. In the present study, a total of 36 ClDof genes were identified in the watermelon genome, which were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that the ClDof proteins could be divided into nine groups, and the members in a particular group had similar motif arrangement and exon-intron structure. We then analyzed the expression patterns of nine selected ClDof genes in eight specific tissues by qRT-PCR, and the results showed that they have tissue-specific expression patterns. We also evaluated the expression levels of the nine selected ClDof genes under salt stress and ABA treatments using qRT-PCR, and they showed differential expression under these treatments, suggesting their important roles in stress response. Taken together, our results provide a basis for future research on the biological functions of Dof genes in watermelon.

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CbPLDγ gene from Chorispora bungeana: Gene cloning, characterization, expression, and expression analysis in drought

10.21203/rs.3.rs-61719/v1 ◽

2020 ◽

Author(s):

Ning Yang ◽

Bo Liu ◽

Pengjun Yang ◽

Hui Li ◽

Yaping Zhou

Keyword(s):

Drought Stress ◽

Gene Family ◽

Imaging System ◽

Subcellular Localisation ◽

Wild Type ◽

Bioinformatics Analyses ◽

Real Time Quantitative Pcr ◽

Qrt Pcr ◽

Chorispora Bungeana ◽

Vector Construction

Abstract Background: Chorispora bungeana (C. bungeana) is a typical subnival alpine species, which shows high tolerance to multiple abiotic stresses. Phospholipase D (PLD) is a crucial enzyme participated in membrane phospholipid catabolism. In this study, to explore the function of CbPLDγ in drought stress, we cloned and characterized a CbPLDγ gene, which is a part of CbPLD gene family and from C. bungeana.Methods: Use the gateway method for vector construction, using DNAstar software, PCR machine, centrifuge, pipette, electrophoresis, gel imaging system, spectrophotometer, confocal microscope, etc. Spss, Orgin software for statistical analysis.Results: The CbPLDγ gene encodes 859 amino acids containing "FIYIENQYF" domain and two HKD domains. Bioinformatics analyses showed that the CbPLDγ is highly homologous with PLDs from other plant species. Real-time quantitative PCR (qRT-PCR) and Beta-glucuronidase (GUS) assay showed that CbPLDγ was accumulated dominantly in roots and stems. Compered with the control, the expression pattern of the CbPLDγ mRNA is in response to low temperature, salt, mannitol, and exogenous ABA have up-regulated. Subcellular localisation analysis showed that the CbPLDγ was localized in the cell membrane. Compared with wild-type Arabidopsis thaliana, CbPLDγ gene overexpression plants showed higher activities of antioxidant enzymes, and lower levels of malonidiadehyde content and electrolyte leakage under drought stress.Conclusions: In this study, novel PLDγ gene was amplification from C. bungeana and was called CbPLDγ. These confirmed that CbPLDγ involved in the response to drought stress, and has the potential to improve the drought tolerance of plants. This is the first report about cloning and characterizing the gene of CbPLDγ from C. bungeana. It laid a foundation for further research and improvement of the PLD gene family of C. bungeana.

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