scholarly journals Molecular Analysis of 14-3-3 Genes in Citrus sinensis and Their Responses to Different Stresses

2021 ◽  
Vol 22 (2) ◽  
pp. 568
Author(s):  
Shiheng Lyu ◽  
Guixin Chen ◽  
Dongming Pan ◽  
Jianjun Chen ◽  
Wenqin She
Keyword(s):  
Stress Responses ◽  
Abiotic Stresses ◽  
Citrus Sinensis ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Interaction Network ◽  
Citrus Canker ◽  
Defense Responses ◽  
Biotic And Abiotic Stresses ◽  
Specific Expression

14-3-3 proteins (14-3-3s) are among the most important phosphorylated molecules playing crucial roles in regulating plant development and defense responses to environmental constraints. No report thus far has documented the gene family of 14-3-3s in Citrus sinensis and their roles in response to stresses. In this study, nine 14-3-3 genes, designated as CitGF14s (CitGF14a through CitGF14i) were identified from the latest C. sinensis genome. Phylogenetic analysis classified them into ε-like and non-ε groups, which were supported by gene structure analysis. The nine CitGF14s were located on five chromosomes, and none had duplication. Publicly available RNA-Seq raw data and microarray databases were mined for 14-3-3 expression profiles in different organs of citrus and in response to biotic and abiotic stresses. RT-qPCR was used for further examining spatial expression patterns of CitGF14s in citrus and their temporal expressions in one-year-old C. sinensis “Xuegan” plants after being exposed to different biotic and abiotic stresses. The nine CitGF14s were expressed in eight different organs with some isoforms displayed tissue-specific expression patterns. Six of the CitGF14s positively responded to citrus canker infection (Xanthomonas axonopodis pv. citri). The CitGF14s showed expressional divergence after phytohormone application and abiotic stress treatments, suggesting that 14-3-3 proteins are ubiquitous regulators in C. sinensis. Using the yeast two-hybrid assay, CitGF14a, b, c, d, g, and h were found to interact with CitGF14i proteins to form a heterodimer, while CitGF14i interacted with itself to form a homodimer. Further analysis of CitGF14s co-expression and potential interactors established a 14-3-3s protein interaction network. The established network identified 14-3-3 genes and several candidate clients which may play an important role in developmental regulation and stress responses in this important fruit crop. This is the first study of 14-3-3s in citrus, and the established network may help further investigation of the roles of 14-3-3s in response to abiotic and biotic constraints.

scholarly journals Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses

2020 ◽  
Author(s):  
Chong Yang ◽  
Juanjuan Li ◽  
Faisal Islam ◽  
Luyang Hu ◽  
Jiansu Wang ◽  
...  
Keyword(s):  
Helianthus Annuus ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Crop Improvement ◽  
Plant Tolerance ◽  
Biotic And Abiotic Stresses

Abstract Background: WRKY transcription factors play important roles in various physiological processes and stress responses in flowering plants. However, the information about WRKY genes in Helianthus annuus L. (common sunflower) is limited. Results: Ninety WRKY (HaWRKY) genes were identified and renamed according to their locations on chromosomes. Further phylogenetic analyses classified them into four main groups including a species-specific WKKY group and HaWRKY genes within same group or subgroup generally showed similar exon-intron structures and motif compositions. The tandem and segmental duplication possibly contributed to the diversity and expansion of HaWRKY gene families. Synteny analyses of sunflower WRKY genes provided deep insight to the evolution of HaWRKY genes. Transcriptomic and qRT-PCR analyses of HaWRKY genes displayed distinct expression patterns in different plant tissues, as well as under various abiotic and biotic stresses. Conclusions: Ninety WRKY (HaWRKY) genes were identified from H. annuus L. and classified into four groups. Structures of HaWRKY proteins and their evolutionary characteristics were also investigated. The characterization of HaWRKY genes and their expression profiles under biotic and abiotic stresses in this study provide a foundation for further functional analyses of these genes. Therefore, these functional genes related to increasing the plant tolerance or improving the crop quality, could be applied for the crop improvement..

scholarly journals Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses

2020 ◽  
Author(s):  
Chong Yang ◽  
Juanjuan Li ◽  
Faisal Islam ◽  
Luyang Hu ◽  
Jiansu Wang ◽  
...  
Keyword(s):  
Helianthus Annuus ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Crop Improvement ◽  
Gene Families ◽  
Biotic And Abiotic Stresses

Abstract Background: WRKY transcription factors play important roles in various physiological processes and stress responses in flowering plants. However, the information about WRKY genes in Helianthus annuus L. (common sunflower) is limited. Results: Ninety WRKY (HaWRKY) genes were identified and renamed according to their locations on chromosomes. Further phylogenetic analyses classified them into four main groups including a species-specific WKKY group and HaWRKY genes within same group or subgroup generally showed similar exon-intron structures and motif compositions. The tandem and segmental duplication possibly contributed to the diversity and expansion of HaWRKY gene families. Synteny analyses of sunflower WRKY genes provided deep insight to the evolution of HaWRKY genes. Transcriptomic and qRT-PCR analyses of HaWRKY genes displayed distinct expression patterns in different plant tissues, as well as under various abiotic and biotic stresses. Conclusions: Ninety WRKY (HaWRKY) genes were identified from H. annuus L. and classified into four groups. Structures of HaWRKY proteins and their evolutionary characteristics were also investigated. The characterization of HaWRKY genes and their expression profiles under biotic and abiotic stresses in this study provide a foundation for further functional analyses of these genes and will be beneficial to crop improvement.

Characterization of moso bamboo (Phyllostachys edulis) Dof transcription factors in floral development and abiotic stress responses

Genome ◽  
2018 ◽  
Vol 61 (3) ◽  
pp. 151-156 ◽  
Author(s):  
Zhanchao Cheng ◽  
Dan Hou ◽  
Jun Liu ◽  
Xiangyu Li ◽  
Lihua Xie ◽  
...  
Keyword(s):  
Stress Responses ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Regulatory Element ◽  
Expression Patterns ◽  
Moso Bamboo ◽  
Phyllostachys Edulis ◽  
Element Analysis ◽  
Specific Expression

The Dof transcription factor (TF) family belongs to a class of plant-specific TFs and is involved in plant growth, development, and response to abiotic stresses. However, there are only very limited reports on the characterization of Dof TFs in moso bamboo (Phyllostachys edulis). In the present research, PheDof TFs showed specific expression profiles based on RNA-seq data analyses. The co-expression network indicated that PheDof12, PheDof14, and PheDof16 might play vital roles during flower development. Cis-regulatory element analysis of these PheDof genes suggested diverse functions. Expression patterns of 12 selected genes from seven different classes under three abiotic stresses (cold, salt, and drought) are further investigated by quantitative real-time PCR. This work will provide useful information for functional analysis and regulation mechanisms of Dof TFs in moso bamboo.

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.

Genome-wide identification and expression analysis of the CaLAX and CaPIN gene families in pepper (Capsicum annuum L.) under various abiotic stresses and hormone treatments

Genome ◽  
2018 ◽  
Vol 61 (2) ◽  
pp. 121-130 ◽  
Author(s):  
Chenghao Zhang ◽  
Wenqi Dong ◽  
Zong-an Huang ◽  
MyeongCheoul Cho ◽  
Qingcang Yu ◽  
...  
Keyword(s):  
Capsicum Annuum ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Families ◽  
Environmental Stresses ◽  
Transcriptional Level ◽  
Specific Expression ◽  
Capsicum Annuum L ◽  
Genome Wide

Auxin plays key roles in regulating plant growth and development as well as in response to environmental stresses. The intercellular transport of auxin is mediated by the following four gene families: ATP-binding cassette family B (ABCB), auxin resistant1/like aux1 (AUX/LAX), PIN-formed (PIN), and PIN-like (PILS). Here, the latest assembled pepper (Capsicum annuum L.) genome was used to characterise and analyse the CaLAX and CaPIN gene families. Genome-wide investigations into these families, including chromosomal distributions, phytogenic relationships, and intron/exon structures, were performed. In total, 4 CaLAX and 10 CaPIN genes were mapped to 10 chromosomes. Most of these genes exhibited varied tissue-specific expression patterns assessed by quantitative real-time PCR. The expression profiles of the CaLAX and CaPIN genes under various abiotic stresses (salt, drought, and cold), exogenous phytohormones (IAA, 6-BA, ABA, SA, and MeJA), and polar auxin transport inhibitor treatments were evaluated. Most CaLAX and CaPIN genes were altered by abiotic stress at the transcriptional level in both shoots and roots, and many CaLAX and CaPIN genes were regulated by exogenous phytohormones. Our study helps to identify candidate auxin transporter genes and to further analyse their biological functions in pepper development and in its adaptation to environmental stresses.

scholarly journals Comprehensive Analysis of the TIFY Gene Family and Its Expression Profiles under Phytohormone Treatment and Abiotic Stresses in Roots of Populus trichocarpa

Forests ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 315
Author(s):  
Hanzeng Wang ◽  
Xue Leng ◽  
Xuemei Xu ◽  
Chenghao Li
Keyword(s):  
Gene Family ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Interaction Network ◽  
Pcr Analysis ◽  
Phylogenetic Tree Analysis ◽  
Element Analysis ◽  
Cis Element

The TIFY gene family is specific to land plants, exerting immense influence on plant growth and development as well as responses to biotic and abiotic stresses. Here, we identify 25 TIFY genes in the poplar (Populus trichocarpa) genome. Phylogenetic tree analysis revealed these PtrTIFY genes were divided into four subfamilies within two groups. Promoter cis-element analysis indicated most PtrTIFY genes possess stress- and phytohormone-related cis-elements. Quantitative real-time reverse transcription polymerase chain reaction (qRT–PCR) analysis showed that PtrTIFY genes displayed different expression patterns in roots under abscisic acid, methyl jasmonate, and salicylic acid treatments, and drought, heat, and cold stresses. The protein interaction network indicated that members of the PtrTIFY family may interact with COI1, MYC2/3, and NINJA. Our results provide important information and new insights into the evolution and functions of TIFY genes in P. trichocarpa.

scholarly journals A genome-wide analysis of the cellulose synthase-like (Csl) gene family in maize (Zea mays)

2018 ◽  
Author(s):  
Yongkai Li ◽  
Xiaojie Cheng ◽  
Yaqin Fu ◽  
Qinqin Wu ◽  
Yuli Guo ◽  
...  
Keyword(s):  
Gene Family ◽  
Abiotic Stresses ◽  
Early Stage ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Cellulose Synthase ◽  
Biotic And Abiotic Stresses ◽  
A Genome ◽  
Evolutionary Features ◽  
Different Tissues

Cell walls play an important role in the structure and morphology of plants as well as stress response, including various biotic and abiotic stresses. Although the comprehensive analysis of genes involved in cellulose synthase have been performed in model plants, such as Arabidopsis thaliana and rice, information regarding cellulose synthase-like (Csl) genes in maize is extremely limited. In this study, a total of 56 members of Csl gene family were identified in maize genome, which were classified into six subfamilies. Analysis of gene structure and conserved motif indicated functional similarities among the ZmCsl proteins within the same subfamily. Additionally, the 56 ZmCsl genes were dispersed on 10 chromosomes. The expression patterns of ZmCsl genes in different tissues using the transcriptome data revealed that most of ZmCsl genes had a relatively high expression in root and tassel tissues. Moreover, the expression profiles of ZmCsl genes under drought and re-watering indicated that the expression of ZmCsl genes were mainly responsive to early stage of drought stress. The protein-protein interaction network of ZmCsl genes proposed some potential interacted proteins. The data presented a comprehensive survey of Csl gene family in maize. The detailed description of maize Csl genes will be beneficial to understand their structural, functional, and evolutionary features. Importantly, we have described the differential expression profiles of these members across different tissues and under drought. This information will provide an important foundation for studying the roles of these ZmCsl genes in response to biotic and abiotic stresses.

scholarly journals Genome-Wide Characterization of the sHsp Gene Family in Salix suchowensis Reveals Its Functions under Different Abiotic Stresses

2018 ◽  
Vol 19 (10) ◽  
pp. 3246 ◽  
Author(s):  
Jianbo Li ◽  
Jin Zhang ◽  
Huixia Jia ◽  
Zhiqiang Yue ◽  
Mengzhu Lu ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Molecular Characteristics ◽  
Specific Expression ◽  
Cis Acting ◽  
Shsp Gene ◽  
Duplication Events

Small heat shock proteins (sHsps) function mainly as molecular chaperones that play vital roles in response to diverse stresses, especially high temperature. However, little is known about the molecular characteristics and evolutionary history of the sHsp family in Salix suchowensis, an important bioenergy woody plant. In this study, 35 non-redundant sHsp genes were identified in S. suchowensis, and they were divided into four subfamilies (C, CP, PX, and MT) based on their phylogenetic relationships and predicted subcellular localization. Though the gene structure and conserved motif were relatively conserved, the sequences of the Hsp20 domain were diversified. Eight paralogous pairs were identified in the Ssu-sHsp family, in which five pairs were generated by tandem duplication events. Ka/Ks analysis indicated that Ssu-sHsps had undergone purifying selection. The expression profiles analysis showed Ssu-Hsps tissue-specific expression patterns, and they were induced by at least one abiotic stress. The expression correlation between two paralogous pairs (Ssu-sHsp22.2-CV/23.0-CV and 23.8-MT/25.6-MT) were less than 0.6, indicating that they were divergent during the evolution. Various cis-acting elements related to stress responses, hormone or development, were detected in the promoter of Ssu-sHsps. Furthermore, the co-expression network revealed the potential mechanism of Ssu-sHsps under stress tolerance and development. These results provide a foundation for further functional research on the Ssu-sHsp gene family in S. suchowensis.

scholarly journals Identification and expression analysis of GRAS transcription factors in the wild relative of sweet potato Ipomoea trifida

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Yao Chen ◽  
Panpan Zhu ◽  
Shaoyuan Wu ◽  
Yan Lu ◽  
Jian Sun ◽  
...  
Keyword(s):  
Sweet Potato ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Raw Material ◽  
Functional Study ◽  
Ipomoea Trifida ◽  
Specific Expression ◽  
Adverse Environmental Condition ◽  
In The Wild

Abstract Background GRAS gene is an important transcription factor gene family that plays a crucial role in plant growth, development, adaptation to adverse environmental condition. Sweet potato is an important food, vegetable, industrial raw material, and biofuel crop in the world, which plays an essential role in food security in China. However, the function of sweet potato GRAS genes remains unknown. Results In this study, we identified and characterised 70 GRAS members from Ipomoea trifida, which is the progenitor of sweet potato. The chromosome distribution, phylogenetic tree, exon-intron structure and expression profiles were analysed. The distribution map showed that GRAS genes were randomly located in 15 chromosomes. In combination with phylogenetic analysis and previous reports in Arabidopsis and rice, the GRAS proteins from I. trifida were divided into 11 subfamilies. Gene structure showed that most of the GRAS genes in I. trifida lacked introns. The tissue-specific expression patterns and the patterns under abiotic stresses of ItfGRAS genes were investigated via RNA-seq and further tested by RT-qPCR. Results indicated the potential functions of ItfGRAS during plant development and stress responses. Conclusions Our findings will further facilitate the functional study of GRAS gene and molecular breeding of sweet potato.

scholarly journals A genome-wide analysis of the cellulose synthase-like (Csl) gene family in maize (Zea mays)

2018 ◽  
Author(s):  
Yongkai Li ◽  
Xiaojie Cheng ◽  
Yaqin Fu ◽  
Qinqin Wu ◽  
Yuli Guo ◽  
...  
Keyword(s):  
Gene Family ◽  
Abiotic Stresses ◽  
Early Stage ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Cellulose Synthase ◽  
Biotic And Abiotic Stresses ◽  
A Genome ◽  
Evolutionary Features ◽  
Different Tissues

Cell walls play an important role in the structure and morphology of plants as well as stress response, including various biotic and abiotic stresses. Although the comprehensive analysis of genes involved in cellulose synthase have been performed in model plants, such as Arabidopsis thaliana and rice, information regarding cellulose synthase-like (Csl) genes in maize is extremely limited. In this study, a total of 56 members of Csl gene family were identified in maize genome, which were classified into six subfamilies. Analysis of gene structure and conserved motif indicated functional similarities among the ZmCsl proteins within the same subfamily. Additionally, the 56 ZmCsl genes were dispersed on 10 chromosomes. The expression patterns of ZmCsl genes in different tissues using the transcriptome data revealed that most of ZmCsl genes had a relatively high expression in root and tassel tissues. Moreover, the expression profiles of ZmCsl genes under drought and re-watering indicated that the expression of ZmCsl genes were mainly responsive to early stage of drought stress. The protein-protein interaction network of ZmCsl genes proposed some potential interacted proteins. The data presented a comprehensive survey of Csl gene family in maize. The detailed description of maize Csl genes will be beneficial to understand their structural, functional, and evolutionary features. Importantly, we have described the differential expression profiles of these members across different tissues and under drought. This information will provide an important foundation for studying the roles of these ZmCsl genes in response to biotic and abiotic stresses.

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