Genome-wide analysis of the AREB/ABF gene lineage in land plants and functional analysis of TaABF3 in Arabidopsis

Abstract Background: Previous studies have shown that ABFs (abscisic acid-responsive transcription factors) are important ABA-signaling components that participate in abiotic stress response. However, little is known about the function of ABFs in Triticum aestivum. In addition, although various ABFs have been identified in other species, the phylogenetic relationship between ABF transcription factors has not been systemically investigated in land plants. Results: In this study, we systemically collected ABFs from land plants and analyzed the phylogenetic relationship of these ABF genes. The ABF genes are present in all the land plants we investigated, including moss, lycophyte, monocots, and eudicots. Furthermore, these ABF genes are phylogenetically divided into seven subgroups, differentiations that are supported by variation in the gene structure, protein properties, and motif patterns. We further demonstrated that the expression of ABF genes varies among different tissues and developmental stages, and are induced by one or more environmental stresses. Furthermore, we found that three wheat ABFs (TaABF1, TaABF2, and TaABF3) were significantly induced by drought stress. Compared with wild-type (WT) plants, transgenic Arabidopsis plants overexpressing TaABF3 displayed enhanced drought tolerance. Conclusions: These results provide important ground work for understanding the phylogenetic relationships between plant ABF genes. Our results also indicate that TaABFs may participate in regulating plant response to abiotic stresses.

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Genome-wide analysis of the AREB/ABF gene lineage in land plants and functional analysis of TaABF3 in Arabidopsis

10.21203/rs.3.rs-19486/v1 ◽

2020 ◽

Author(s):

Fangfang Li ◽

Fangming Mei ◽

Yifang Zhang ◽

Shumin Li ◽

Hude Mao

Keyword(s):

Transcription Factors ◽

Phylogenetic Relationship ◽

Developmental Stages ◽

Land Plants ◽

Wild Type ◽

Abiotic Stress Response ◽

Genome Wide ◽

Protein Properties ◽

Relationship Of ◽

Signaling Components

Abstract Background: Previous studies have shown that ABFs (abscisic acid-responsive transcription factors) are important ABA-signaling components that participate in abiotic stress response. However, little is known about the function of ABFs in Triticum aestivum. In addition, although various ABFs have been identified in other species, the phylogenetic relationship between ABF transcription factors has not been systemically investigated in land plants. Results: In this study, we systemically collected ABFs from land plants and analyzed the phylogenetic relationship of these ABF genes. The ABF genes are present in all the land plants we investigated, including moss, lycophyte, monocots, and eudicots. Furthermore, these ABF genes are phylogenetically divided into seven subgroups, differentiations that are supported by variation in the gene structure, protein properties, and motif patterns. We further demonstrated that the expression of ABF genes varies among different tissues and developmental stages, and are induced by one or more environmental stresses. Furthermore, we found that three wheat ABFs (TaABF1, TaABF2, and TaABF3) were significantly induced by drought stress. Compared with wild-type (WT) plants, transgenic Arabidopsis plants overexpressing TaABF3 displayed enhanced drought tolerance. Conclusions: These results provide important ground work for understanding the phylogenetic relationships between plant ABF genes. Our results also indicate that TaABFs may participate in regulating plant response to abiotic stresses.

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Genome-wide analysis of the AREB/ABF gene lineage in land plants and functional analysis of TaABF3 in Arabidopsis

10.21203/rs.3.rs-19486/v2 ◽

2020 ◽

Author(s):

Fangfang Li ◽

Fangming Mei ◽

Yifang Zhang ◽

Shumin Li ◽

Zhensheng Kang ◽

...

Keyword(s):

Transcription Factors ◽

Phylogenetic Relationship ◽

Developmental Stages ◽

Land Plants ◽

Wild Type ◽

Abiotic Stress Response ◽

Genome Wide ◽

Protein Properties ◽

Relationship Of ◽

Signaling Components

Abstract Background: Previous studies have shown that ABFs (abscisic acid-responsive transcription factors) are important ABA-signaling components that participate in abiotic stress response. However, little is known about the function of ABFs in Triticum aestivum. In addition, although various ABFs have been identified in other species, the phylogenetic relationship between ABF transcription factors has not been systemically investigated in land plants. Results: In this study, we systemically collected ABFs from land plants and analyzed the phylogenetic relationship of these ABF genes. The ABF genes are present in all the land plants we investigated, including moss, lycophyte, monocots, and eudicots. Furthermore, these ABF genes are phylogenetically divided into seven subgroups, differentiations that are supported by variation in the gene structure, protein properties, and motif patterns. We further demonstrated that the expression of ABF genes varies among different tissues and developmental stages, and are induced by one or more environmental stresses. Furthermore, we found that three wheat ABFs (TaABF1, TaABF2, and TaABF3) were significantly induced by drought stress. Compared with wild-type (WT) plants, transgenic Arabidopsis plants overexpressing TaABF3 displayed enhanced drought tolerance. Conclusions: These results provide important ground work for understanding the phylogenetic relationships between plant ABF genes. Our results also indicate that TaABFs may participate in regulating plant response to abiotic stresses.

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Genome-wide analysis of the AREB/ABF gene lineage in land plants and functional analysis of TaABF3 in Arabidopsis

10.21203/rs.3.rs-19486/v3 ◽

2020 ◽

Author(s):

Fangfang Li ◽

Fangming Mei ◽

Yifang Zhang ◽

Shumin Li ◽

Zhensheng Kang ◽

...

Keyword(s):

Transcription Factors ◽

Phylogenetic Relationship ◽

Developmental Stages ◽

Land Plants ◽

Wild Type ◽

Abiotic Stress Response ◽

Genome Wide ◽

Protein Properties ◽

Relationship Of ◽

Signaling Components

Abstract Background: Previous studies have shown that ABFs (abscisic acid-responsive transcription factors) are important ABA-signaling components that participate in abiotic stress response. However, little is known about the function of ABFs in Triticum aestivum. In addition, although various ABFs have been identified in other species, the phylogenetic relationship between ABF transcription factors has not been systemically investigated in land plants. Results: In this study, we systemically collected ABFs from land plants and analyzed the phylogenetic relationship of these ABF genes. The ABF genes are present in all the land plants we investigated, including moss, lycophyte, monocots, and eudicots. Furthermore, these ABF genes are phylogenetically divided into seven subgroups, differentiations that are supported by variation in the gene structure, protein properties, and motif patterns. We further demonstrated that the expression of ABF genes varies among different tissues and developmental stages, and are induced by one or more environmental stresses. Furthermore, we found that three wheat ABFs (TaABF1, TaABF2, and TaABF3) were significantly induced by drought stress. Compared with wild-type (WT) plants, transgenic Arabidopsis plants overexpressing TaABF3 displayed enhanced drought tolerance. Conclusions: These results provide important ground work for understanding the phylogenetic relationships between plant ABF genes. Our results also indicate that TaABFs may participate in regulating plant response to abiotic stresses.

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GENETIC DIVERSITY, POPULATION STRUCTURE AND PHYLOGENETIC RELATIONSHIP OF RACE, SPORTS, DRAFT, AND WILD TYPE HORSES

The Pakistan Journal of Agricultural Sciences ◽

10.21162/pakjas/17.5087 ◽

2018 ◽

Author(s):

Iqra Atiq

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Phylogenetic Relationship ◽

Wild Type ◽

Relationship Of

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Molecular Characterization and Phylogenetic Relationship of Wild Type 1 Poliovirus Strains Circulating across Pakistan and Afghanistan Bordering Areas during 2010–2012

PLoS ONE ◽

10.1371/journal.pone.0107697 ◽

2014 ◽

Vol 9 (9) ◽

pp. e107697 ◽

Cited By ~ 6

Author(s):

Shahzad Shaukat ◽

Mehar Angez ◽

Muhammad Masroor Alam ◽

Salmaan Sharif ◽

Adnan Khurshid ◽

...

Keyword(s):

Molecular Characterization ◽

Phylogenetic Relationship ◽

Wild Type ◽

Relationship Of

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Genome-wide regulation of light-controlled seedling morphogenesis by three families of transcription factors

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1803861115 ◽

2018 ◽

Vol 115 (25) ◽

pp. 6482-6487 ◽

Cited By ~ 27

Author(s):

Hui Shi ◽

Mohan Lyu ◽

Yiwen Luo ◽

Shoucheng Liu ◽

Yue Li ◽

...

Keyword(s):

Transcription Factors ◽

Continuous Light ◽

Specific Protein ◽

Bhlh Protein ◽

Wild Type ◽

Morphological Aspects ◽

Genome Wide ◽

Wide Range ◽

Transcriptional Changes ◽

Bzip Proteins

Three families of transcription factors have been reported to play key roles in light control of Arabidopsis seedling morphogenesis. Among them, bHLH protein PIFs and plant-specific protein EIN3/EIN3-LIKE 1 (EIN3/EIL1) accumulate in the dark to maintain skotomorphogenesis. On the other hand, HY5 and HY5 HOMOLOG (HYH), two related bZIP proteins, are stabilized in light and promote photomorphogenic development. To systemically investigate the transcriptional regulation of light-controlled seedling morphogenesis, we generated HY5ox/pifQein3eil1, which contained mutations of EIN3/EIL1 and four PIF genes (pifQein3eil1) and overexpression of HY5. Our results show that dark-grown HY5ox/pifQein3eil1 seedlings display a photomorphogenesis highly similar to that of wild-type seedlings grown in continuous light, with remarkably enhanced photomorphogenic phenotypes compared with the pifQ mutants. Consistent with the genetic evidence, transcriptome analysis indicated that PIFs, EIN3/EIL1, and HY5 are dominant transcription factors in collectively mediating a wide range of light-caused genome-wide transcriptional changes. Moreover, PIFs and EIN3/EIL1 independently control the expression of light-regulated genes such as HLS1 to cooperatively regulate apical hook formation, hypocotyl elongation, and cotyledon opening and expansion. This study illustrates a comprehensive regulatory network of transcription activities that correspond to specific morphological aspects in seedling skotomorphogenesis and photomorphogenesis.

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Comparative transcriptome analysis of hard and tender fruit spines of cucumber to identify genes involved in morphological development of fruit spines

10.21203/rs.3.rs-31353/v2 ◽

2020 ◽

Author(s):

Duo Lv ◽

Yao Yu ◽

Liang-Rong Xiong ◽

Gang Wang ◽

Jin-An Pang ◽

...

Keyword(s):

Transcription Factors ◽

Molecular Mechanisms ◽

Developmental Stages ◽

Developmental Process ◽

Stage Iii ◽

Morphological Development ◽

Wild Type ◽

Polar Transport ◽

Cucumber Fruit ◽

Auxin Polar Transport

Abstract Background: The trichomes of cucumber fruits are also called spines. Cucumber has important commercial value, and its fruit spines represent a classical tissue with which to study the cell division and differentiation mode of multicellular trichomes. Although there have been many studies on the development of unicellular trichomes in model plants, the molecular mechanism of multicellular trichome formation remains elusive. In this study, we used a pair of cucumber materials defined as having hard (Ts, wild type) or tender (ts, mutant) spines in a previous study. The whole developmental process of fruit spines was continuously observed by microscopy and SEM. In an attempt to define the developmental stages of fruit spines, transcriptome profiles at different stages were determined to explore the molecular mechanisms underlying the process of spine development. Results: According to significant phenotypic differences, the developmental process of fruit spines was clearly defined as involving four stages. Comparison of transcriptome profiles showed that 803 and 722 genes were upregulated in the stalk (stage II and stage III) and base (stage IV) developmental stages of fruit spines, respectively. Functional analysis of differentially expressed genes (DEGs) showed that for all developmental stages of fruit spines, lipid metabolism, amino acid metabolism, and signal transduction were the most noticeable pathways. However, during the development of the stalk, genes related to auxin polar transport and HD-ZIP transcription factors were significantly upregulated. bHLH transcription factors and cytoskeleton-related genes were significantly upregulated during the development of the base. In addition, stage III was the key point for differentiating between the wild type and mutant. We detected 628 DEGs between the wild type and mutant at this stage. These DEGs are mainly involved in calcium signaling of the cytoskeleton and auxin polar transport, indicating that the main reason for the disorder of the fruit spine developmental pattern in the mutant was a change in cell polarity caused by blocked intercellular signal transmission.Conclusions: Our study defines in great detail the developmental stages of cucumber fruit spines. At the same time, transcriptome profiles are used to present the gene regulatory networks at different developmental stages of cucumber fruit spines. In addition, we analyzed transcriptomic data of a wild type and mutant to elucidate the biological pathways involving C-type lectin receptor-like kinase that regulate the development of fruit spines.

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GENETIC DIVERSITY, POPULATION STRUCTURE AND PHYLOGENETIC RELATIONSHIP OF RACE, SPORTS, DRAFT AND WILD TYPE HORSES

The Pakistan Journal of Agricultural Sciences ◽

10.21162/pakjas/18.6702 ◽

2018 ◽

Vol 55 (01) ◽

pp. 155-158

Author(s):

Iqra Atiq

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Phylogenetic Relationship ◽

Wild Type ◽

Relationship Of

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Genome-Wide Identification of Stress-Associated Proteins (SAPs) Encoding A20/AN1 Zinc Finger in Almond (Prunus dulcis) and Their Differential Expression during Fruit Development

Plants ◽

10.3390/plants11010117 ◽

2021 ◽

Vol 11 (1) ◽

pp. 117

Author(s):

Sidra Fatima ◽

Zeeshan Zafar ◽

Alvina Gul ◽

Muhammad Faraz Bhatti

Keyword(s):

Zinc Finger ◽

Developmental Stages ◽

Evolutionary Relationship ◽

Prunus Dulcis ◽

Regulatory Elements ◽

Genome Wide ◽

Upstream Promoter ◽

Associated Proteins ◽

Upstream Promoter Region ◽

Relationship Of

Stress-associated proteins (SAPs) are zinc finger proteins involved in the regulation of various stresses in a variety of plant species. A total of nine PdSAP genes were identified in Prunus dulcis. Phylogenetic and synteny analyses were performed to analyze the homology and evolutionary relationship of PdSAP genes. The functions of PdSAP genes were assessed by further analyses, including cis-regulatory elements, gene duplication, gene ontology, gene structure, subcellular localization, and motif pattern. This study found that PdSAP genes were unevenly distributed on chromosomes 2, 3, 6, and 7. Phylogenetic analysis of PdSAP genes with Arabidopsis thaliana and Oryza sativa suggested that six subgroups have a similar pattern of AN1 and A20 domains in each subgroup. PdSAP genes lacked duplicated blocks. The majority of PdSAP genes were localized in the nucleus region. Three hormonal and five stress cis-regulatory elements were found in the upstream promoter region of the PdSAP gene family. RNA-seq analysis revealed differential gene expression of PdSAP genes at days 12, 17, 22, 27, 32, and 37 of fruitlet development after flowering. This study identifies the SAP genes in P. dulcis and also provides insights into the expression of PdSAP genes in abnormal fruitlets with diapause atrophic growth at various developmental stages.

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