scholarly journals Genome-wide identification and transcriptional expression analysis of superoxide dismutase (SOD) family in wheat (Triticum aestivum)

2018 ◽  
Author(s):  
Wenqiang J. Jiang ◽  
Lei Y. Yang ◽  
Yiqin H. He ◽  
Haotian Z. Zhang ◽  
Wei L. Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Phylogenetic Analyses ◽  
Composition Analysis ◽  
Distribution Analysis ◽  
Motif Analysis ◽  
Chromosomal Distribution ◽  
Critical Function ◽  
Genome Wide ◽  
A Genome ◽  
Sod Gene Family

Superoxide dismutases (SODs) are a key antioxidant enzyme family, which plays a critical function in plant growth and development. Previously, this gene family has been investigated in Arabidopsis and rice. In the present study, it was the first time for us to perform a genome-wide analysis of SOD gene family in wheat. And using bioinformatics-based methods, 26 SOD genes were identified from the whole genome of wheat, including 17 Cu/Zn-SODs, 6 Fe-SODs, and 3 Mn-SODs. The chromosomal distribution analysis revealed that SOD genes are only distributed on 2, 4 and 7 chromosomes of wheat. Phylogenetic analyses with SODs from wheat and several other species revealed that these SOD proteins can divided into two major categories. SOD1 is mainly composed of Cu/Zn-SODs, and SOD2 is mainly composed of Fe-SODs and Mn-SODs. Gene structure and motif analysis indicated that most of the SOD genes have relatively conserved exon/intron arrangement and motif composition. Analysis of transcriptional data indicated that most of the wheat SOD genes are expressed in almost all the tested tissues and it possibly have important function in abiotic stress. Taken together, our results provide a basis for further functional research on SOD gene family in wheat and facilitate their potential applications in the genetic improvement of wheat.

scholarly journals Genome-wide identification and transcriptional expression analysis of superoxide dismutase (SOD) family in wheat (Triticum aestivum)

2018 ◽  
Author(s):  
Wenqiang J. Jiang ◽  
Lei Y. Yang ◽  
Yiqin H. He ◽  
Haotian Z. Zhang ◽  
Wei L. Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Phylogenetic Analyses ◽  
Composition Analysis ◽  
Distribution Analysis ◽  
Motif Analysis ◽  
Chromosomal Distribution ◽  
Critical Function ◽  
Genome Wide ◽  
A Genome ◽  
Sod Gene Family

Superoxide dismutases (SODs) are a key antioxidant enzyme family, which plays a critical function in plant growth and development. Previously, this gene family has been investigated in Arabidopsis and rice. In the present study, it was the first time for us to perform a genome-wide analysis of SOD gene family in wheat. And using bioinformatics-based methods, 26 SOD genes were identified from the whole genome of wheat, including 17 Cu/Zn-SODs, 6 Fe-SODs, and 3 Mn-SODs. The chromosomal distribution analysis revealed that SOD genes are only distributed on 2, 4 and 7 chromosomes of wheat. Phylogenetic analyses with SODs from wheat and several other species revealed that these SOD proteins can divided into two major categories. SOD1 is mainly composed of Cu/Zn-SODs, and SOD2 is mainly composed of Fe-SODs and Mn-SODs. Gene structure and motif analysis indicated that most of the SOD genes have relatively conserved exon/intron arrangement and motif composition. Analysis of transcriptional data indicated that most of the wheat SOD genes are expressed in almost all the tested tissues and it possibly have important function in abiotic stress. Taken together, our results provide a basis for further functional research on SOD gene family in wheat and facilitate their potential applications in the genetic improvement of wheat.

scholarly journals Genome-wide identification and transcriptional expression analysis of superoxide dismutase (SOD) family in wheat (Triticum aestivum)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8062 ◽  
Author(s):  
Wenqiang Jiang ◽  
Lei Yang ◽  
Yiqin He ◽  
Haotian Zhang ◽  
Wei Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Phylogenetic Analyses ◽  
Pcr Analysis ◽  
Response Patterns ◽  
Qrt Pcr ◽  
Genome Wide ◽  
A Genome ◽  
Almost All ◽  
Location Mapping ◽  
Sod Gene Family

Superoxide dismutases (SODs) are a family of key antioxidant enzymes that play a crucial role in plant growth and development. Previously, this gene family has been investigated in Arabidopsis and rice. In the present study, a genome-wide analysis of the SOD gene family in wheat were performed. Twenty-six SOD genes were identified from the whole genome of wheat, including 17 Cu/Zn-SODs, six Fe-SODs, and three Mn-SODs. The chromosomal location mapping analysis indicated that these three types of SOD genes were only distributed on 2, 4, and 7 chromosomes, respectively. Phylogenetic analyses of wheat SODs and several other species revealed that these SOD proteins can be assigned to two major categories. SOD1 mainly comprises of Cu/Zn-SODs, and SOD2 mainly comprises of Fe-SODs and Mn-SODs. Gene structure and motif analyses indicated that most of the SOD genes showed a relatively conserved exon/intron arrangement and motif composition. Analyses of transcriptional data indicated that most of the wheat SOD genes were expressed in almost all of the examined tissues and had important functions in abiotic stress resistance. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) analysis was used to reveal the regulating roles of wheat SOD gene family in response to NaCl, mannitol, and polyethylene glycol stresses. qRT-PCR showed that eight randomly selected genes with relatively high expression levels responded to all three stresses based on released transcriptome data. However, their degree of response and response patterns were different. Interestingly, among these genes, TaSOD1.7, TaSOD1.9, TaSOD2.1, and TaSOD2.3 feature research value owing to their remarkable expression-fold change in leaves or roots under different stresses. Overall, our results provide a basis of further functional research on the SOD gene family in wheat and facilitate their potential use for applications in the genetic improvement on wheat in drought and salt stress environments.

scholarly journals Genome-Wide Characterization and Expression Profiles of the Superoxide Dismutase Gene Family inGossypium

2016 ◽  
Vol 2016 ◽  
pp. 1-11 ◽  
Author(s):  
Jingbo Zhang ◽  
Bo Li ◽  
Yang Yang ◽  
Wenran Hu ◽  
Fangyuan Chen ◽  
...  
Keyword(s):  
Superoxide Dismutase ◽  
Gene Family ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Distribution Analysis ◽  
Gossypium Arboreum ◽  
Genome Wide ◽  
A Genome ◽  
Gossypium Raimondii ◽  
Sod Gene Family

Superoxide dismutase (SOD) as a group of significant and ubiquitous enzymes plays a critical function in plant growth and development. Previously this gene family has been investigated inArabidopsisand rice; it has not yet been characterized in cotton. In our study, it was the first time for us to perform a genome-wide analysis of SOD gene family in cotton. Our results showed that 10 genes of SOD gene family were identified inGossypium arboreumandGossypium raimondii, including 6 Cu-Zn-SODs, 2 Fe-SODs, and 2 Mn-SODs. The chromosomal distribution analysis revealed that SOD genes are distributed across 7 chromosomes inGossypium arboreumand 8 chromosomes inGossypium raimondii. Segmental duplication is predominant duplication event and major contributor for expansion of SOD gene family. Gene structure and protein structure analysis showed that SOD genes have conserved exon/intron arrangement and motif composition. Microarray-based expression analysis revealed that SOD genes have important function in abiotic stress. Moreover, the tissue-specific expression profile reveals the functional divergence of SOD genes in different organs development of cotton. Taken together, this study has imparted new insights into the putative functions of SOD gene family in cotton. Findings of the present investigation could help in understanding the role of SOD gene family in various aspects of the life cycle of cotton.

scholarly journals Genome wide analysis of kinesin gene family in Citrullus lanatus reveals an essential role in early fruit development

2020 ◽  
Author(s):  
Shujuan Tian ◽  
Jiao Jiang ◽  
Guo-qi Xu ◽  
Tan Wang ◽  
Qiyan Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Fruit Development ◽  
Developmental Stages ◽  
Citrullus Lanatus ◽  
Current Data ◽  
Comprehensive Analysis ◽  
Binding Motif ◽  
Distribution Analysis ◽  
Motif Analysis ◽  
Chromosomal Distribution

Abstract BackgroundKinesin (KIN) as a motor protein is a versatile nano-machine and involved in diverse essential processes in plant growth and development. However, the kinesin gene family has not been identified in watermelon, a valued and nutritious fruit, and yet their functions has not been characterized. Especially, their involvement in early fruit development, which directly determines the size, shape, yield and quality of the watermelon fruit, remains unclear.ResultsIn this study, we performed a whole-genome search and comprehensive analysis in C. lanatus. In total, 48 kinesins were identified and categorized into 10 kinesin subfamilies groups based on phylogenetic analysis. Their uneven distribution on 11 chromosomes was revealed by chromosomal distribution analysis. Conserved motif analysis showed that the ATP-binding motif of kinesins was conserved within all subfamilies, but not the microtubule-binding motif. 10 segmental duplication pairs genes were detected by the syntenic and phylogenetic approaches, which explains the expansion of the kinesin gene family in C. lanatus genome. Moreover, 5 ClKINs genes are specifically and abundantly expressed in early fruit developmental stages according to comprehensive expression profile analysis, indicating their critical regulatory roles during early fruit development. Our current data also demonstrated that the majority of kinesin genes were responsive to plant hormones, implying their involvement in the signaling pathways of plant hormones.ConclusionsThis study is the first comprehensive analysis of the kinesin gene family in watermelon, which establishes a foundation for further functional investigation of C. lanatus kinesin genes and provides novel insights into their biological functions. In addition, these results will provide a useful resource for further selecting an artificial regulator of fruit development in C. lanatus.

scholarly journals Genome-wide Identification and Expression Analysis of the Cucumber PP2C Genes Family

2021 ◽  
Author(s):  
Guobin Zhang ◽  
Zeyu Zhang ◽  
Shilei Luo ◽  
Xia Li ◽  
Jian Lyu ◽  
...  
Keyword(s):  
Gene Family ◽  
Gene Structure ◽  
Expression Patterns ◽  
Cold Treatment ◽  
Negative Regulator ◽  
Motif Analysis ◽  
Response Elements ◽  
Genome Wide ◽  
A Genome ◽  
Duplication Events

Abstract Background: Type 2C protein phosphatase (PP2Cs) is a negative regulator of ABA signaling pathway, which play important roles in stress signal transduction in plants. However, cucumber (Cucumis sativus L.), as an important economic vegetable, has little research on its PP2C genes family. Results: This study conducted a genome-wide investigation of CsPP2C gene family. Through bioinformatics analysis, 56 CsPP2C genes were identified in cucumber. Based on phylogenetic analysis, the PP2C genes of cucumber and Arabidopsis were divided into 13 groups. Gene structure and conserved motif analysis showed that CsPP2C genes in the same group had similar gene structure and conserved domains. Collinearity analysis showed that segmental duplication events played a key role in the expansion of cucumber PP2C genes family. In addition, the expression of CsPP2Cs under different abiotic treatments was analyzed by qRT-PCR. The results showed that CsPP2C family genes showed different expression patterns under ABA, drought, salt and cold treatment, and a significantly responsive gene CsPP2Cs was obtained (CsPP2C3). By predicting the cis-elements in the promoter, we found that all CsPP2C members contained ABA response elements (ABRE) and drought response elements (MYC). Additionally, the expression patterns of CsPP2C genes were specific in different tissues. Conclusions: The results of this study provide a reference for the genome-wide identification of PP2C gene family in other species, and provide a basis for future studies on the function of PP2C gene in cucumber.

scholarly journals Genome-wide analysis and expression patterns of lipid phospholipid phospholipase gene family in Brassica napus L.

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wei Su ◽  
Ali Raza ◽  
Liu Zeng ◽  
Ang Gao ◽  
Yan Lv ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Stress Conditions ◽  
Motif Analysis ◽  
Genome Wide Analysis ◽  
Group I ◽  
Genome Wide ◽  
A Genome

Abstract Background Lipid phosphate phosphatases (LPP) are critical for regulating the production and degradation of phosphatidic acid (PA), an essential signaling molecule under stress conditions. Thus far, the LPP family genes have not been reported in rapeseed (Brassica napus L.). Results In this study, a genome-wide analysis was carried out to identify LPP family genes in rapeseed that respond to different stress conditions. Eleven BnLPPs genes were identified in the rapeseed genome. Based on phylogenetic and synteny analysis, BnLPPs were classified into four groups (Group I-Group IV). Gene structure and conserved motif analysis showed that similar intron/exon and motifs patterns occur in the same group. By evaluating cis-elements in the promoters, we recognized six hormone- and seven stress-responsive elements. Further, six putative miRNAs were identified targeting three BnLPP genes. Gene ontology analysis disclosed that BnLPP genes were closely associated with phosphatase/hydrolase activity, membrane parts, phosphorus metabolic process, and dephosphorylation. The qRT-PCR based expression profiles of BnLPP genes varied in different tissues/organs. Likewise, several gene expression were significantly up-regulated under NaCl, PEG, cold, ABA, GA, IAA, and KT treatments. Conclusions This is the first report to describe the comprehensive genome-wide analysis of the rapeseed LPP gene family. We identified different phytohormones and abiotic stress-associated genes that could help in enlightening the plant tolerance against phytohormones and abiotic stresses. The findings unlocked new gaps for the functional verification of the BnLPP gene family during stresses, leading to rapeseed improvement.

scholarly journals Systematic analysis of NAC transcription factors in Gossypium barbadense uncovers their roles in response to Verticillium wilt

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7995 ◽  
Author(s):  
Zhanji Liu ◽  
Mingchuan Fu ◽  
Hao Li ◽  
Yizhen Chen ◽  
Liguo Wang ◽  
...  
Keyword(s):  
Gene Family ◽  
Verticillium Wilt ◽  
Stress Responses ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Hormone Regulation ◽  
Genome Wide ◽  
A Genome

As one of the largest plant-specific gene families, the NAC transcription factor gene family plays important roles in various plant physiological processes that are related to plant development, hormone signaling, and biotic and abiotic stresses. However, systematic investigation of the NAC gene family in sea-island cotton (Gossypium babardense L.) has not been reported, to date. The recent release of the complete genome sequence of sea-island cotton allowed us to perform systematic analyses of G. babardense NAC GbNAC) genes. In this study, we performed a genome-wide survey and identified 270 GbNAC genes in the sea-island cotton genome. Genome mapping analysis showed that GbNAC genes were unevenly distributed on 26 chromosomes. Through phylogenetic analyses of GbNACs along with their Arabidopsis counterparts, these proteins were divided into 10 groups (I–X), and each contained a different number of GbNACs with a similar gene structure and conserved motifs. One hundred and fifty-four duplicated gene pairs were identified, and almost all of them exhibited strong purifying selection during evolution. In addition, various cis-acting regulatory elements in GbNAC genes were found to be related to major hormones, defense and stress responses. Notably, transcriptome data analyses unveiled the expression profiles of 62 GbNAC genes under Verticillium wilt (VW) stress. Furthermore, the expression profiles of 15 GbNAC genes tested by quantitative real-time PCR (qPCR) demonstrated that they were sensitive to methyl jasmonate (MeJA) and salicylic acid (SA) treatments and that they could be involved in pathogen-related hormone regulation. Taken together, the genome-wide identification and expression profiling pave new avenues for systematic functional analysis of GbNAC candidates, which may be useful for improving cotton defense against VW.

scholarly journals Genome-wide identification and expression analysis of sucrose nonfermenting-1-related protein kinase (SnRK) genes in Triticum aestivum in response to abiotic stress

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shefali Mishra ◽  
Pradeep Sharma ◽  
Rajender Singh ◽  
Ratan Tiwari ◽  
Gyanendra Pratap Singh
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Abiotic Stresses ◽  
Phylogenetic Analyses ◽  
Abiotic Stress Tolerance ◽  
Functional Characterization ◽  
Protein Motif ◽  
Element Analysis ◽  
Genome Wide ◽  
A Genome

AbstractThe SnRK gene family is a key regulator that plays an important role in plant stress response by phosphorylating the target protein to regulate subsequent signaling pathways. This study was aimed to perform a genome-wide analysis of the SnRK gene family in wheat and the expression profiling of SnRKs in response to abiotic stresses. An in silico analysis identified 174 SnRK genes, which were then categorized into three subgroups (SnRK1/2/3) on the basis of phylogenetic analyses and domain types. The gene intron–exon structure and protein-motif composition of SnRKs were similar within each subgroup but different amongst the groups. Gene duplication and synteny between the wheat and Arabidopsis genomes was also investigated in order to get insight into the evolutionary aspects of the TaSnRK family genes. The result of cis-acting element analysis showed that there were abundant stress- and hormone-related cis-elements in the promoter regions of 129 SnRK genes. Furthermore, quantitative real-time PCR data revealed that heat, salt and drought treatments enhanced TaSnRK2.11 expression, suggesting that it might be a candidate gene for abiotic stress tolerance. We also identified eight microRNAs targeting 16 TaSnRK genes which are playing important role across abiotic stresses and regulation in different pathways. These findings will aid in the functional characterization of TaSnRK genes for further research.

scholarly journals Genome-Wide Analysis and Expression Profile of Superoxide Dismutase (SOD) Gene Family in Rapeseed (Brassica napus L.) under Different Hormones and Abiotic Stress Conditions

Antioxidants ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1182
Author(s):  
Wei Su ◽  
Ali Raza ◽  
Ang Gao ◽  
Ziqi Jia ◽  
Yi Zhang ◽  
...  
Keyword(s):  
Superoxide Dismutase ◽  
Abiotic Stress ◽  
Brassica Napus ◽  
Gene Family ◽  
Expression Profiles ◽  
Protein Structures ◽  
Brassica Napus L ◽  
Genome Wide ◽  
A Genome ◽  
Sod Gene Family

Superoxide dismutase (SOD) is an important enzyme that acts as the first line of protection in the plant antioxidant defense system, involved in eliminating reactive oxygen species (ROS) under harsh environmental conditions. Nevertheless, the SOD gene family was yet to be reported in rapeseed (Brassica napus L.). Thus, a genome-wide investigation was carried out to identify the rapeseed SOD genes. The present study recognized 31 BnSOD genes in the rapeseed genome, including 14 BnCSDs, 11 BnFSDs, and six BnMSDs. Phylogenetic analysis revealed that SOD genes from rapeseed and other closely related plant species were clustered into three groups based on the binding domain with high bootstrap values. The systemic analysis exposed that BnSODs experienced segmental duplications. Gene structure and motif analysis specified that most of the BnSOD genes displayed a relatively well-maintained exon–intron and motif configuration within the same group. Moreover, we identified five hormones and four stress- and several light-responsive cis-elements in the promoters of BnSODs. Thirty putative bna-miRNAs from seven families were also predicted, targeting 13 BnSODs. Gene ontology annotation outcomes confirm the BnSODs role under different stress stimuli, cellular oxidant detoxification processes, metal ion binding activities, SOD activity, and different cellular components. Twelve BnSOD genes exhibited higher expression profiles in numerous developmental tissues, i.e., root, leaf, stem, and silique. The qRT-PCR based expression profiling showed that eight genes (BnCSD1, BnCSD3, BnCSD14, BnFSD4, BnFSD5, BnFSD6, BnMSD2, and BnMSD10) were significantly up-regulated under different hormones (ABA, GA, IAA, and KT) and abiotic stress (salinity, cold, waterlogging, and drought) treatments. The predicted 3D structures discovered comparable conserved BnSOD protein structures. In short, our findings deliver a foundation for additional functional investigations on the BnSOD genes in rapeseed breeding programs.

scholarly journals Catalase (CAT) Gene Family in Rapeseed (Brassica napus L.): Genome-Wide Analysis, Identification and Expression Pattern in Response to Multiple Hormones and Abiotic Stress Conditions

2021 ◽  
Vol 22 (8) ◽  
pp. 4281
Author(s):  
Ali Raza ◽  
Su Wei ◽  
Gao Ang ◽  
Sundas Saher Mehmood ◽  
Muhammad Azhar Hussain ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Enrichment Analysis ◽  
Motif Analysis ◽  
Brassica Napus L ◽  
Group Iii ◽  
Group I ◽  
Genome Wide ◽  
A Genome ◽  
Cat Gene

Catalase (CAT) is an antioxidant enzyme expressed by the CAT gene family and exists in almost all aerobic organisms. Environmental stresses induce the generation of reactive oxygen species (ROS) that eventually hinder plant growth and development. The CAT enzyme translates the hydrogen peroxide (H2O2) to water (H2O) and reduce the ROS levels to shelter the cells' death. So far, the CAT gene family has not been reported in rapeseed (Brassica napus L.). Therefore, a genome-wide comprehensive analysis was conducted to classify the CAT genes in the rapeseed genome. The current study identified 14 BnCAT genes in the rapeseed genome. Based on phylogenetic and synteny analysis, the BnCATs belong to four groups (Groups I–IV). A gene structure and conserved motif analysis showed that Group I, Group II, and Group IV possess almost the same intron/exon pattern, and an equal number of motifs, while Group III contains diverse structures and contain 15 motifs. By analyzing the cis-elements in the promoters, we identified five hormone-correlated responsive elements and four stress-related responsive elements. Further, six putative bna-miRNAs were also identified, targeting three genes (BnCAT4, BnCAT6, and BnCAT8). Gene ontology (GO) enrichment analysis showed that the BnCAT genes were largely related to cellular organelles, ROS response, stimulus response, stress response, and antioxidant enzymes. Almost 10 BnCAT genes showed higher expression levels in different tissues, i.e., root, leaf, stem, and silique. The expression analysis showed that BnCAT1–BnCAT3 and BnCAT11–BnCAT13 were significantly upregulated by cold, salinity, abscisic acid (ABA), and gibberellic acid (GA) treatment, but not by drought and methyl jasmonate (MeJA). Notably, most of the genes were upregulated by waterlogging stress, except BnCAT6, BnCAT9, and BnCAT10. Our results opened new windows for future investigations and provided insights into the CAT family genes in rapeseed.

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