scholarly journals Whole Genome Analysis of Cyclin Dependent Kinase (CDK) Gene Family in Cotton and Functional Evaluation of the Role of CDKF4 Gene in Drought and Salt Stress Tolerance in Plants

2018 ◽  
Vol 19 (9) ◽  
pp. 2625 ◽  
Author(s):  
Richard Magwanga ◽  
Pu Lu ◽  
Joy Kirungu ◽  
Xiaoyan Cai ◽  
Zhongli Zhou ◽  
...  
Keyword(s):  
Salt Stress ◽  
Gene Family ◽  
Transgenic Arabidopsis ◽  
Stress Factors ◽  
Functional Evaluation ◽  
Whole Genome ◽  
Evolutionary Analysis ◽  
Cotton Production ◽  
Whole Genome Analysis ◽  
Drought And Salt Stress

Cotton (Gossypium spp.) is the number one crop cultivated for fiber production and the cornerstone of the textile industry. Drought and salt stress are the major abiotic stresses, which can have a huge economic impact on cotton production; this has been aggravated with continued climate change, and compounded by pollution. Various survival strategies evolved by plants include the induction of various stress responsive genes, such as cyclin dependent kinases (CDKs). In this study, we performed a whole-genome identification and analysis of the CDK gene family in cotton. We identified 31, 12, and 15 CDK genes in G. hirsutum, G. arboreum, and G. raimondii respectively, and they were classified into 6 groups. CDK genes were distributed in 15, 10, and 9 linkage groups of AD, D, and A genomes, respectively. Evolutionary analysis revealed that segmental types of gene duplication were the primary force underlying CDK genes expansion. RNA sequence and RT-qPCR validation revealed that Gh_D12G2017 (CDKF4) was strongly induced by drought and salt stresses. The transient expression of Gh_D12G2017-GFP fusion protein in the protoplast showed that Gh_D12G2017 was localized in the nucleus. The transgenic Arabidopsis lines exhibited higher concentration levels of the antioxidant enzymes measured, including peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) concentrations under drought and salt stress conditions with very low levels of oxidants. Moreover, cell membrane stability (CMS), excised leaf water loss (ELWL), saturated leaf weight (SLW), and chlorophyll content measurements showed that the transgenic Arabidopsis lines were highly tolerant to either of the stress factors compared to their wild types. Moreover, the expression of the stress-related genes was also significantly up-regulated in Gh_D12G2017 (CDKF4) transgenic Arabidopsis plants under drought and salt conditions. We infer that CDKF-4s and CDKG-2s might be the primary regulators of salt and drought responses in cotton.

scholarly journals Genome-wide identification of ZF-HD gene family in Triticum aestivum: Molecular evolution mechanism and function analysis

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0256579
Author(s):  
Hongli Niu ◽  
Pengliang Xia ◽  
Yifeng Hu ◽  
Chuang Zhan ◽  
Yiting Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Function Analysis ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Wheat Evolution ◽  
New Perspective ◽  
Almost All ◽  
And Function

ZF-HD family genes play important roles in plant growth and development. Studies about the whole genome analysis of ZF-HD gene family have been reported in some plant species. In this study, the whole genome identification and expression profile of the ZF-HD gene family were analyzed for the first time in wheat. A total of 37 TaZF-HD genes were identified and divided into TaMIF and TaZHD subfamilies according to the conserved domain. The phylogeny tree of the TaZF-HD proteins was further divided into six groups based on the phylogenetic relationship. The 37 TaZF-HDs were distributed on 18 of 21 chromosomes, and almost all the genes had no introns. Gene duplication and Ka/Ks analysis showed that the gene family may have experienced powerful purification selection pressure during wheat evolution. The qRT-PCR analysis showed that TaZF-HD genes had significant expression patterns in different biotic stress and abiotic stress. Through subcellular localization experiments, we found that TaZHD6-3B was located in the nucleus, while TaMIF4-5D was located in the cell membrane and nucleus. Our research contributes to a comprehensive understanding of the TaZF-HD family, provides a new perspective for further research on the biological functions of TaZF-HD genes in wheat.

scholarly journals A member of wheat class III peroxidase gene family, TaPRX-2A, enhanced the tolerance of salt stress

2020 ◽  
Author(s):  
Peisen Su ◽  
Jun Yan ◽  
Wen Li ◽  
Liang Wang ◽  
Jinxiao Zhao ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Gene Family ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Evolutionary Model ◽  
Evolutionary Analysis ◽  
Class Iii ◽  
Expression Levels ◽  
Stress Related Genes

Abstract Background: Salt and drought are the main abiotic stresses that restrict the yield of crops. Peroxidases (PRXs) are involved in various abiotic stress responses. Furthermore, only few wheat PRXs have been characterized in the mechanism of the abiotic stress response.Results: In this study, a novel wheat peroxidase (PRX) gene named TaPRX-2A, a member of wheat class III PRX gene family, was cloned and its response to salt stress was characterized. Based on the identification and evolutionary analysis of class III PRXs in 12 plants, we proposed an evolutionary model for TaPRX-2A, suggesting that occurrence of some exon fusion events during evolution. We also detected the positive selection of PRX domain in 13 PRXs involving our evolutionary model, and found 2 or 6 positively selected sites during TaPRX-2A evolution. Quantitative reverse transcription–polymerase chain reaction (qRT–PCR) results showed that TaPRX-2A exhibited relatively higher expression levels in root tissue than those exhibited in leaf and stem tissues. TaPRX-2A expression was also induced by abiotic stresses and hormone treatments such as polyethylene glycol 6000, NaCl, hydrogen peroxide (H2O2), salicylic acid (SA), methyljasmonic acid (MeJA) and abscisic acid (ABA). Transgenic wheat plants with overexpression of TaPRX-2A showed higher tolerance to salt stress than wild-type (WT) plants. Confocal microscopy revealed that TaPRX-2A-eGFP was mainly localized in cell nuclei. Survival rate, relative water content, and shoot length were higher in TaPRX-2A-overexpressing wheat than in the WT wheat, whereas root length was not significantly different. The activities of s superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) were enhanced in TaPRX-2A-overexpressing wheat compared with those in the WT wheat, resulting in the reduction of reactive oxygen species (ROS) accumulation and malondialdehyde (MDA) content. The expression levels of downstream stress-related genes showed that RD22, TLP4, ABAI, GST22, FeSOD, and CAT exhibited higher expressions in TaPRX-2A-overexpressing wheat than in WT under salt stress.Conclusions: The results show that TaPRX-2A plays a positive role in the response to salt stress by scavenging ROS and regulating stress-related genes.

Genome-wide investigation of the AP2/ERF superfamily and their expression under salt stress in Chinese willow (Salix matsudana)

2020 ◽  
Author(s):  
Yanhong Chen ◽  
Yuna Jiang ◽  
Guoyuan Liu ◽  
Chunmei Yu ◽  
Bolin Lian ◽  
...  
Keyword(s):  
Salt Stress ◽  
Expression Profiles ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Evolutionary Analysis ◽  
Sequencing Data ◽  
Genome Wide ◽  
Salix Matsudana

Abstract Background: AP2/ERF transcription factors (TFs) play indispensable roles in plant growth, development, and especially in various abiotic stresses responses. The AP2/ERF TF family has been discovered and classified in more than 50 species, including model plants, horticulture plants, crops, and trees. Many AP2/ERF TFs from various species have been functionally characterized. However, little is known about the AP2/ERF gene family of Chinese willow (Salix matsudana), which is a tetraploid ornamental tree species that is widely planted and is also considered a species that can improve the soil salinity of coastal beaches. The recently produced whole genome sequencing data of Salix matsudana allowed us to conduct an evolutionary analysis on the AP2/ERF genes during polyploidization and study the genome-wide expression profiles of AP2/ERF genes in Salix matsudana under salt stress. Results: In this study, 364 AP2/ERF genes of Salix matsudana (SmAP2/ERF) were identified and renamed according to the chromosomal location of the SmAP2/ERF genes. After phylogenetic analysis with known categories of genes from other species, the AP2/ERF genes were divided into three subfamilies: AP2 (55 members), ERF (301 members), and RAV (six members). Two Soloist genes were also identified. Gene structure and conserved motifs were analyzed in AP2/ERF genes, and introns were not found in most genes of the ERF subfamily, although some unique motifs were found to be important for the function of AP2/ERF genes. Syntenic relationships between the SmAP2/ERF genes and AP2/ERF genes from other species were also investigated to elucidate their evolutionary relationships during polyploidization. Moreover, analyses on the expression profiles under salt stress were also conducted.Conclusion: The progenitors of Salix matsudana underwent whole genome duplication not more than 10 Mya. Synteny analysis with other species showed macrosynteny between willow and poplar AP2/ERF genes and that Salix matsudana is genetically more closely related to Populus trichocarpa than to Salix purpurea. Further investigation of the AP2/ERF TFs demonstrated that differential expression patterns during salt stress and this information can help reveal the mechanism of salt tolerance regulation in Salix matsudana.

scholarly journals A member of wheat class III peroxidase gene family, TaPRX-2A, enhanced the tolerance of salt stress

2020 ◽  
Author(s):  
Peisen Su ◽  
Jun Yan ◽  
Wen Li ◽  
Liang Wang ◽  
Jinxiao Zhao ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Gene Family ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Evolutionary Model ◽  
Evolutionary Analysis ◽  
Class Iii ◽  
Expression Levels ◽  
Stress Related Genes

Abstract Background: Salt and drought are the main abiotic stresses that restrict the yield of crops. Peroxidases (PRXs) are involved in various abiotic stress responses. Furthermore, only few wheat PRXs have been characterized in the mechanism of the abiotic stress response.Results: In this study, a novel wheat peroxidase (PRX) gene named TaPRX-2A, a member of wheat class III PRX gene family, was cloned and its response to salt stress was characterized. Based on the identification and evolutionary analysis of class III PRXs in 12 plants, we proposed an evolutionary model for TaPRX-2A, suggesting that occurrence of some exon fusion events during evolution. We also detected the positive selection of PRX domain in 13 PRXs involving our evolutionary model, and found 2 or 6 positively selected sites during TaPRX-2A evolution. Quantitative reverse transcription–polymerase chain reaction (qRT–PCR) results showed that TaPRX-2A exhibited relatively higher expression levels in root tissue than those exhibited in leaf and stem tissues. TaPRX-2A expression was also induced by abiotic stresses and hormone treatments such as polyethylene glycol 6000, NaCl, hydrogen peroxide (H2O2), salicylic acid (SA), methyljasmonic acid (MeJA) and abscisic acid (ABA). Transgenic wheat plants with overexpression of TaPRX-2A showed higher tolerance to salt stress than wild-type (WT) plants. Confocal microscopy revealed that TaPRX-2A-eGFP was mainly localized in cell nuclei. Survival rate, relative water content, and shoot length were higher in TaPRX-2A-overexpressing wheat than in the WT wheat, whereas root length was not significantly different. The activities of s superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) were enhanced in TaPRX-2A-overexpressing wheat compared with those in the WT wheat, resulting in the reduction of reactive oxygen species (ROS) accumulation and malondialdehyde (MDA) content. The expression levels of downstream stress-related genes showed that RD22, TLP4, ABAI, GST22, FeSOD, and CAT exhibited higher expressions in TaPRX-2A-overexpressing wheat than in WT under salt stress.Conclusions: The results show that TaPRX-2A plays a positive role in the response to salt stress by scavenging ROS and regulating stress-related genes.

scholarly journals Genome-Wide Identification and Evolutionary Analysis of AOMT Gene Family in Pomegranate (Punica granatum)

Agronomy ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 318
Author(s):  
Xinhui Zhang ◽  
Weicheng Yuan ◽  
Yujie Zhao ◽  
Yuan Ren ◽  
Xueqing Zhao ◽  
...  
Keyword(s):  
Gene Family ◽  
Gene Evolution ◽  
Punica Granatum ◽  
Gene Family Evolution ◽  
Raw Material ◽  
Whole Genome ◽  
Evolutionary Analysis ◽  
New Genes ◽  
Genome Wide ◽  
Duplication Events

Gene duplication is the major resource with which to generate new genes, which provide raw material for novel functions evolution. Thus, to elucidate the gene family evolution after duplication events is of vital importance. Anthocyanin O-methyltransferases (AOMTs) have been recognized as being capable of anthocyanin methylation, which increases anthocyanin diversity and stability and improves the protection of plants from environmental stress. Meanwhile, no detailed identification or genome-wide analysis of the AOMT gene family members in pomegranate (Punicagranatum) have been reported. Three published pomegranate genome sequences offer substantial resources with which to explore gene evolution based on the whole genome. Altogether, 58 identified OMTs from pomegranate and five other species were divided into the AOMT group and the OMT group, according to their phylogenetic tree and AOMTs derived from OMTs. AOMTs in the same subclade have a similar gene structure and protein conserved motifs. The PgAOMT family evolved and expanded primarily via whole-genome duplication (WGD) and tandem duplication. PgAOMTs expression pattern in peel and aril development by qRT-PCR verification indicated that PgAOMTs had tissue-specific patterns. The main fates of AOMTs were neo- or non-functionalization after duplication events. High expression genes of PgOMT04 and PgOMT09 were speculated to contribute to “Taishanhong” pomegranate’s bright red peel color. Finally, we integrated the above analysis in order to infer the evolutionary scenario of AOMT family.

scholarly journals Evolution and Stress Responses of CLO Genes and Potential Function of the GhCLO06 Gene in Salt Resistance of Cotton

2022 ◽  
Vol 12 ◽  
Author(s):  
Xiaokang Fu ◽  
Yonglin Yang ◽  
Meng Kang ◽  
Hengling Wei ◽  
Boying Lian ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Gene Family ◽  
Stress Responses ◽  
Calcium Binding ◽  
Algal Species ◽  
Evolutionary Analysis ◽  
Qrt Pcr ◽  
Green Algal ◽  
Cotton Species

The caleosin (CLO) protein family displays calcium-binding properties and plays an important role in the abiotic stress response. Here, a total of 107 CLO genes were identified in 15 plant species, while no CLO genes were detected in two green algal species. Evolutionary analysis revealed that the CLO gene family may have evolved mainly in terrestrial plants and that biological functional differentiation between species and functional expansion within species have occurred. Of these, 56 CLO genes were identified in four cotton species. Collinearity analysis showed that CLO gene family expansion mainly occurred through segmental duplication and whole-genome duplication in cotton. Sequence alignment and phylogenetic analysis showed that the CLO proteins of the four cotton species were mainly divided into two types: H-caleosins (class I) and L-caleosins (class II). Cis-acting element analysis and quantitative RT–PCR (qRT–PCR) suggested that GhCLOs might be regulated by abscisic acid (ABA) and methyl jasmonate (MeJA). Moreover, transcriptome data and qRT–PCR results revealed that GhCLO genes responded to salt and drought stresses. Under salt stress, gene-silenced plants (TRV: GhCLO06) showed obvious yellowing and wilting, higher malondialdehyde (MDA) content accumulation, and significantly lower activities of superoxide dismutase (SOD) and peroxidase (POD), indicating that GhCLO06 plays a positive regulatory role in cotton salt tolerance. In gene-silenced plants (TRV: GhCLO06), ABA-related genes (GhABF2, GhABI5, and GhNAC4) were significantly upregulated after salt stress, suggesting that the regulation of salt tolerance may be related to the ABA signaling pathway. This research provides an important reference for further understanding and analyzing the molecular regulatory mechanism of CLOs for salt tolerance.

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