scholarly journals Genome-wide analysis of the superoxide dismutase (SOD) gene family in Zostera marina and expression profile analysis under temperature stress

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9063
Author(s):  
Yu Zang ◽  
Jun Chen ◽  
Ruoxi Li ◽  
Shuai Shang ◽  
Xuexi Tang
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Zostera Marina ◽  
Profile Analysis ◽  
Protein Structures ◽  
Pcr Analysis ◽  
Primary Role ◽  
Sequence Motifs ◽  
Systematic Analysis ◽  
Sod Gene Family

Superoxide dismutases (SODs) serve as the first line of defense in the plant antioxidant enzyme system, and play a primary role in the removal of reactive oxygen species (ROS). However, our understanding of the functions of the SOD family in Zostera marina is limited. In this study, a systematic analysis was conducted on the characteristics of the SOD genes in Z. marina at the whole-genome level. Five SOD genes were identified, consisting of two Cu/ZnSODs, two FeSODs, and one MnSOD. Phylogenetic analysis showed that ZmSOD proteins could be divided into two major categories (Cu/ZnSODs and Fe-MnSODs). Sequence motifs, gene structure, and the 3D-modeled protein structures further supported the phylogenetic analysis, with each subgroup having similar motifs, exon-intron structures, and protein structures. Additionally, several cis-elements were identified that may respond to biotic and abiotic stresses. Transcriptome analysis revealed expression diversity of ZmSODs in various tissues. Moreover, qRT-PCR analysis showed that the expression level of most ZmSOD genes trended to decreased expression with the increase of temperature, indicating that heat stress inhibits expression of ZmSODs and may result in reduced ability of ZmSODs to scavenge ROS. Our results provide a basis for further functional research on the SOD gene family in Z. marina, which will help to determine the molecular mechanism of ZmSOD genes in response to environmental stress.

Genome-Wide Characterization of PDI Gene Family in Medicago truncatula and their Roles in Response to ER stress

Genome ◽  
2020 ◽  
Author(s):  
Zhe Meng ◽  
Yuwei Zhao ◽  
Lijie Liu ◽  
Xihua Du
Keyword(s):  
Protein Folding ◽  
Er Stress ◽  
Gene Family ◽  
Medicago Truncatula ◽  
Environmental Changes ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Protein Structures ◽  
Pcr Analysis ◽  
Model Legume

Protein disulfide isomerases (PDIs) are pivotal protein folding catalysts in the endoplasmic reticulum (ER) through formation of disulfide bond, isomerization, and inhibition of misfolded protein aggregation. When protein folding capacity is overwhelmed by the demands during transitions between growth phases or under environmental changes, the accumulation of unfolded or misfolded proteins in the ER triggers ER stress. However, little is known about PDI gene family in the model legume, Medicago truncatula, especially the responses to ER stress. Therefore, we identified 17 putative PDIs from the genome of M. truncatula and presented their gene and protein structures, phylogenetic relationships, chromosomal distributions, and synteny analysis with the orthologs in other four eudicot species inculding A. thaliana, G. max, B. rapa, and V. vinifera. Moreover, expression profiles derived from transcriptome data showed distinct expression patterns of MtPDI genes among plant organs, while real-time quantitative PCR analysis and data from the proteome revealed the potential roles of MtPDIs in response to ER stress. Our study provides a foundation for further investigations of the biological roles of PDIs in Medicago, especially their roles in response to ER stress.

scholarly journals In Silico and Transcription Analysis of Trehalose-6-Phosphate Phosphatase Gene Family of Wheat: Trehalose Synthesis Genes Contribute to Salinity, Drought Stress and Leaf Senescence

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1652
Author(s):  
Md Ashraful Islam ◽  
Md Mustafizur Rahman ◽  
Md Mizanor Rahman ◽  
Xiujuan Jin ◽  
Lili Sun ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Tolerance ◽  
Leaf Senescence ◽  
Brachypodium Distachyon ◽  
Protein Structures ◽  
Regulatory Elements ◽  
Transcriptional Analysis ◽  
Pcr Analysis ◽  
Evolutionary Status ◽  
Transcription Analysis

Trehalose-6-phosphate phosphatase (TPP) genes take part in trehalose metabolism and also in stress tolerance, which has been well documented in many species but poorly understood in wheat. The present research has identified a family of 31 TPP genes in Triticum aestivum L. through homology searches and classified them into five clades by phylogenetic tree analysis, providing evidence of an evolutionary status with Hordeum vulgare, Brachypodium distachyon and Oryza sativa. The exon-intron distribution revealed a discrete evolutionary history and projected possible gene duplication occurrences. Furthermore, different computational approaches were used to analyze the physical and chemical properties, conserved domains and motifs, subcellular and chromosomal localization, and three-dimensional (3-D) protein structures. Cis-regulatory elements (CREs) analysis predicted that TaTPP promoters consist of CREs related to plant growth and development, hormones, and stress. Transcriptional analysis revealed that the transcription levels of TaTPPs were variable in different developmental stages and organs. In addition, qRT-PCR analysis showed that different TaTPPs were induced under salt and drought stresses and during leaf senescence. Therefore, the findings of the present study give fundamental genomic information and possible biological functions of the TaTPP gene family in wheat and will provide the path for a better understanding of TaTPPs involvement in wheat developmental processes, stress tolerance, and leaf senescence.

Genome-wide Survey of bHLH Super Gene Family in Brassica napus and Their Roles in Roots

2019 ◽  
Author(s):  
Yunzhuo Ke ◽  
Yunwen Wu ◽  
Hongjun Zhou ◽  
Ping Chen ◽  
Mangmang Wang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Expression Profiles ◽  
Joint Analysis ◽  
Pcr Analysis ◽  
Sequence Motifs ◽  
Intron Insertion ◽  
Under Five ◽  
Helix Loop Helix ◽  
Root Hair Development

Abstract Background: Basic helix-loop-helix (bHLH) gene family is one of the largest transcription factors in plants and are functionally characterized in diverse species. However, less is known about their functions in the economically important allopolyploid oil crop, Brassica napus . Results : We identified 602 potential bHLHs in B. napus genome ( BnbHLHs ) and categorized them into 36 subfamilies, including seven newly separated subfamilies, based on phylogeny, protein structure and exon-intron organization analysis. The intron insertion patterns of this gene family were corrected and a total of eight types were identified in the bHLH regions of BnbHLHs . Chromosome distribution and synteny analyses revealed that hybridization between Brassica rapa and Brassica oleracea was the main expansion mechanism for BnbHLHs . Expression analyses showed that BnbHLHs were wide and formed six main patterns, suggesting they may participate in various aspects in B. napus during the development. The expression profiles under five hormone treatments (IAA, ABA, ACC, GA3, 6-BA) in roots further revealed the active response of BnbHLHs with a large proportion of which being induced. qRT-PCR analysis confirmed the expression profiles of five candidate BnbHLHs under five hormone inductions. Up to 246 BnbHLHs from nine subfamilies were predicted to have potential roles relating to root development by joint analysis of expression profile and homolog function. Further, the MYB/bHLH/WD40 (MBW) protein complex regulating root hair development were verified in B. napus by yeast two-hybrid experiment. Conclusion: The 602 BnbHLHs identified from B. napus could be classed into 36 subfamilies, and those members from the same subfamily generally have similar sequence motifs. BnbHLHs may widely involve in root biological process in B. napus . Overall, this study provides important insights into the characterization and potential functions of B. napus bHLH super gene family and thus will be useful in future gene function research.

scholarly journals Genome-Wide Analysis of the WOX Gene Family and Function Exploration of GmWOX18 in Soybean

Plants ◽  
2019 ◽  
Vol 8 (7) ◽  
pp. 215 ◽  
Author(s):  
Qingnan Hao ◽  
Ling Zhang ◽  
Yanyan Yang ◽  
Zhihui Shan ◽  
Xin-an Zhou
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Function Analysis ◽  
Expression Patterns ◽  
Protein Structures ◽  
Pcr Analysis ◽  
Regeneration Ability ◽  
Functional Identification ◽  
Phylogenetic Tree Analysis ◽  
Wox Genes

WUSCHEL-related homeobox (WOX) is a family of transcription factors that are unique to plants and is characterized by the presence of a homeodomain. The WOX transcription factor plays an important role in regulating plant growth and development and the response to abiotic stress. Soybean is one of the most important oil crops worldwide. In this study, based on the available genome data of soybean, the WOX gene family was identified by bioinformatics analysis. The chromosome distribution, gene and protein structures, phylogenetic relationship and gene expression patterns of this family were comprehensively compared. The results showed that a total of 33 putative WOX genes in the soybean genome were found and then designated as GmWOX1- GmWOX33, which were distributed across 19 chromosomes except chromosome 16. Multiple sequence analysis of the GmWOX gene family revealed a highly conserved homeodomain. Phylogenetic tree analysis showed that 33 WOX genes could be divided into three major clades (modern/WUS, intermediate and ancient) in soybean. Of these 33 WOX genes, some showed differential expression patterns in the tested tissues (leaves, pods, unopen and open flowers, nodules, seed, roots, root hairs, stems, shoot apical meristems and shoot tips). In addition, the expression profile and qRT-PCR analysis showed that most of the GmWOX genes responded to different abiotic stress treatments (cold and drought). According to the expression pattern of GmWOX genes in the high regeneration capacity soybean material P3, overexpression of GmWOX18 was selected for function analysis. The overexpression of GmWOX18 increased the regeneration ability of clustered buds. The results will provide valuable information for further studies on the roles of WOX genes in regulating soybean growth, development and responses to abiotic stress, as well as a basis for the functional identification and analysis of WOX genes in soybean.

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.

Isolation and characterisation of six putative wheat cell wall-associated kinases

2006 ◽  
Vol 33 (9) ◽  
pp. 811 ◽  
Author(s):  
Yong Liu ◽  
Dongcheng Liu ◽  
Haiying Zhang ◽  
Hongbo Gao ◽  
Xiaoli Guo ◽  
...  
Keyword(s):  
Cell Wall ◽  
Gene Family ◽  
Plant Cell Wall ◽  
Expression Patterns ◽  
Protein Structures ◽  
Family Members ◽  
Intact Protein ◽  
Pcr Analysis ◽  
Structure Conservation ◽  
Nucleotide Mutation

The plant cell wall-associated kinase (WAK) and WAK-like kinase (WAKL) make up a unique group in the receptor-like protein kinase (RLK) superfamily. Previous studies on Arabidopsis have revealed that the WAK gene family members play an important role in both cell elongation and stress response signalling. Here we show that four putative WAKs (TaWAK1, TaWAKL2, TaWAKL3, and TaWAK4) and two WAKLs (TaWAKL1 and TaWAKL2) were isolated from wheat based on the DNA sequence similarity and the protein structure conservation of Arabidopsis WAKs genes. TaWAK1, TaWAK2, TaWAK3 and TaWAKL1 each encode a putative intact protein with the characteristic of the WAK / WAKL gene family members, except for the abbreviated TaWAK4 and TaWAKL2 which were caused by nucleotide mutation and alternative splicing, respectively. Southern analysis revealed that TaWAKL1, TaWAK1, TaWAK2 and TaWAK3 are all multiple-copy members. Real-time PCR analysis revealed that the TaWAK1 and TaWAK3 displayed similar expression patterns, while expressions of TaWAKL1, TaWAKL2, and TaWAK2 were organ specific. Further, we analysed the conservation of introns and intron–exon structure and the putative protein structures between wheat and Arabidopsis, which showed the putative wheat WAKs are different from those of Arabidopsis and make up a new subgroup in the polygenetic tree.

scholarly journals Duplication of the Phytoene Synthase Gene in the Carotenoid Biosynthetic Pathway of Watermelon

HortScience ◽  
2006 ◽  
Vol 41 (4) ◽  
pp. 1007A-1007 ◽  
Author(s):  
Haejeen Bang ◽  
Sunggil Kim ◽  
Daniel I. Leskovar ◽  
Angela Davis ◽  
Stephen R. King
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Gene Expression Pattern ◽  
Gene Families ◽  
Phytoene Synthase ◽  
Pcr Analysis ◽  
Long Time ◽  
Phytoene Synthase Gene ◽  
Relationship Of ◽  
Identification And Characterization

Gene identification and characterization can be utilized for the identification of respective functions and their relationship to flesh color inheritance. Phytoene synthase (PSY), which converts two molecules of GGPP into phytoene, is the first committed step of the pathway. Previous phylogenetic analysis of PSY has indicated that PSY duplication is common in Poaceae, but rare in dicots. Degenerate PCR and RACE were used for PSY cloning. Three members of PSY gene family (PSY-A, PSY-B and PSY-C) were identified. PSY-A shared higher identity with PSY-C than PSY-B. PSYC shared 96% identity with melon PSY. PSY-C also showed a high homology with tomato PSY1, even higher than PSY-A and PSY-B. It showed a similar gene expression pattern, so we propose that PSY-C is a homologue to PSY1. RT-PCR analysis indicated that PSY-B has a different transcriptional behavior from PSY-A, similar to tomato PSY2. Therefore, PSY genes appear to be under different regulatory mechanisms. Deduced protein sequence of PSY1 or PSY2 between species has higher homology than between PSY1 and PSY2 within species. Phylogenetic analysis indicated that watermelon PSY gene family is very distantly related. Watermelon and carrot PSY gene families did not appear to cluster as closely as in Poaceae or tomato. This indicates that watermelon and carrot PSY genes are not conserved as much as PSY in tomato or Poaceae. There was no particular pattern in phylogenetic relationship of dicots. Poaceae PSY genes showed a clustering into a PSY1 group and PSY2 group. PSY duplication in watermelon provides additional evidence that PSY duplication may be a common phenomenon in dicots. They are likely to be duplicated evolutionarily a long time ago, possibly even prior to the evolution of monocot and dicot divergence.

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

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Shujuan Tian ◽  
Jiao Jiang ◽  
Guo-qi Xu ◽  
Tan Wang ◽  
Qiyan Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Plant Hormones ◽  
Fruit Development ◽  
Developmental Stages ◽  
Profile Analysis ◽  
Citrullus Lanatus ◽  
Binding Motif ◽  
Distribution Analysis ◽  
Motif Analysis ◽  
Expression Profile Analysis

Abstract Background Kinesin (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 have 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. Results In this study, we performed a whole-genome investigation and comprehensive analysis of kinesin genes 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 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 showed the expansion of the kinesin gene family in C. lanatus genome during evolution. Moreover, 5 ClKINs genes are specifically and abundantly expressed in early fruit developmental stages according to comprehensive expression profile analysis, implying their critical regulatory roles during early fruit development. Our data also demonstrated that the majority of kinesin genes were responsive to plant hormones, revealing their potential involvement in the signaling pathways of plant hormones. Conclusions Kinesin gene family in watermelon was comprehensively analyzed in this study, 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 also provide useful information for understanding the relationship between plant hormone and kinesin genes in C. lanatus.

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