scholarly journals Genome-wide identification and comprehensive analysis of the NAC transcription factor family in sunflower during salt and drought stress

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wenhui Li ◽  
Youling Zeng ◽  
Fangliu Yin ◽  
Ran Wei ◽  
Xiaofei Mao
Keyword(s):  
Phylogenetic Analysis ◽  
Abiotic Stress ◽  
Drought Stress ◽  
Tissue Specificity ◽  
Large Family ◽  
Strong Response ◽  
Genome Wide ◽  
A Genome ◽  
Salt And Drought Stress ◽  
Nac Family

AbstractThe NAC (NAM, ATAF1/2, and CUC2), is a large family of plant-specific transcription factors (TFs) that exert crucial regulatory roles in various physiological processes and abiotic stresses. There is scanty information on the role of the NAC family in sunflower (Helianthus annuus L.). In this study, we conducted a genome-wide survey and expression analysis of the NAC family in sunflower. A total of 150 HaNACs were identified in sunflower. Phylogenetic analysis to compare HaNACs with Arabidopsis NACs generated 15 clusters. Among them, eight membrane-bound NAC TFs with transmembrane helixes were found (designated as NTLs), which were suggested to be localized in the membrane and transferred to the nucleus through proteolysis. Notably, 12 HaNACs were potentially regulated via miR164 cleavage or translational inhibition. By analyzing RNA-seq data from Sequence Read Archive (SRA), the expression of HaNACs showed tissue specificity and strong response to drought stress. Additionally, phylogenetic analysis of 150 HaNACs with the previously reported NACs related to abiotic stress revealed that 75% of the abiotic stress-related NACs were clustered into the SNAC (abiotic stress-related NAC) group, and only 25% were in the Non-SNAC group. qRT-PCR further demonstrated that about 75% of the HaNACs in the SNAC subgroup were induced by salt and drought stress, and the expression of some HaNACs showed tissue specificity. These findings provide valuable information that can deepen the understanding of how NAC TFs in sunflower respond to abiotic stress.

Genome-wide identification of citrus calmodulin-like genes and their expression in response to arbuscular mycorrhizal fungi colonization and drought

2021 ◽  
Author(s):  
Bo Shu ◽  
YaChao Xie ◽  
Fei Zhang ◽  
Dejian Zhang ◽  
Chunyan Liu ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Drought Stress ◽  
Arbuscular Mycorrhizal Fungi ◽  
Stress Responses ◽  
Mycorrhizal Fungi ◽  
Expression Patterns ◽  
Arbuscular Mycorrhizal ◽  
Biotic And Abiotic Stress ◽  
Genome Wide ◽  
A Genome

Calmodulin-like (CML) proteins represent a diverse family of protein in plants, and play significant roles in biotic and abiotic stress responses. However, the involvement of citrus CMLs in plant responses to drought stress (abiotic stress) and arbuscular mycorrhizal fungi (AMF) colonization remain relatively unknown. We characterized the citrus CML genes by analyzing the EF-hand domains and a genome-wide search, and identified a total of 38 such genes, distributed across at least nine chromosomes. Six tandem duplication clusters were observed in the CsCMLs, and 12 CsCMLs exhibited syntenic relationships with Arabidopsis thaliana CMLs. Gene expression analysis showed that 29 CsCMLs were expressed in the roots, and exhibited differential expression patterns. The regulation of CsCMLs expression was not consistent with the cis-elements identified in their promoters. CsCML2, 3, and 5 were upregulated in response to drought stress, and AMF colonization repressed the expression of CsCML7, 9, 12, 13,20, 27, 28, and 35,and induced that of CsCML1, 2, 3, 5, 8, 10, 11, 14, 15, 16, 18, 25, 30, 33, and 37. Furthermore, AMF colonization and drought stress exerted a synergistic effect, evident from the enhanced repression of CsCML7, 9, 12, 13, 27, 28, and 35 and enhanced expression of CsCML2, 3, and 5 under AMF colonization and drought stress. The present study provides valuable insights into the CsCML gene family and its responses to AMF colonization and drought stress.

scholarly journals Overexpression of PheNAC3 from moso bamboo promotes leaf senescence and enhances abiotic stress tolerance in Arabidopsis

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8716
Author(s):  
Lihua Xie ◽  
Miaomiao Cai ◽  
Xiangyu Li ◽  
Huifang Zheng ◽  
Yali Xie ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Drought Stress ◽  
Leaf Senescence ◽  
Stress Responses ◽  
Abiotic Stress Tolerance ◽  
Moso Bamboo ◽  
Biotic And Abiotic Stress ◽  
Phyllostachys Edulis ◽  
Salt And Drought Stress ◽  
Nac Family

The NAC family is one of the largest transcription factor families unique to plants, which regulates the growth and development, biotic and abiotic stress responses, and maturation and senescence in plants. In this study, PheNAC3, a NAC gene, was isolated and characterized from moso bamboo (Phyllostachys edulis). PheNAC3 belong to the NAC1 subgroup and has a conserved NAC domain on the N-terminus, which with 88.74% similarity to ONAC011 protein. PheNAC3 localized in the nucleus and exhibited transactivation activity. PheNAC3 was upregulated during the process of senescence of leaves and detected shoots. PheNAC3 was also induced by ABA, MeJA, NaCl and darkness, but it had no remarkable response to PEG and SA treatments. Overexpression of PheNAC3 could cause precocious senescence in Arabidopsis. Transgenic Arabidopsis displayed faster seed germination, better seedling growth, and a higher survival rate than the wild-type under salt or drought stress conditions. Moreover, AtSAG12 associated with senescence and AtRD29A and AtRD29b related to ABA were upregulated by PheNAC3 overexpression, but AtCAB was inhibited. These findings show that PheNAC3 may participate in leaf senescence and play critical roles in the salt and drought stress response.

scholarly journals Genome-wide identification and expression analysis of Raffinose synthetase family in cotton

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ruifeng Cui ◽  
Xiaoge Wang ◽  
Waqar Afzal Malik ◽  
Xuke Lu ◽  
Xiugui Chen ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Plant Leaves ◽  
Motif Analysis ◽  
Expression Levels ◽  
Genome Wide ◽  
Salt And Drought Stress ◽  
Key Genes ◽  
Stress Gene

Abstract Background The Raffinose synthetase (RAFS) genes superfamily is critical for the synthesis of raffinose, which accumulates in plant leaves under abiotic stress. However, it remains unclear whether RAFS contributes to resistance to abiotic stress in plants, specifically in the Gossypium species. Results In this study, we identified 74 RAFS genes from G. hirsutum, G. barbadense, G. arboreum and G. raimondii by using a series of bioinformatic methods. Phylogenetic analysis showed that the RAFS gene family in the four Gossypium species could be divided into four major clades; the relatively uniform distribution of the gene number in each species ranged from 12 to 25 based on species ploidy, most likely resulting from an ancient whole-genome polyploidization. Gene motif analysis showed that the RAFS gene structure was relatively conservative. Promoter analysis for cis-regulatory elements showed that some RAFS genes might be regulated by gibberellins and abscisic acid, which might influence their expression levels. Moreover, we further examined the functions of RAFS under cold, heat, salt and drought stress conditions, based on the expression profile and co-expression network of RAFS genes in Gossypium species. Transcriptome analysis suggested that RAFS genes in clade III are highly expressed in organs such as seed, root, cotyledon, ovule and fiber, and under abiotic stress in particular, indicating the involvement of genes belonging to clade III in resistance to abiotic stress. Gene co-expressed network analysis showed that GhRFS2A-GhRFS6A, GhRFS6D, GhRFS7D and GhRFS8A-GhRFS11A were key genes, with high expression levels under salt, drought, cold and heat stress. Conclusion The findings may provide insights into the evolutionary relationships and expression patterns of RAFS genes in Gossypium species and a theoretical basis for the identification of stress resistance materials in cotton.

scholarly journals Genome- Wide Identification, Structure Characterization and Expression Pattern Profiling of the Aquaporin Gene Family in Betula pendula

2021 ◽  
Vol 22 (14) ◽  
pp. 7269
Author(s):  
Jean-Stéphane Venisse ◽  
Eele Õunapuu-Pikas ◽  
Maxime Dupont ◽  
Aurélie Gousset-Dupont ◽  
Mouadh Saadaoui ◽  
...  
Keyword(s):  
Cold Stress ◽  
Gene Family ◽  
Betula Pendula ◽  
Large Family ◽  
Biochemical Properties ◽  
Silver Birch ◽  
Structure Characterization ◽  
Transcriptional Expression ◽  
Genome Wide ◽  
A Genome

Aquaporin water channels (AQPs) constitute a large family of transmembrane proteins present throughout all kingdoms of life. They play key roles in the flux of water and many solutes across the membranes. The AQP diversity, protein features, and biological functions of silver birch are still unknown. A genome analysis of Betula pendula identified 33 putative genes encoding full-length AQP sequences (BpeAQPs). They are grouped into five subfamilies, representing ten plasma membrane intrinsic proteins (PIPs), eight tonoplast intrinsic proteins (TIPs), eight NOD26-like intrinsic proteins (NIPs), four X intrinsic proteins (XIPs), and three small basic intrinsic proteins (SIPs). The BpeAQP gene structure is conserved within each subfamily, with exon numbers ranging from one to five. The predictions of the aromatic/arginine selectivity filter (ar/R), Froger’s positions, specificity-determining positions, and 2D and 3D biochemical properties indicate noticeable transport specificities to various non-aqueous substrates between members and/or subfamilies. Nevertheless, overall, the BpePIPs display mostly hydrophilic ar/R selective filter and lining-pore residues, whereas the BpeTIP, BpeNIP, BpeSIP, and BpeXIP subfamilies mostly contain hydrophobic permeation signatures. Transcriptional expression analyses indicate that 23 BpeAQP genes are transcribed, including five organ-related expressions. Surprisingly, no significant transcriptional expression is monitored in leaves in response to cold stress (6 °C), although interesting trends can be distinguished and will be discussed, notably in relation to the plasticity of this pioneer species, B. pendula. The current study presents the first detailed genome-wide analysis of the AQP gene family in a Betulaceae species, and our results lay a foundation for a better understanding of the specific functions of the BpeAQP genes in the responses of the silver birch trees to cold stress.

scholarly journals Genome-Wide Characterization of Glutathione Peroxidase (GPX) Gene Family in Rapeseed (Brassica napus L.) Revealed Their Role in Multiple Abiotic Stress Response and Hormone Signaling

Antioxidants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1481
Author(s):  
Wei Li ◽  
Xuemin Huai ◽  
Peitao Li ◽  
Ali Raza ◽  
Muhammad Salman Mubarik ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Brassica Napus ◽  
Gene Family ◽  
Antioxidant Defense ◽  
Main Role ◽  
Brassica Napus L ◽  
Group I ◽  
Genome Wide ◽  
A Genome ◽  
Antioxidant Defense Systems

Plant glutathione peroxidases (GPXs) are the main enzymes in the antioxidant defense system that sustain H2O2 homeostasis and normalize plant reaction to abiotic stress conditions. To understand the major roles of the GPX gene family in rapeseed (Brassica napus L.), for the first time, a genome-wide study identified 25 BnGPX genes in the rapeseed genome. The phylogenetic analysis discovered that GPX genes were grouped into four major groups (Group I–Group IV) from rapeseed and three closely interrelated plant species. The universal investigation uncovered that the BnGPXs gene experienced segmental duplications and positive selection pressure. Gene structure and motifs examination recommended that most of the BnGPX genes demonstrated a comparatively well-maintained exon-intron and motifs arrangement within the identical group. Likewise, we recognized five hormones-, four stress-, and numerous light-reactive cis-elements in the promoters of BnGPXs. Five putative bna-miRNAs from two families were also prophesied, targeting six BnGPXs genes. Gene ontology annotation results proved the main role of BnGPXs in antioxidant defense systems, ROS, and response to stress stimulus. Several BnGPXs genes revealed boosted expression profiles in many developmental tissues/organs, i.e., root, seed, leaf, stem, flower, and silique. The qRT-PCR based expression profiling exhibited that two genes (BnGPX21 and BnGPX23) were suggestively up-regulated against different hormones (ABA, IAA, and MeJA) and abiotic stress (salinity, cold, waterlogging, and drought) treatments. In short, our discoveries provide a basis for additional functional studies on the BnGPX genes in future rapeseed breeding programs.

scholarly journals Overexpression of the ThTPS gene enhanced T. hispida salt and drought stress tolerance

2020 ◽  
Author(s):  
PeiLong Wang ◽  
XiaoJin Lei ◽  
JiaXin Lv ◽  
caiqiu gao
Keyword(s):  
Abiotic Stress ◽  
Drought Stress ◽  
Stress Tolerance ◽  
Abiotic Stress Tolerance ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Drought Stress Tolerance ◽  
Trehalose Metabolism ◽  
Physiological Indexes ◽  
Salt And Drought Stress

Abstract Background: Trehalose is a nonreducing disaccharide with high stability and strong water absorption properties that can improve the resistance of organisms to various abiotic stresses. Trehalose-6-phosphate synthase (TPS) plays important roles in trehalose metabolism and signaling. Results: A full-length cDNA of ThTPS was cloned from Tamarix hispida. The phylogenetic tree among ThTPS and 11 AtTPS in Arabidopsis indicates that the ThTPS protein had a close evolutionary relationship with AtTPS7. However, the function of AtTPS7 has not been determined. To analyze the abiotic stress tolerance function of ThTPS, the expression patterns of ThTPS were monitored under salt and drought stress and JA, ABA and GA3 hormone stimulation in T. hispida by qRT-PCR. The results showed that ThTPS expression was clearly induced by these 5 kinds of treatments at at least one studied point. Particularly under salt stress, ThTPS was highly induced in the roots of T. hispda. Furthermore, the ThTPS gene was transiently overexpressed in T. hispida. The results of physiological indexes and staining showed that overexpression of the ThTPS gene increased T. hispida salt and drought stress tolerance. Conclusion: The ThTPS gene can respond to abiotic stress such as salt and drought, and overexpression of ThTPS gene can significantly improve salt and drought tolerance. These findings establish a foundation to better understand the response of TPS genes to abiotic stress in plants.

scholarly journals Genome-Wide Phylogenetic Analysis, Expression Pattern, and Transcriptional Regulatory Network of the Pig C/EBP Gene Family

2021 ◽  
Vol 17 ◽  
pp. 117693432110413
Author(s):  
Chaoxin Zhang ◽  
Tao Wang ◽  
Tongyan Cui ◽  
Shengwei Liu ◽  
Bing Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Phylogenetic Analysis ◽  
Regulatory Network ◽  
Target Genes ◽  
Transcriptional Regulatory Network ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Genome Wide ◽  
A Genome

The CCAAT/enhancer binding protein (C/EBP) transcription factors (TFs) regulate many important biological processes, such as energy metabolism, inflammation, cell proliferation etc. A genome-wide gene identification revealed the presence of a total of 99 C/EBP genes in pig and 19 eukaryote genomes. Phylogenetic analysis showed that all C/EBP TFs were classified into 6 subgroups named C/EBPα, C/EBPβ, C/EBPδ, C/EBPε, C/EBPγ, and C/EBPζ. Gene expression analysis showed that the C/EBPα, C/EBPβ, C/EBPδ, C/EBPγ, and C/EBPζ genes were expressed ubiquitously with inconsistent expression patterns in various pig tissues. Moreover, a pig C/EBP regulatory network was constructed, including C/EBP genes, TFs and miRNAs. A total of 27 feed-forward loop (FFL) motifs were detected in the pig C/EBP regulatory network. Based on the RNA-seq data, gene expression patterns related to FFL sub-network were analyzed in 27 adult pig tissues. Certain FFL motifs may be tissue specific. Functional enrichment analysis indicated that C/EBP and its target genes are involved in many important biological pathways. These results provide valuable information that clarifies the evolutionary relationships of the C/EBP family and contributes to the understanding of the biological function of C/EBP genes.

Genome-Wide Identification and Expression Profile Analysis of WRKY Family Genes in Teak (Tectona Grandis)

2020 ◽  
Author(s):  
Xi-Yang Wang ◽  
Jie Song ◽  
Jia-Hui Xing ◽  
Jun-Feng Liang ◽  
Bi-ying Ke
Keyword(s):  
Profile Analysis ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Large Family ◽  
Tectona Grandis ◽  
Duplication Event ◽  
Whole Genome Sequence ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
A Genome

Abstract Background: WRKY proteins comprise a large family of transcription factors that play vital roles in many aspects of physiological processes and adaption to environment. However, little information was available about the WRKY genes in teak (Tectona grandis). The recent release of the whole-genome sequence of teak allowed us to perform a genome-wide investigation into the organization and expression profiling of teak WRKY genes. Results: In the present study, 102 teak WRKY (TgWRKY) genes were identified and renamed as per their positions on chromosome and scaffolds. According to their structural and phylogenetic analysis, the 102 TgWRKYs were further classified into three main groups with seceral subgroups. The segmental duplication event played a major role in the expansion of teak WRKY gene family and three WGD events were inferred. Expression profiles derived from transcriptome data exhibited distinct expression patterns of TgWRKY genes in various tissues and inresponse to different abiotic stress.Conclusions: 102 TgWRKY genes were identified in teak and the structure of their encoded proteins, their evolutionary characteristics and expression patterns were examined in this study. This study generated an important resource that will provide helpful information for further exploration of the TgWRKY genes role in the regulatory mechanism in response to abiotic stresses.

scholarly journals Identification of Maize CC-Type Glutaredoxins That Are Associated with Response to Drought Stress

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 610
Author(s):  
Ding ◽  
He ◽  
Tang ◽  
Du ◽  
Wang
Keyword(s):  
Drought Stress ◽  
Active Sites ◽  
Expression Profiles ◽  
Maize Genome ◽  
Tblastn Search ◽  
Redox Active ◽  
Genome Wide ◽  
A Genome ◽  
Maize Cultivation ◽  
Conservative Domain

Global maize cultivation is often adversely affected by drought stress. The CC-type glutaredoxin (GRX) genes form a plant-specific subfamily that regulate plant growth and respond to environmental stresses. However, how maize CC-type GRX (ZmGRXCC) genes respond to drought stress remains unclear. We performed a TBLASTN search to identify ZmGRXCCs in the maize genome and verified the identified sequences using the NCBI conservative domain database (CDD). We further established a phylogenetic tree using Mega7 and surveyed known cis-elements in the promoters of ZmGRXCCs using the PlantCARE database. We found twenty-one ZmGRXCCs in the maize genome by a genome-wide investigation and compared their phylogenetic relationships with rice, maize, and Arabidopsis. The analysis of their redox active sites showed that most of the 21 ZmGRXCCs share similar structures with their homologs. We assessed their expression at young seedlings and adult leaves under drought stress and their expression profiles in 15 tissues, and found that they were differentially expressed, indicating that different ZmGRXCC genes have different functions. Notably, ZmGRXCC14 is up-regulated at seedling, V12, V14, V16, and R1 stages. Importantly, significant associations between genetic variation in ZmGRXCC14 and drought tolerance are found at the seedling stage. These results will help to advance the study of the function of ZmGRXCCs genes under drought stress and understand the mechanism of drought resistance in maize.

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