scholarly journals Genome-wide characterization of the Zn(II)2Cys6 zinc cluster-encoding gene family in Pleurotus ostreatus and expression analyses of this family during developmental stages and under heat stress

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9336
Author(s):  
Zhihao Hou ◽  
Qiang Chen ◽  
Mengran Zhao ◽  
Chenyang Huang ◽  
Xiangli Wu
Keyword(s):  
Heat Stress ◽  
Pleurotus Ostreatus ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Regulatory Mechanisms ◽  
Fruiting Body Formation ◽  
Zinc Cluster ◽  
Genome Wide ◽  
A Genome

Pleurotus ostreatus is one of the most widely cultivated mushrooms in China. The regulatory mechanisms of fruiting body formation and the response to heat stress in P. ostreatus are main research focuses. The Zn(II)2Cys6 family is one of the largest families of transcriptional factors and plays important roles in multiple biological processes in fungi. In this study, we identified 66 zinc cluster proteins in P. ostreatus (PoZCPs) through a genome-wide search. The PoZCPs were classified into 15 types according to their zinc cluster domain. Physical and chemical property analyses showed a huge diversity among the PoZCPs. Phylogenetic analysis of PoZCPs classified these proteins into six groups and conserved motif combinations and similar gene structures were observed in each group. The expression profiles of these PoZCP genes during different developmental stages and under heat stress were further investigated by RNA-sequencing (RNA-seq), revealing diverse expression patterns. A total of 13 PoZCPs that may participate in development or the heat stress response were selected for validation of their expression levels through real-time quantitative PCR (RT-qPCR) analysis, and some developmental stage-specific and heat stress-responsive candidates were identified. The findings contribute to our understanding of the roles and regulatory mechanisms of ZCPs in P. ostreatus.

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 Systematic Analysis of Gibberellin Pathway Components in Medicago truncatula Reveals the Potential Application of Gibberellin in Biomass Improvement

2020 ◽  
Vol 21 (19) ◽  
pp. 7180
Author(s):  
Hongfeng Wang ◽  
Hongjiao Jiang ◽  
Yiteng Xu ◽  
Yan Wang ◽  
Lin Zhu ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Ectopic Expression ◽  
Feedback Regulation ◽  
Specific Expression ◽  
Systematic Analysis ◽  
Model Legume ◽  
Genome Wide ◽  
A Genome

Gibberellins (GAs), a class of phytohormones, act as an essential natural regulator of plant growth and development. Many studies have shown that GA is related to rhizobial infection and nodule organogenesis in legume species. However, thus far, GA metabolism and signaling components are largely unknown in the model legume Medicago truncatula. In this study, a genome-wide analysis of GA metabolism and signaling genes was carried out. In total 29 components, including 8 MtGA20ox genes, 2 MtGA3ox genes, 13 MtGA2ox genes, 3 MtGID1 genes, and 3 MtDELLA genes were identified in M. truncatula genome. Expression profiles revealed that most members of MtGAox, MtGID1, and MtDELLA showed tissue-specific expression patterns. In addition, the GA biosynthesis and deactivation genes displayed a feedback regulation on GA treatment, respectively. Yeast two-hybrid assays showed that all the three MtGID1s interacted with MtDELLA1 and MtDELLA2, suggesting that the MtGID1s are functional GA receptors. More importantly, M. truncatula exhibited increased plant height and biomass by ectopic expression of the MtGA20ox1, suggesting that enhanced GA response has the potential for forage improvement.

scholarly journals Genome-wide investigation of the AP2/ERF gene family in  ginger: evolution and expression profiles during rhizome and inflorescence development

2021 ◽  
Author(s):  
Haitao Xing ◽  
Yusong Jiang ◽  
Xiaoling Long ◽  
Xiaoli Wu ◽  
Yun Ren ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Whole Genome Sequence ◽  
Chromosomal Distribution ◽  
Inflorescence Development ◽  
Systematic Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Erf Transcription Factors

Abstract Background:AP2/ERF transcription factors perform indispensable functions in various biological processes, such as plant growth, development, biotic and abiotic stresses responses. The AP2/ERF transcription factor family has been identified in many plants, and several AP2/ERF transcription factors from Arabidopsis (Arabidopsis thaliana) have been functionally characterized. However, little research has been conducted on the AP2/ERF genes of ginger (Zingiber officinale), which is an important edible and medicinal horticultural plant. The recently published whole genome sequence of ginger allowed us to study the tissue and expression profiles of AP2/ERF genes in ginger on a genome-wide basis.Results:In this study, 163 AP2/ERF genes of ginger (ZoAP2/ERF) were identified and renamed according to the chromosomal distribution of the ZoAP2/ERF genes. According to the number conserved domains and gene structure, the AP2/ERF genes were divided into three subfamilies by phylogenetic analysis, namely, AP2 (35 members), ERF (125 members) and RAV (3 members). A total of 10 motifs were detected in ginger AP2/ERF genes, and some of the unique motifs were found to be important for the function of ZoAP2/ERF genes.Conclusion:A comprehensive analysis of AP2/ERF gene expression patterns in different tissues and rhizome development stages by transcriptom sequence and quantitative real-time PCR (qRT-PCR) showed that they played an important role in the growth and development of ginger, and genes that might regulate rhizome and flower development were preliminarily identified. This systematic analysis establishes a foundation for further studies of the functional characteristics of ZoAP2/ERF genes and improvement of ginger.

scholarly journals Expression patterns of two pal genes of Pleurotus ostreatus across developmental stages and under heat stress

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Ludan Hou ◽  
Lining Wang ◽  
Xiangli Wu ◽  
Wei Gao ◽  
Jinxia Zhang ◽  
...  
Keyword(s):  
Heat Stress ◽  
Pleurotus Ostreatus ◽  
Growth Stage ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Phenylpropanoid Pathway ◽  
Regulatory Pathways ◽  
Defense Systems ◽  
Key Enzyme ◽  
Organismal Development

Abstract Background Phenylalanine ammonia-lyase (PAL, EC 4.3.1.24) is the first key enzyme in the phenylpropanoid pathway. The pal gene has been widely studied in plants and participates in plant growth, development and defense systems. However, in Pleurotus ostreatus, the biological functions of pal during organismal development and exposure to abiotic stress have not been reported. Results In this study, we cloned and characterized the pal1 (2232 bp) and pal2 (2244 bp) genes from the basidiomycete P. ostreatus CCMSSC 00389. The pal1 and pal2 genes are interrupted by 6 and 10 introns, respectively, and encode proteins of 743 and 747 amino acids, respectively. Furthermore, prokaryotic expression experiments showed that PAL enzymes catalyzed the conversion of L-phenylalanine to trans-cinnamic acid. The function of pal1 and pal2 was determined by constructing overexpression (OE) and RNA interference (RNAi) strains. The results showed that the two pal genes had similar expression patterns during different developmental stages. The expression of pal genes was higher in the reproductive growth stage than in the vegetative growth stage. And the interference of pal1 and pal2 delayed the formation of primordia. The results of heat stress assays showed that the RNAi-pal1 strains had enhanced mycelial tolerance to high temperature, while the RNAi-pal2 strains had enhanced mycelial resistance to H2O2. Conclusions These results indicate that two pal genes may play a similar role in the development of P. ostreatus fruiting bodies, but may alleviate stress through different regulatory pathways under heat stress.

scholarly journals Genome-Wide Identification, Characterization and Expression Analysis of TCP Transcription Factors in Petunia

2020 ◽  
Vol 21 (18) ◽  
pp. 6594
Author(s):  
Shuting Zhang ◽  
Qin Zhou ◽  
Feng Chen ◽  
Lan Wu ◽  
Baojun Liu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Leaf Morphogenesis ◽  
Systematic Analysis ◽  
Genome Wide ◽  
A Genome

The plant-specific TCP transcription factors are well-characterized in both monocots and dicots, which have been implicated in multiple aspects of plant biological processes such as leaf morphogenesis and senescence, lateral branching, flower development and hormone crosstalk. However, no systematic analysis of the petunia TCP gene family has been described. In this work, a total of 66 petunia TCP genes (32 PaTCP genes in P. axillaris and 34 PiTCP genes in P. inflata) were identified. Subsequently, a systematic analysis of 32 PaTCP genes was performed. The phylogenetic analysis combined with structural analysis clearly distinguished the 32 PaTCP proteins into two classes—class Ι and class Ⅱ. Class Ⅱ was further divided into two subclades, namely, the CIN-TCP subclade and the CYC/TB1 subclade. Plenty of cis-acting elements responsible for plant growth and development, phytohormone and/or stress responses were identified in the promoter of PaTCPs. Distinct spatial expression patterns were determined among PaTCP genes, suggesting that these genes may have diverse regulatory roles in plant growth development. Furthermore, differential temporal expression patterns were observed between the large- and small-flowered petunia lines for most PaTCP genes, suggesting that these genes are likely to be related to petal development and/or petal size in petunia. The spatiotemporal expression profiles and promoter analysis of PaTCPs indicated that these genes play important roles in petunia diverse developmental processes that may work via multiple hormone pathways. Moreover, three PaTCP-YFP fusion proteins were detected in nuclei through subcellular localization analysis. This is the first comprehensive analysis of the petunia TCP gene family on a genome-wide scale, which provides the basis for further functional characterization of this gene family in petunia.

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.

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