scholarly journals Genome-wide analysis of the C3H zinc finger family reveals its functions in salt stress responses of Pyrus betulaefolia

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9328
Author(s):  
Chunxiao Liu ◽  
Xiaoyang Xu ◽  
Jialiang Kan ◽  
Zong ming Cheng ◽  
Youhong Chang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Stress Responses ◽  
Structural Characteristics ◽  
Expression Profiles ◽  
Purifying Selection ◽  
Regulate Gene Expression ◽  
Genome Wide ◽  
Complex Functions ◽  
Gene Structures ◽  
Environmental Responses

Transcription factors regulate gene expression in response to various external and internal cues by activating or suppressing downstream genes. Significant progress has been made in identifying and characterizing the Cysteine3Histidine (C3H) gene family in several dicots and monocots. They are characterized by their signature motif of three cysteine and one histidine residues, and reportedly play important roles in regulation of plant growth, developmental processes and environmental responses. In this study, we performed genome-wide and deep analysis of putative C3H genes, and a total of 117 PbeC3H members, were identified in P. betulaefolia and classified into 12 groups. Results were supported by the gene structural characteristics and phylogenetic analysis. These genes were unevenly distributed on 17 chromosomes. The gene structures of the C3H genes were relatively complex but conserved in each group. The C3H genes experienced a WGD event that occurred in the ancestor genome of P. betulaefolia and apple before their divergence based on the synonymous substitutions (Ks) values. There were 35 and 37 pairs of paralogous genes in the P. betulaefolia and apple genome, respectively, and 87 pairs of orthologous genes between P. betulaefolia and apple were identified. Except for one orthologous pairs PbeC3H66 and MD05G1311700 which had undergone positive selection, the other C3H genes had undergone purifying selection. Expression profiles showed that high salinity stress could influence the expression level of C3H genes in P. betulaefolia. Four members were responsive to salt stress in roots, nine were responsive to salt stress in leaves and eight showed inhibited expression in leaves. Results suggested important roles of PbeC3H genes in response to salt stress and will be useful for better understanding the complex functions of the C3H genes, and will provide excellent candidates for salt-tolerance 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.

scholarly journals Mungbean DIRIGENT Gene Subfamilies and Their Expression Profiles Under Salt and Drought Stresses

2021 ◽  
Vol 12 ◽  
Author(s):  
Wenying Xu ◽  
Tong Liu ◽  
Huiying Zhang ◽  
Hong Zhu
Keyword(s):  
Stress Responses ◽  
Expression Profiles ◽  
Pfam Domain ◽  
Vascular Plant ◽  
Expression Patterns ◽  
Promoter Regions ◽  
Genome Wide ◽  
A Genome ◽  
Salt And Drought Stress ◽  
Gene Structures

DIRIGENT (DIR) genes are key players in environmental stress responses that have been identified in many vascular plant species. However, few studies have examined the VrDIR genes in mungbean. In this study, we characterized 37 VrDIR genes in mungbean using a genome-wide identification method. VrDIRs were distributed on seven of the 11 mungbean chromosomes, and chromosome three contained the most VrDIR genes, with seven members. Thirty-two of the 37 VrDIRs contained a typical DIR gene structure, with one exon; the conserved DIR domain (i.e., Pfam domain) occupied most of the protein in 33 of the 37 VrDIRs. The gene structures of VrDIR genes were analyzed, and a total of 19 distinct motifs were detected. VrDIR genes were classified into five groups based on their phylogenetic relationships, and 13 duplicated gene pairs were identified. In addition, a total of 92 cis-acting elements were detected in all 37 VrDIR promoter regions, and VrDIR genes contained different numbers and types of cis-acting elements. As a result, VrDIR genes showed distinct expression patterns in different tissues and in response to salt and drought stress.

scholarly journals Genome-Wide Identification, Evolution, and Expression Analysis of TPS and TPP Gene Families in Brachypodium distachyon

Plants ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 362 ◽  
Author(s):  
Song Wang ◽  
Kai Ouyang ◽  
Kai Wang
Keyword(s):  
Stress Responses ◽  
Brachypodium Distachyon ◽  
Interaction Network ◽  
Purifying Selection ◽  
Gene Interaction ◽  
Gene Families ◽  
Gene Interaction Network ◽  
Genome Wide ◽  
Duplication Events ◽  
Gene Structures

Trehalose biosynthesis enzyme homologues in plants contain two families, trehalose-6-phosphate synthases (TPSs) and trehalose-6-phosphate phosphatases (TPPs). Both families participate in trehalose synthesis and a variety of stress-resistance processes. Here, nine BdTPS and ten BdTPP genes were identified based on the Brachypodium distachyon genome, and all genes were classified into three classes. The Class I and Class II members differed substantially in gene structures, conserved motifs, and protein sequence identities, implying varied gene functions. Gene duplication analysis showed that one BdTPS gene pair and four BdTPP gene pairs are formed by duplication events. The value of Ka/Ks (non-synonymous/synonymous) was less than 1, suggesting purifying selection in these gene families. The cis-elements and gene interaction network prediction showed that many family members may be involved in stress responses. The quantitative real-time reverse transcription (qRT-PCR) results further supported that most BdTPSs responded to at least one stress or abscisic acid (ABA) treatment, whereas over half of BdTPPs were downregulated after stress treatment, implying that BdTPSs play a more important role in stress responses than BdTPPs. This work provides a foundation for the genome-wide identification of the B. distachyon TPS–TPP gene families and a frame for further studies of these gene families in abiotic stress responses.

scholarly journals Genome-wide identification, characterization, and expression patterns analysis of the SBP-box gene family in wheat (Triticum aestivum L.)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ying Li ◽  
Qilu Song ◽  
Yamin Zhang ◽  
Zheng Li ◽  
Jialin Guo ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Tandem Duplication ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Triticum Aestivum L ◽  
Genome Wide ◽  
Related Development ◽  
Gene Structures

Abstract SQUAMOSA promoter-binding protein (SBP)-box genes encode a family of plant-specific transcription factors that play roles in plant growth and development. The characteristics of SBP-box genes in rice (Oryza sativa) and Arabidopsis have been reported, but their potential roles in wheat (Triticum aestivum) are not fully understood. In this study, 48 SBP-box genes (TaSBPs) were identified; they were located in all wheat chromosomes except for 4B and 4D. Six TaSBPs were identified as tandem duplication genes that formed three tandem duplication pairs, while 22 were segmentally duplicated genes that formed 16 segmental duplication pairs. Subcellular localization prediction showed TaSBPs were located in nucleus. Among the 48 TaSBPs, 24 were predicted to be putative targets of TamiR156. Phylogenetic analysis showed that TaSBPs, AtSBPs, and OsSBPs that shared similar functions were clustered into the same subgroups. The phylogenetic relationships between the TaSBPs were supported by the identification of highly conserved motifs and gene structures. Four types of cis-elements––transcription-related, development-related, hormone-related, and abiotic stress-related elements––were found in the TaSBP promoters. Expression profiles indicated most TaSBPs participate in flower development and abiotic stress responses. This study establishes a foundation for further investigation of TaSBP genes and provides novel insights into their biological functions.

scholarly journals Genome-Wide Characterization of DNA Demethylase Genes and Their Association with Salt Response in Pyrus

Genes ◽  
2018 ◽  
Vol 9 (8) ◽  
pp. 398 ◽  
Author(s):  
Chunxiao Liu ◽  
Hui Li ◽  
Jing Lin ◽  
Ying Wang ◽  
Xiaoyang Xu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Salt Stress ◽  
Structural Characteristics ◽  
Regulation Of Gene Expression ◽  
Duplication Event ◽  
Genome Duplication Event ◽  
Genome Wide ◽  
Complex Functions ◽  
Genome Protection

DNA methylation plays important roles in genome protection and the regulation of gene expression and it is associated with plants’ responses to environments. DNA demethylases are very important proteins in DNA methylation regulation. In this study, we performed genome-wide and deep analysis of putative demethylases (DMEs) in pear. Seven DME genes were found in the pear genome and were defined as PbDME1–7 based on their domain organization. Results were supported by the gene structural characteristics and phylogenetic analysis. The gene structure of the DME genes were relatively complex and the DME7 proteins didn’t contain the Perm_CXXC domain. The DME genes experienced a whole genome duplication event (WGD) that occurred in the ancestor genome of pear and apple before their divergence based on the Ks values. Expression results showed that high salinity stress could influence the expression level of DMEs and salt-responsive genes in Pyrus betulaefolia. Furthermore, the methylation levels of salt-responsive genes changed under salt stress treatment. Results suggested important roles of PbDME genes in response to salt stress and are useful for better understanding the complex functions of this DME genes, which will facilitate epigenetic studies in pear trees salt tolerance.

scholarly journals Genome-Wide Identification and Analysis of CC-NBS-LRR Family in Response to Downy Mildew and Black Rot in Chinese Cabbage

2021 ◽  
Vol 22 (8) ◽  
pp. 4266
Author(s):  
Yan Liu ◽  
Dalong Li ◽  
Na Yang ◽  
Xiaolong Zhu ◽  
Kexin Han ◽  
...  
Keyword(s):  
Downy Mildew ◽  
Chinese Cabbage ◽  
Plant Disease Resistance ◽  
Expression Profiles ◽  
Black Rot ◽  
Genome Wide ◽  
Pathogenesis Related ◽  
Effector Triggered Immunity ◽  
Gene Structures ◽  
Bacteria And Fungi

The nucleotide-binding site–leucine-rich repeat (NBS–LRR) gene family is the largest group of plant disease resistance (R) genes widespread in response to viruses, bacteria, and fungi usually involved in effector triggered immunity (ETI). Forty members of the Chinese cabbage CC type NBS–LRR family were investigated in this study. Gene and protein characteristics, such as distributed locations on chromosomes and gene structures, were explored through comprehensive analysis. CC–NBS–LRR proteins were classified according to their conserved domains, and the phylogenetic relationships of CC–NBS–LRR proteins in Brassica rapa, Arabidopsis thaliana, and Oryza sativa were compared. Moreover, the roles of BrCC–NBS–LRR genes involved in pathogenesis-related defense were studied and analyzed. First, the expression profiles of BrCC–NBS–LRR genes were detected by inoculating with downy mildew and black rot pathogens. Second, sensitive and resistant Chinese cabbage inbred lines were screened by downy mildew and black rot. Finally, the differential expression levels of BrCC–NBS–LRR genes were monitored at 0, 1, 3, 6, 12 and 24 h for short and 0, 3, 5, 7, 10 and 14 days for long inoculation time. Our study provides information on BrCC–NBS–LRR genes for the investigation of the functions and mechanisms of CC-NBS-LRR genes in Chinese cabbage.

scholarly journals Genome-Wide Identification of Soybean ABC Transporters Relate to Aluminum Toxicity

2021 ◽  
Vol 22 (12) ◽  
pp. 6556
Author(s):  
Junjun Huang ◽  
Xiaoyu Li ◽  
Xin Chen ◽  
Yaru Guo ◽  
Weihong Liang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Abc Transporters ◽  
Developmental Stages ◽  
Aluminum Toxicity ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Purifying Selection ◽  
Biotic Stresses ◽  
Genome Wide ◽  
New Germplasm

ATP-binding cassette (ABC) transporter proteins are a gene super-family in plants and play vital roles in growth, development, and response to abiotic and biotic stresses. The ABC transporters have been identified in crop plants such as rice and buckwheat, but little is known about them in soybean. Soybean is an important oil crop and is one of the five major crops in the world. In this study, 255 ABC genes that putatively encode ABC transporters were identified from soybean through bioinformatics and then categorized into eight subfamilies, including 7 ABCAs, 52 ABCBs, 48 ABCCs, 5 ABCDs, 1 ABCEs, 10 ABCFs, 111 ABCGs, and 21 ABCIs. Their phylogenetic relationships, gene structure, and gene expression profiles were characterized. Segmental duplication was the main reason for the expansion of the GmABC genes. Ka/Ks analysis suggested that intense purifying selection was accompanied by the evolution of GmABC genes. The genome-wide collinearity of soybean with other species showed that GmABCs were relatively conserved and that collinear ABCs between species may have originated from the same ancestor. Gene expression analysis of GmABCs revealed the distinct expression pattern in different tissues and diverse developmental stages. The candidate genes GmABCB23, GmABCB25, GmABCB48, GmABCB52, GmABCI1, GmABCI5, and GmABCI13 were responsive to Al toxicity. This work on the GmABC gene family provides useful information for future studies on ABC transporters in soybean and potential targets for the cultivation of new germplasm resources of aluminum-tolerant soybean.

scholarly journals Genome-Wide Analysis of Poplar SQUAMOSA-Promoter-Binding Protein (SBP) Family under Salt Stress

Forests ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 413
Author(s):  
Qing Guo ◽  
Li Li ◽  
Kai Zhao ◽  
Wenjing Yao ◽  
Zihan Cheng ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Growth And Development ◽  
Binding Protein ◽  
Gene Segment ◽  
Gene Expression Pattern ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Squamosa Promoter Binding Protein

SQUAMOSA promoter binding protein (SBP) is a kind of plant-specific transcription factor, which plays a crucial role in stress responses and plant growth and development by activating and inhibiting the transcription of multiple target genes. In this study, a total of 30 SBP genes were identified from Populus trichocarpa genome and randomly distributed on 16 chromosomes in poplar. According to phylogenetic analysis, the PtSBPs can be divided into six categories, and 14 out of the genes belong to VI. Furthermore, the SBP genes in VI were proved to have a targeting relationship with miR156. The homeopathic element analysis showed that the promoters of poplar SBP genes mainly contain the elements involved in growth and development, abiotic stress and hormone response. In addition, there existed 10 gene segment duplication events in the SBP gene duplication analysis. Furthermore, there were four poplar and Arabidopsis orthologous gene pairs among the poplar SBP members. What is more, poplar SBP gene family has diverse gene expression pattern under salt stress. As many as nine SBP members were responding to high salt stress and six members possibly participated in growth development and abiotic stress. Yeast two-hybrid experiments indicated that PtSBPs can form heterodimers to interact in the transcriptional regulatory networks. The genome-wide analysis of poplar SBP family will contribute to function characterization of SBP genes in woody plants.

scholarly journals Genome-wide Identification and Expression Analysis of the YTH Domain-containing RNA-binding Protein Family in Citrus Sinensis

2019 ◽  
Vol 144 (2) ◽  
pp. 79-91 ◽  
Author(s):  
Zhigang Ouyang ◽  
Huihui Duan ◽  
Lanfang Mi ◽  
Wei Hu ◽  
Jianmei Chen ◽  
...  
Keyword(s):  
Stress Responses ◽  
Messenger Rna ◽  
Citrus Sinensis ◽  
Rna Binding ◽  
Developmental Stages ◽  
Rna Binding Proteins ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Genome Wide ◽  
Yth Domain

In eukaryotic systems, messenger RNA regulations, including splicing, 3′-end formation, editing, localization, and translation, are achieved by different RNA-binding proteins and noncoding RNAs. The YTH domain is a newly identified RNA-binding domain that was identified by comparing its sequence with that of splicing factor YT521-B. Previous study showed that the YTH gene plays an important role in plant resistance to abiotic and biotic stress. In this study, 211 YTH genes were identified in 26 species that represent four major plant lineages. Phylogenetic analysis revealed that these genes could be divided into eight subgroups. All of the YTH genes contain a YT521 domain and have different structures. Ten YTH genes were identified in navel orange (Citrus sinensis). The expression profiles of these CitYTH genes were analyzed in different tissues and at different fruit developmental stages, and CitYTH genes displayed distinct expression patterns under heat, cold, salt, and drought stress. Furthermore, expression of the CitYTH genes in response to exogenous hormones was measured. Nuclear localization was also confirmed for five of the proteins encoded by these genes after transient expression in Nicotiana benthamiana cells. This study provides valuable information on the role of CitYTHs in the signaling pathways involved in environmental stress responses in Citrus.

scholarly journals Genome-Wide Identification of Brassinosteroid Signaling Downstream Genes in Nine Rosaceae Species and Analyses of Their Roles in Stem Growth and Stress Response in Apple

2021 ◽  
Vol 12 ◽  
Author(s):  
Liwei Zheng ◽  
Yingli Yang ◽  
Shengjie Ma ◽  
Wenming Wang ◽  
Jimeng Zhang ◽  
...  
Keyword(s):  
Stress Responses ◽  
Agronomic Traits ◽  
Purifying Selection ◽  
Short Shoot ◽  
Gene Expansion ◽  
Rosaceae Species ◽  
Genome Wide ◽  
Brassinosteroid Signaling ◽  
Stress Signals ◽  
External Signals

Brassinosteroid signaling downstream genes regulate many important agronomic traits in rice. However, information on such genes is limited in Arabidopsis and Rosaceae species. We identified these genes in Arabidopsis and nine Rosaceae species. They were, respectively, named based on chromosomal locations. Segmental duplication and whole-genome duplication under purifying selection, as determined by Ka/Ks analysis, likely contributed to Rosaceae gene expansion. Apple (Malus domestica), Arabidopsis, and rice genes were generally similar, while several Rosaceae genes differed from their rice homologs in various characteristics, such as gene length, subcellular localization, transmembrane topology, conserved domains, secondary structures, and responses to external signals. The brassinosteroid downstream genes in apple were, respectively, induced or repressed by five phytohormones. Furthermore, these apple downstream genes were differentially expressed in different apple grafting combinations (“Nagafu No. 2”/“Malling 9” and “Nagafu No. 2”/“Nagafu No. 2”) and long–short shoot varieties (“Yanfu No. 6” and “Nagafu No. 2”). Responses of the MdBZR genes to diverse stress signals were examined and candidate hub genes were identified. These findings indicated that several brassinosteroid signaling downstream genes in Rosaceae functionally differed from their rice homologs, and certain apple genes may play roles in plant height and stress responses. This study provided valuable information and presented enriched biological theories on brassinosteroid signaling downstream genes in apple. Identification of such genes serve to help expand apple breeding and growth. This study provides useful information for brassinosteroid signaling downstream genes.

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