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

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.

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

10.7287/peerj.preprints.27402v1 ◽

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.

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Genome-Wide Identification, Characterization and Evolution of BBX Gene Family in Cotton

10.21203/rs.3.rs-120586/v1 ◽

2020 ◽

Author(s):

Jun-Shan Gao ◽

Pei-pei Wang ◽

Na Sun ◽

Jessica-Maguy ◽

MIENANDI NKODIA ◽

...

Keyword(s):

Gene Family ◽

Gene Structure ◽

Cotton Fibers ◽

Pcr Analysis ◽

Conserved Domains ◽

Qrt Pcr ◽

Genome Wide ◽

A Genome ◽

Phylogenetic Evolution ◽

Genome Wide Survey

Abstract Background: The B-BOX (BBX) proteins have important functions in the regulation of photomorphogenesis. The BBX gene family has been identified in several plants, such as rice, Arabidopsis and tomato. However, there still lack a genome-wide survey of BBX genes in cotton. Results: In our present study, 63 GhBBX genes were identified in cotton. The analyses of phylogenetic evolution and gene structure showed that the GhBBX genes were divided into five subfamilies, and contained B-box conserved domains. qRT-PCR analysis releaved that both GhBBX27 and GhBBX33 had potential roles in proanthocyanidin synthesis of brown cotton fibers.Conclusions: This study provides a genome-wide survey of the BBX gene family in cotton and highlights its role in proanthocyanidin synthesis. This result will help us to further understand the complexity of the BBX gene family and the functional characteristics of its members.

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

10.7287/peerj.preprints.27402 ◽

2018 ◽

Cited By ~ 1

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

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Genome-Wide Analysis and Cloning of the Apple Stress-Associated Protein Gene Family Reveals MdSAP15, Which Confers Tolerance to Drought and Osmotic Stresses in Transgenic Arabidopsis

International Journal of Molecular Sciences ◽

10.3390/ijms19092478 ◽

2018 ◽

Vol 19 (9) ◽

pp. 2478 ◽

Cited By ~ 15

Author(s):

Qinglong Dong ◽

Dingyue Duan ◽

Shuang Zhao ◽

Bingyao Xu ◽

Jiawei Luo ◽

...

Keyword(s):

Drought Tolerance ◽

Gene Family ◽

Transgenic Arabidopsis ◽

Abiotic Stress Tolerance ◽

Expression Patterns ◽

Pcr Analysis ◽

Sequence Alignments ◽

Genome Wide Analysis ◽

Genome Wide ◽

A Genome

Stress-associated proteins (SAPs) are novel A20/AN1 zinc finger domain-containing proteins that are now favorable targets to improve abiotic stress tolerance in plants. However, the SAP gene family and their biological functions have not been identified in the important fruit crop apple (Malus × domestica Borkh.). We conducted a genome-wide analysis and cloning of this gene family in apple and determined that the overexpression of MdSAP15 enhances drought tolerance in Arabidopsis plants. We identified 30 SAP genes in the apple genome. Phylogenetic analysis revealed two major groups within that family. Results from sequence alignments and analyses of 3D structures, phylogenetics, genomics structure, and conserved domains indicated that apple SAPs are highly and structurally conserved. Comprehensive qRT-PCR analysis found various expression patterns for MdSAPs in different tissues and in response to a water deficit. A transgenic analysis showed that the overexpression of MdSAP15 in transgenic Arabidopsis plants markedly enhanced their tolerance to osmotic and drought stresses. Our results demonstrate that the SAP genes are highly conserved in plant species, and that MdSAP15 can be used as a target gene in genetic engineering approaches to improve drought tolerance.

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The TIFY Gene Family in Wheat and its Progenitors: Genome-wide Identification, Evolution and Expression Analysis

Current Genomics ◽

10.2174/1389202920666191018114557 ◽

2019 ◽

Vol 20 (5) ◽

pp. 371-388

Author(s):

Songfeng Xie ◽

Licao Cui ◽

Xiaole Lei ◽

Guang Yang ◽

Jun Li ◽

...

Keyword(s):

Gene Family ◽

Expression Profiles ◽

Regulatory Element ◽

Aegilops Tauschii ◽

Vital Role ◽

Pcr Analysis ◽

Protein Motif ◽

Genome Wide ◽

A Genome ◽

As Stress

Background: The TIFY gene family is a group of plant-specific proteins involved in the jasmonate (JA) metabolic process, which plays a vital role in plant growth and development as well as stress response. Although it has been extensively studied in many species, the significance of this family is not well studied in wheat. Objective: To comprehensively understand the genome organization and evolution of TIFY family in wheat, a genome-wide identification was performed in wheat and its two progenitors using updated genome information provided here. Results: In total, 63, 13 and 17 TIFY proteins were identified in wheat, Triticum urartu and Aegilops tauschii respectively. Phylogenetic analysis clustered them into 18 groups with 14 groups possessing A, B and D copies in wheat, demonstrating the completion of the genome as well as the two rounds of allopolyploidization events. Gene structure, conserved protein motif and cis-regulatory element divergence of A, B, D homoeologous copies were also investigated to gain insight into the evolutionary conservation and divergence of homoeologous genes. Furthermore, the expression profiles of the genes were detected using the available RNA-seq and the expression of 4 drought-responsive candidates was further validated through qRT-PCR analysis. Finally, the co-expression network was constructed and a total of 22 nodes with 121 edges of gene pairs were found. Conclusion: This study systematically reported the characteristics of the wheat TIFY family, which ultimately provided important targets for further functional analysis and also facilitated the elucidation of the evolution mechanism of TIFY genes in wheat and more.

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

PeerJ ◽

10.7717/peerj.7995 ◽

2019 ◽

Vol 7 ◽

pp. e7995 ◽

Cited By ~ 3

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.

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Genome-Wide Identification and Transcriptional Expression Analysis of Cucumber Superoxide Dismutase (SOD) Family in Response to Various Abiotic Stresses

International Journal of Genomics ◽

10.1155/2017/7243973 ◽

2017 ◽

Vol 2017 ◽

pp. 1-14 ◽

Cited By ~ 19

Author(s):

Yong Zhou ◽

Lifang Hu ◽

Hao Wu ◽

Lunwei Jiang ◽

Shiqiang Liu

Keyword(s):

Superoxide Dismutase ◽

Expression Analysis ◽

Stress Responses ◽

Phylogenetic Analyses ◽

Promoter Sequence ◽

Pcr Analysis ◽

Motif Analysis ◽

Genome Wide ◽

Potential Applications ◽

Almost All

Superoxide dismutase (SOD) proteins are widely present in the plant kingdom and play important roles in different biological processes. However, little is known about the SOD genes in cucumber. In this study, night SOD genes were identified from cucumber (Cucumis sativus) using bioinformatics-based methods, including 5 Cu/ZnSODs, 3 FeSODs, and 1 MnSOD. Gene structure and motif analysis indicated that most of the SOD genes have relatively conserved exon/intron arrangement and motif composition. Phylogenetic analyses with SODs from cucumber and several other species revealed that these SOD proteins can be traced back to two ancestral SODs before the divergence of monocot and dicot plants. Many cis-elements related to stress responses and plant hormones were found in the promoter sequence of each CsSOD gene. Gene expression analysis revealed that most of the CsSOD genes are expressed in almost all the tested tissues. qRT-PCR analysis of 8 selected CsSOD genes showed that these genes could respond to heat, cold, osmotic, and salt stresses. Our results provide a basis for further functional research on SOD gene family in cucumber and facilitate their potential applications in the genetic improvement of cucumber.

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

Scientific Reports ◽

10.1038/s41598-021-99639-5 ◽

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.

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Genome-Wide Identification and Expression Analysis of Flavonoid 3'-Hydroxylase Gene Family in Carthamus Tinctorius L.

10.21203/rs.3.rs-575863/v1 ◽

2021 ◽

Author(s):

Hoàng Việt Nguyễn Quốc ◽

Kong Jie ◽

Naveed Ahmad ◽

Yang Zhuoda ◽

Wang Nan ◽

...

Keyword(s):

Expression Analysis ◽

Phylogenetic Analyses ◽

Evolutionary Relationship ◽

Pcr Analysis ◽

Genetic Evolution ◽

Significant Information ◽

Protein Motifs ◽

Qrt Pcr ◽

Digital Expression ◽

Genome Wide

Abstract ObjectiveThrough experiments and bioinformatic analysis clearly demonstrate considerable information about the genetic evolution of the flavonoid 3'-hydroxylase (F3'H) gene in Safflower and in plants.ResultsHere, we performed genome wide survey of safflower genome and identified a total of 22 CtF3'H enzyme encoding genes. Phylogenetic analyses revealed the classifications of these CtF3'Hs into nine subgroups demonstrating their evolutionary relationship. The distribution of the conserved protein motifs, and cis-regulatory units of CtF3'Hs indicated essential structure-to-function components leading to the final function of protein or its interactions. Furthermore, the results of digital expression analysis and the qRT-PCR pattern of 22 putative CtF3’H genes during different flowering stages suggested their requisite roles in safflower petal pigmentation. In addition, the fusions construct of plant expression vector pCAMBIA1302-GFP-CtF3’H5 in onion epidermal cells verified the subcellular localization of CtF3’H5 to the plasma membrane. Subsequently, the prokaryotic expression and western blot hybridization of CtF3’H5 resulted in a stable 50.3kD target protein. These results partly demonstrate the influence of F3'Hs on plants.ConclusionsIn this study, the results of digital expression and qRT-PCR analysis of 22 putative CtF3'H genes in different flowering stages indicate their essential role in safflower petal pigmentation. clearly demonstrates significant information on the genetic evolution of important enzyme-coding genes and will provide a pathway for future functional studies of F3'Hs in safflower as well as in plants.

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

International Journal of Genomics ◽

10.1155/2016/8740901 ◽

2016 ◽

Vol 2016 ◽

pp. 1-11 ◽

Cited By ~ 6

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.

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