Genome-wide Analysis of Phosphoenolpyruvate Carboxylase Gene Family and Their Response to Abiotic Stresses in Soybean

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.

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

Scientific Reports ◽

10.1038/s41598-021-93383-6 ◽

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.

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Genome‐wide analysis of mitogen‐activated protein ( MAP ) kinase gene family expression in response to biotic and abiotic stresses in sugarcane

Physiologia Plantarum ◽

10.1111/ppl.13208 ◽

2020 ◽

Vol 171 (1) ◽

pp. 86-107

Author(s):

Ahmad Ali ◽

Na Chu ◽

Panpan Ma ◽

Talha Javed ◽

Uroosa Zaheer ◽

...

Keyword(s):

Gene Family ◽

Map Kinase ◽

Abiotic Stresses ◽

Biotic And Abiotic Stresses ◽

Kinase Gene ◽

Genome Wide Analysis ◽

Genome Wide ◽

Protein Map ◽

Mitogen Activated Protein

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Genome-Wide Identification and Analysis of the Phosphoenolpyruvate Carboxylase Gene Family in Suaeda aralocaspica, an Annual Halophyte With Single-Cellular C4 Anatomy

Frontiers in Plant Science ◽

10.3389/fpls.2021.665279 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jing Cao ◽

Gang Cheng ◽

Lu Wang ◽

Tayier Maimaitijiang ◽

Haiyan Lan

Keyword(s):

Gene Family ◽

Phosphoenolpyruvate Carboxylase ◽

Abiotic Stresses ◽

Expression Patterns ◽

Substrate Affinity ◽

Photosynthetic Pathway ◽

Genome Wide ◽

A Genome ◽

Chlorenchyma Cell

Phosphoenolpyruvate carboxylase (PEPC) plays pivotal roles in the carbon fixation of photosynthesis and a variety of metabolic and stress pathways. Suaeda aralocaspica belongs to a single-cellular C4 species and carries out a photosynthetic pathway in an unusually elongated chlorenchyma cell, which is expected to have PEPCs with different characteristics. To identify the different isoforms of PEPC genes in S. aralocaspica and comparatively analyze their expression and regulation patterns as well as the biochemical and enzymatic properties in this study, we characterized a bacterial-type PEPC (BTPC; SaPEPC-4) in addition to the two plant-type PEPCs (PTPCs; SaPEPC-1 and SaPEPC-2) using a genome-wide identification. SaPEPC-4 presented a lower expression level in all test combinations with an unknown function; two SaPTPCs showed distinct subcellular localizations and different spatiotemporal expression patterns but positively responded to abiotic stresses. Compared to SaPEPC-2, the expression of SaPEPC-1 specifically in chlorenchyma cell tissues was much more active with the progression of development and under various stresses, particularly sensitive to light, implying the involvement of SaPEPC-1 in a C4 photosynthetic pathway. In contrast, SaPEPC-2 was more like a non-photosynthetic PEPC. The expression trends of two SaPTPCs in response to light, development, and abiotic stresses were also matched with the changes in PEPC activity in vivo (native) or in vitro (recombinant), and the biochemical properties of the two recombinant SaPTPCs were similar in response to various effectors while the catalytic efficiency, substrate affinity, and enzyme activity of SaPEPC-2 were higher than that of SaPEPC-1 in vitro. All the different properties between these two SaPTPCs might be involved in transcriptional (e.g., specific cis-elements), posttranscriptional [e.g., 5′-untranslated region (5′-UTR) secondary structure], or translational (e.g., PEPC phosphorylation/dephosphorylation) regulatory events. The comparative studies on the different isoforms of the PEPC gene family in S. aralocaspica may help to decipher their exact role in C4 photosynthesis, plant growth/development, and stress resistance.

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