scholarly journals Comprehensive Genome-Wide Analysis of The Catalase Enzyme Toolbox In Potato (Solanum Tuberosum L.)

2021 ◽  
Author(s):  
Rania Jbir Koubaa ◽  
Mariem Ayadi ◽  
Mohamed Najib Saidi ◽  
Safa Charfeddine ◽  
Radhia Gargouri Bouzid ◽  
...  
Keyword(s):  
Stress Responses ◽  
Expression Profiling ◽  
Phylogenetic Trees ◽  
Solanum Tuberosum L ◽  
Potato Cultivar ◽  
Promoter Sequence ◽  
3D Protein Structure ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

Abstract As antioxidant enzymes, catalase (CAT) protects organisms from oxidative stress via the production of reactive oxygen species (ROS). These enzymes play important roles in diverse biological processes. However, little is known about the CAT genes in potato plants despite its important economical rank of this crop in the world. Yet, abiotic and biotic stresses severely hinder growth and development of the plants which affects the production and quality of the crop. To define the possible roles of CAT genes under various stresses, a genome-wide analysis of CAT gene family has been performed in potato plant.In this study, the StCAT gene’s structure, secondary and 3D protein structure, physicochemical properties, synteny analysis, phylogenetic tree and also expression profiling under various developmental and environmental cues were predicted using bioinformatics tools. The expression analysis by RT-PCR was performed using commercial potato cultivar. Three genes encoding StCAT that code for three proteins each of size 492 aa, interrupted by seven introns have been identified in potatoes. StCAT proteins were found to be localized in the peroxisome which is judged as the main H2O2 cell production site during different processes. Many regulating cis-elements related to stress responses and plant hormones signaling were found in the promoter sequence of each gene. The analysis of motifs and phylogenetic trees showed that StCAT are closer to their homologous in S. lycopersicum and share a 41% – 95% identity with other plants’ CATs. Expression profiling revealed that StCAT1 is the constitutively expressive member; while StCAT2 and StCAT3 are the stress-responsive members.

scholarly journals Expression Profiling of the Dof Gene Family Under Abiotic Stresses in Spinach

2021 ◽  
Author(s):  
Hongying Yu ◽  
Yaying Ma ◽  
Yijing Lu ◽  
Jingjing Yue ◽  
Ray Ming
Keyword(s):  
Transcription Factors ◽  
Gene Family ◽  
Stress Responses ◽  
Expression Profiling ◽  
Abiotic Stresses ◽  
Specific Expression ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Male Flowers

Abstract DNA-binding with one finger (Dof) transcription factors are plant-specific transcription factors involved in numerous pathways of plant development, especially in respond to abiotic stresses. Although genome-wide analysis of this gene family has been performed in many species, Dof genes in spinach have not been thoroughly analyzed. We performed a genome-wide analysis and characterization of Dof gene family in spinach. Twenty two Dof genes were identified and classified into four groups with nine subgroups, which was further corroborated by gene structure and motif analyses. Ka/Ks analysis revealed that SoDofs were subjected to purify selection. Using Cis-acting elements analysis, SoDofs were involved in plant growth and development, plant hormones and stress responses. Expression profiling demonstrated that SoDofs expressed in leaf and inflorescence, and responded to cold, heat, and drought stresses. SoDof22 expressed the highest level in male flowers and under cold stress. These results provided a genome-wide analysis of SoDof genes, their gender- and tissue-specific expression, and response to abiotic stresses. The knowledge and resources gained from these analyses will benefit spinach improvement.

scholarly journals Expression profiling of the Dof gene family under abiotic stresses in spinach

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hongying Yu ◽  
Yaying Ma ◽  
Yijing Lu ◽  
Jingjing Yue ◽  
Ray Ming
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Profiling ◽  
Abiotic Stresses ◽  
Spinacia Oleracea ◽  
Purifying Selection ◽  
Specific Expression ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

AbstractDNA-binding with one finger (Dof) are plant-specific transcription factors involved in numerous pathways of plant development, such as abiotic stresses responses. Although genome-wide analysis of Dof genes has been performed in many species, but these genes in spinach have not been analyzed yet. We performed a genome-wide analysis and characterization of Dof gene family in spinach (Spinacia oleracea L.). Twenty-two Dof genes were identified and classified into four groups with nine subgroups, which was further corroborated by gene structure and motif analyses. Ka/Ks analysis revealed that SoDofs were subjected to purifying selection. Using cis-acting elements analysis, SoDofs were involved in plant growth and development, plant hormones, and stress responses. Expression profiling demonstrated that SoDofs expressed in leaf and inflorescence, and responded to cold, heat, and drought stresses. SoDof22 expressed the highest level in male flowers and under cold stress. These results provided a genome-wide analysis of SoDof genes, their gender- and tissue-specific expression, and response to abiotic stresses. The knowledge and resources gained from these analyses will benefit spinach improvement.

scholarly journals Genome-Wide Analysis of the TCP Gene Family in Switchgrass (Panicum virgatum L.)

2019 ◽  
Vol 2019 ◽  
pp. 1-13 ◽  
Author(s):  
Yuzhu Huo ◽  
Wangdan Xiong ◽  
Kunlong Su ◽  
Yu Li ◽  
Yawen Yang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Panicum Virgatum ◽  
Expression Profiles ◽  
Specific Expression ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

The plant-specific transcription factor TCPs play multiple roles in plant growth, development, and stress responses. However, a genome-wide analysis of TCP proteins and their roles in salt stress has not been declared in switchgrass (Panicum virgatum L.). In this study, 42 PvTCP genes (PvTCPs) were identified from the switchgrass genome and 38 members can be anchored to its chromosomes unevenly. Nine PvTCPs were predicted to be microRNA319 (miR319) targets. Furthermore, PvTCPs can be divided into three clades according to the phylogeny and conserved domains. Members in the same clade have the similar gene structure and motif localization. Although all PvTCPs were expressed in tested tissues, their expression profiles were different under normal condition. The specific expression may indicate their different roles in plant growth and development. In addition, approximately 20 cis-acting elements were detected in the promoters of PvTCPs, and 40% were related to stress response. Moreover, the expression profiles of PvTCPs under salt stress were also analyzed and 29 PvTCPs were regulated after NaCl treatment. Taken together, the PvTCP gene family was analyzed at a genome-wide level and their possible functions in salt stress, which lay the basis for further functional analysis of PvTCPs in switchgrass.

Genome-Wide Analysis and Expression Profiling of the ERF Transcription Factor Family in Potato (Solanum tuberosum L.)

2014 ◽  
Vol 57 (4) ◽  
pp. 348-358 ◽  
Author(s):  
Mariam Charfeddine ◽  
Mohamed Najib Saïdi ◽  
Safa Charfeddine ◽  
Asma Hammami ◽  
Radhia Gargouri Bouzid
Keyword(s):  
Transcription Factor ◽  
Solanum Tuberosum ◽  
Expression Profiling ◽  
Solanum Tuberosum L ◽  
Transcription Factor Family ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Erf Transcription Factor

scholarly journals Identification and expression profiling of flax (Linum usitatissimum L.) polyamine oxidase genes in response to stimuli

2018 ◽  
Vol 77 (1) ◽  
pp. 97-101 ◽  
Author(s):  
Seung Hee Eom ◽  
Jae Kook Lee ◽  
Dong-Ho Kim ◽  
Heekyu Kim ◽  
Keum-Il Jang ◽  
...  
Keyword(s):  
Stress Responses ◽  
Linum Usitatissimum ◽  
Expression Profiling ◽  
Biological Activities ◽  
Genome Wide Analysis ◽  
Linum Usitatissimum L ◽  
Physiological Processes ◽  
Genome Wide ◽  
Amino Oxidase ◽  
Polyamine Oxidases

AbstractPolyamine oxidases (PAOs) are known to be involved in either the terminal catabolism or the back conversion of polyamines, which affect a range of physiological processes, including growth, development, and stress responses. In this study, based on genome-wide analysis, we identified five putative PAO genes (LuPAO1toLuPAO5) in flax (Linum usitatissimumL.) that contain the amino-oxidase domain and FAD-binding-domain. The expression analysis using quantitative real-time PCR revealed spatial variations in the expression ofLuPAOsin different organs. In addition, the expression level ofLuPAOsin the flax cell suspension culture was increased by treatment with methyl-jasmonate (MeJA) or pectin, but not with salicylic acid or chitosan. This indicates that LuPAOs might be involved in the MeJA-mediated biological activities. Taken together, our genome-wide analysis of PAO genes and expression profiling of these genes provide the first step toward the functional dissection of LuPAOs.

Genome-wide identification and expression profiling of microRNAs genes during SE and in different organs/tissues in Dimocarpus longan Lour.

2019 ◽  
Author(s):  
Yuling Lin ◽  
Yan Chen ◽  
Youjing Zeng ◽  
Shuting Zhang ◽  
Zihao Zhang ◽  
...  
Keyword(s):  
Stress Responses ◽  
Expression Profiling ◽  
Economic Value ◽  
Future Research ◽  
Element Analysis ◽  
Mirna Genes ◽  
Loop Region ◽  
Genome Wide ◽  
A Genome ◽  
Dimocarpus Longan

Abstract Background MicroRNAs (miRNAs) is a conserved class of single-stranded noncoding RNAs, which regulate growth and development, hormone response, and stress responses in plant. Longan (Dimocarpus longan Lour.) is an important fruit tree with medicinal value and considerable economic value. However, there is no research on genome-wide identification of miRNAs genes in longan.Results Here, we conducted a genome-wide survey of longan miRNA genes, characterizing their structure and expression. A total of 88 miRNA precursors comprised of 30 known miRNA families and three undefined miRNA families were obtained. Of the 30 known longan miRNA families, 16 were represented by multiple loci in longan genome, which were also found more diverse in genome loci numbers in other plants; and four of them, involving miR395, -399, -477, and -3627 families, were identified as miRNA clusters genes; Among the 16 miRNA families, the conserved region as mature miRNA, as would be expected, and the loop region sequences of miRNA genes were divergent. Further, amplification and characterization of the longan pri-miRNA genes were carried out, and the upstream transcription 5 'region of 19 miRNAs and the downstream transcription 3' region of 12 miRNAs with typical poly (a) tails were obtained, showing that longan miRNAs genes possess multiple transcription start sites (TSSs) or polymorphism trait, suggesting pri-miRNA has similar transcription specialty as protein-encoding genes. Subsequently, promoter cis-element analysis on longan miRNA genes showed that the top three most abundant cis-elements were light-responsive elements, stress- responsive elements, and hormone responsive elements. Quantitative real-time PCR showed that pre-miRNAs were differentially expressed during the early stages of longan somatic embryogenesis, and the most number of highly expressed pre-miRNAs were detected in anther samples in different organs/tissues types of longan,Conclusion This is the first report concerning genome-wide identification and expression profiling of microRNAs genes, and will serve as a foundation for future research into the functional roles of miRNA genes in longan.

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