Characterization of the GRAS gene family reveals their contribution to the high adaptability of wheat

GRAS transcription factors play important roles in many processes of plant development as well as abiotic and biotic stress responses. However, little is known about this gene family in bread wheat (Triticum aestivum), one of the most important crops worldwide. The completion of a quality draft genome allows genome-wide detection and evolutionary analysis of the GRAS gene family in wheat. In this study, 188 TaGRAS genes were detected and divided into 12 subfamilies based on phylogenetic analyses: DELLA, DLT, HAM, LISCL, SCL3, SCL4/7, SCR, SHR, PAT1, Os19, Os4 and LAS. Tandem and segmental duplications are the main contributors to the expansion of TaGRAS, which may contribute to the adaptation of wheat to various environmental conditions. A high rate of homoeolog retention during hexaploidization was detected, suggesting the nonredundancy and biological importance of TaGRAS homoeologs. Systematic analyses of TaGRAS indicated the conserved expression pattern and function of the same subfamily during evolution. In addition, we detected five genes belonging to the LISCL subfamily induced by both biotic and abiotic stresses and they may be potential targets for further research through gene editing. Using degradome and ChIP-seq data, we identified the targets of miR171 and histone modifications and further analyzed the contribution of epigenetic modification to the subfunctionalization of TaGRAS. This study laid a foundation for further functional elucidation of TaGRAS genes.

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Genome-Wide Identification, Evolutionary Analysis, and Stress Responses of the GRAS Gene Family in Castor Beans

International Journal of Molecular Sciences ◽

10.3390/ijms17071004 ◽

2016 ◽

Vol 17 (7) ◽

pp. 1004 ◽

Cited By ~ 24

Author(s):

Wei Xu ◽

Zexi Chen ◽

Naeem Ahmed ◽

Bing Han ◽

Qinghua Cui ◽

...

Keyword(s):

Gene Family ◽

Stress Responses ◽

Evolutionary Analysis ◽

Genome Wide ◽

Gras Gene

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Genome-Wide Identification and Expression Profile Analysis of the NF-Y Transcription Factor Gene Family in Petunia hybrida

Plants ◽

10.3390/plants9030336 ◽

2020 ◽

Vol 9 (3) ◽

pp. 336 ◽

Cited By ~ 1

Author(s):

Qian Wei ◽

Shiyun Wen ◽

Chuying Lan ◽

Yixun Yu ◽

Guoju Chen

Keyword(s):

Stress Response ◽

Gene Family ◽

Stress Responses ◽

Petunia Hybrida ◽

Profile Analysis ◽

Phylogenetic Analyses ◽

Expression Patterns ◽

Draft Genome ◽

Rna Seq ◽

Expression Profile Analysis

Nuclear Factor Ys (NF-Ys) are a class of heterotrimeric transcription factors that play key roles in many biological processes, such as abiotic stress responses, flowering time, and root development. The petunia (Petunia hybrida) is a model ornamental plant, and its draft genome has been published. However, no details regarding the NF-Y gene family in petunias are available. Here, 27 NF-Y members from the petunia genome were identified, including 10 PhNF-YAs, 13 PhNF-YBs, and 4 PhNF-YCs. Multiple alignments showed that all PhNF-Y proteins had clear conserved core regions flanked by non-conserved sequences. Phylogenetic analyses identified five pairs of orthologues NF-YB proteins from Petunia and Arabidopsis, and six pairs of paralogues NF-Y proteins in Petunia. Analysis of the gene structure and conserved motifs further confirmed the closer relationship in each subfamily. Bioinformatics analysis revealed that 16 PhNF-Ys could be targeted by 18 miRNA families. RNA-seq results showed that expression patterns of PhNF-Ys among four major organs (leaf, stem, flower, and root) were clustered into six major groups. The stress response pattern of PhNF-Ys was identified under cold, heat, drought, and salinity treatments. Based on the RNA-seq data, we found that 3 genes responded to drought, 4 genes responded to salt, 10 genes responded to cold, and 9 genes responded to hot. In conclusion, this study provides useful information for further studying the functions of NF-Ys in stress response.

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Genome-wide identification of sucrose nonfermenting-1-related protein kinase (SnRK) genes in barley and RNA-seq analyses of their expression in response to abscisic acid treatment

BMC Genomics ◽

10.1186/s12864-021-07601-6 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Zhiwei Chen ◽

Longhua Zhou ◽

Panpan Jiang ◽

Ruiju Lu ◽

Nigel G. Halford ◽

...

Keyword(s):

Abscisic Acid ◽

Gene Family ◽

Stress Responses ◽

Phylogenetic Analyses ◽

Regulatory Elements ◽

Gene Promoters ◽

Related Protein ◽

Rna Seq ◽

Response Elements ◽

Genome Data

Abstract Background Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) play important roles in regulating metabolism and stress responses in plants, providing a conduit for crosstalk between metabolic and stress signalling, in some cases involving the stress hormone, abscisic acid (ABA). The burgeoning and divergence of the plant gene family has led to the evolution of three subfamilies, SnRK1, SnRK2 and SnRK3, of which SnRK2 and SnRK3 are unique to plants. Therefore, the study of SnRKs in crops may lead to the development of strategies for breeding crop varieties that are more resilient under stress conditions. In the present study, we describe the SnRK gene family of barley (Hordeum vulgare), the widespread cultivation of which can be attributed to its good adaptation to different environments. Results The barley HvSnRK gene family was elucidated in its entirety from publicly-available genome data and found to comprise 50 genes. Phylogenetic analyses assigned six of the genes to the HvSnRK1 subfamily, 10 to HvSnRK2 and 34 to HvSnRK3. The search was validated by applying it to Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) genome data, identifying 50 SnRK genes in rice (four OsSnRK1, 11 OsSnRK2 and 35 OsSnRK3) and 39 in Arabidopsis (three AtSnRK1, 10 AtSnRK2 and 26 AtSnRK3). Specific motifs were identified in the encoded barley proteins, and multiple putative regulatory elements were found in the gene promoters, with light-regulated elements (LRE), ABA response elements (ABRE) and methyl jasmonate response elements (MeJa) the most common. RNA-seq analysis showed that many of the HvSnRK genes responded to ABA, some positively, some negatively and some with complex time-dependent responses. Conclusions The barley HvSnRK gene family is large, comprising 50 members, subdivided into HvSnRK1 (6 members), HvSnRK2 (10 members) and HvSnRK3 (34 members), showing differential positive and negative responses to ABA.

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Genome-wide identification and evolutionary analysis of RLKs involved in the response to aluminium stress in peanut

BMC Plant Biology ◽

10.1186/s12870-021-03031-4 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Xin Wang ◽

Ming-Hua Wu ◽

Dong Xiao ◽

Ruo-Lan Huang ◽

Jie Zhan ◽

...

Keyword(s):

Stress Responses ◽

Segmental Duplication ◽

Tandem Duplication ◽

Expression Patterns ◽

Purifying Selection ◽

Segmental Duplications ◽

Evolutionary Analysis ◽

Gene Pairs ◽

Al Stress ◽

Peanut Genome

Abstract Background As an important cash crop, the yield of peanut is influenced by soil acidification and pathogen infection. Receptor-like protein kinases play important roles in plant growth, development and stress responses. However, little is known about the number, location, structure, molecular phylogeny, and expression of RLKs in peanut, and no comprehensive analysis of RLKs in the Al stress response in peanuts have been reported. Results A total of 1311 AhRLKs were identified from the peanut genome. The AhLRR-RLKs and AhLecRLKs were further divided into 24 and 35 subfamilies, respectively. The AhRLKs were randomly distributed across all 20 chromosomes in the peanut. Among these AhRLKs, 9.53% and 61.78% originated from tandem duplications and segmental duplications, respectively. The ka/ks ratios of 96.97% (96/99) of tandem duplication gene pairs and 98.78% (646/654) of segmental duplication gene pairs were less than 1. Among the tested tandem duplication clusters, there were 28 gene conversion events. Moreover, all total of 90 Al-responsive AhRLKs were identified by mining transcriptome data, and they were divided into 7 groups. Most of the Al-responsive AhRLKs that clustered together had similar motifs and evolutionarily conserved structures. The gene expression patterns of these genes in different tissues were further analysed, and tissue-specifically expressed genes, including 14 root-specific Al-responsive AhRLKs were found. In addition, all 90 Al-responsive AhRLKs which were distributed unevenly in the subfamilies of AhRLKs, showed different expression patterns between the two peanut varieties (Al-sensitive and Al-tolerant) under Al stress. Conclusions In this study, we analysed the RLK gene family in the peanut genome. Segmental duplication events were the main driving force for AhRLK evolution, and most AhRLKs subject to purifying selection. A total of 90 genes were identified as Al-responsive AhRLKs, and the classification, conserved motifs, structures, tissue expression patterns and predicted functions of Al-responsive AhRLKs were further analysed and discussed, revealing their putative roles. This study provides a better understanding of the structures and functions of AhRLKs and Al-responsive AhRLKs.

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Genome-Wide Identification and Expression Analysis of the Histone Deacetylase Gene Family in Wheat (Triticum aestivum L.)

Plants ◽

10.3390/plants10010019 ◽

2020 ◽

Vol 10 (1) ◽

pp. 19

Author(s):

Peng Jin ◽

Shiqi Gao ◽

Long He ◽

Miaoze Xu ◽

Tianye Zhang ◽

...

Keyword(s):

Abiotic Stress ◽

Gene Family ◽

Mosaic Virus ◽

Stress Responses ◽

Viral Infections ◽

Phylogenetic Analyses ◽

Plant Viruses ◽

Gene Family Evolution ◽

Yellow Mosaic Virus ◽

Wheat Yellow Mosaic Virus

Histone acetylation is a dynamic modification process co-regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs). Although HDACs play vital roles in abiotic or biotic stress responses, their members in Triticumaestivum and their response to plant viruses remain unknown. Here, we identified and characterized 49 T. aestivumHDACs (TaHDACs) at the whole-genome level. Based on phylogenetic analyses, TaHDACs could be divided into 5 clades, and their protein spatial structure was integral and conserved. Chromosomal location and synteny analyses showed that TaHDACs were widely distributed on wheat chromosomes, and gene duplication has accelerated the TaHDAC gene family evolution. The cis-acting element analysis indicated that TaHDACs were involved in hormone response, light response, abiotic stress, growth, and development. Heatmaps analysis of RNA-sequencing data showed that TaHDAC genes were involved in biotic or abiotic stress response. Selected TaHDACs were differentially expressed in diverse tissues or under varying temperature conditions. All selected TaHDACs were significantly upregulated following infection with the barley stripe mosaic virus (BSMV), Chinese wheat mosaic virus (CWMV), and wheat yellow mosaic virus (WYMV), suggesting their involvement in response to viral infections. Furthermore, TaSRT1-silenced contributed to increasing wheat resistance against CWMV infection. In summary, these findings could help deepen the understanding of the structure and characteristics of the HDAC gene family in wheat and lay the foundation for exploring the function of TaHDACs in plants resistant to viral infections.

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Genome-wide identification, phylogeny and function analysis of GRAS gene family in Dendrobium catenatum (Orchidaceae)

Gene ◽

10.1016/j.gene.2019.04.038 ◽

2019 ◽

Vol 705 ◽

pp. 5-15 ◽

Cited By ~ 4

Author(s):

Xu Zeng ◽

Hong Ling ◽

Xiaomei Chen ◽

Shunxing Guo

Keyword(s):

Gene Family ◽

Function Analysis ◽

Genome Wide ◽

And Function ◽

Gras Gene

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Genome-wide survey and expression analysis of the SLAC/SLAH gene family in pear (Pyrus bretschneideri) and other members of the Rosaceae

10.1101/288308 ◽

2018 ◽

Author(s):

Guodong Chen ◽

Xiaolong Li ◽

Xin qiao ◽

Jiaming Li ◽

Li Wang ◽

...

Keyword(s):

Gene Family ◽

Stress Responses ◽

Prunus Persica ◽

Higher Plants ◽

Chloride Transport ◽

Structural Characteristics ◽

Evolutionary Analysis ◽

Anion Channels ◽

Genome Wide ◽

A Genome

AbstractS-type anion channels (SLAC/SLAHs), which play important roles in plant anion (such as nitrate and chloride) transport, growth and development, abiotic stress responses and hormone signaling. However, there is far less information about this family in Rosaceae species. We performed a genome-wide analysis and identified SLAC/SLAH gene family members in pear (Pyrus bretschneideri) and four other species of Rosaceae (Malus domestica, Prunus persica, Fragaria vesca and Prunus mume). A total of 21 SLAC/SLAH genes were identified from the five Rosaceae species. Based on the structural characteristics and a phylogenetic analysis of these genes, the SLAC/SLAH gene family could be classified into three main groups (I, II and III). The evolutionary analysis showed that the SLAC/SLAH gene family was comparatively conserved during the evolution of Rosaceae species. Transcriptome data demonstrated that PbrSLAC/SLAH genes were detected in all parts of the pear. However, PbrSLAC1 showed a higher expression level in leaf, while PbrSLAH2/3 was mainly expressed in roots. In addition, PbrSLAC/SLAH genes were only located on the plasma membrane in transient expression experiments in Arabidopsis protoplasts cells. These results provide valuable information that increases our understanding of the evolution, expression and functions of the SLAC/SLAH gene family in higher plants.

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Genome-wide identification and characterization of lectin receptor-like kinase gene family in cucumber and expression profiling analysis under different treatments

10.21203/rs.2.20023/v1 ◽

2020 ◽

Author(s):

Duo Lv ◽

Gang Wang ◽

Yue Chen ◽

Liang-Rong Xiong ◽

Jing-Xian Sun ◽

...

Keyword(s):

Gene Family ◽

Stress Responses ◽

Expression Patterns ◽

Regulatory Elements ◽

Kinase Gene ◽

Cucumis Sativus L ◽

Lectin Receptor ◽

Genome Wide ◽

Cucumber Genome ◽

And Function

Abstract Background Lectin receptor-like kinases (LecRLKs) are a class of membrane proteins found in plants that are involved in diverse functions, including plant development and stress responses. Although LecRLK families have been identified in a variety of plants, a comprehensive analysis has not yet been undertaken in cucumber ( Cucumis sativus L.).Results In this study, 46 putative LecRLK genes were identified in cucumber genome, including 23 G-type, 22 L-type and 1 C-type LecRLK genes. They unequally distributed on all 7 chromosomes with a clustering trendency. Most of the genes in the cucumber LecRLK (Cs LecRLK) gene family lacked introns. In addition, there were many regulatory elements associated with phytohormone and stress on these genes’ promoters. Transcriptome data demonstrated that distinct expression patterns of CsLecRLK genes in various tissues. Furthermore, we found that each member of the CsLecRLK family had its own unique expression pattern under hormone and stress treatment by the quantitative real time PCR (qRT-PCR) analysis.Conclusion This study provides a better understanding of the evolution and function of LecRLK gene family in cucumber, and opens the possibility to explore the roles that LecRLK s might play in the life cycle of cucumber.

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Genome-wide identification and expression analysis of the 14-3-3 gene family in soybean (Glycine max)

PeerJ ◽

10.7717/peerj.7950 ◽

2019 ◽

Vol 7 ◽

pp. e7950 ◽

Cited By ~ 2

Author(s):

Yongbin Wang ◽

Lei Ling ◽

Zhenfeng Jiang ◽

Weiwei Tan ◽

Zhaojun Liu ◽

...

Keyword(s):

Plant Growth ◽

Gene Family ◽

Stress Responses ◽

Growth And Development ◽

Genomic Data ◽

Evolutionary Analysis ◽

Rna Seq ◽

Plant Growth And Development ◽

Genome Wide ◽

Gene Structures

In eukaryotes, proteins encoded by the 14-3-3 genes are ubiquitously involved in the plant growth and development. The 14-3-3 gene family has been identified in several plants. In the present study, we identified 22 GmGF14 genes in the soybean genomic data. On the basis of the evolutionary analysis, they were clustered into ε and non-ε groups. The GmGF14s of two groups were highly conserved in motifs and gene structures. RNA-seq analysis suggested that GmGF14 genes were the major regulator of soybean morphogenesis. Moreover, the expression level of most GmGF14s changed obviously in multiple stress responses (drought, salt and cold), suggesting that they have the abilities of responding to multiple stresses. Taken together, this study shows that soybean 14-3-3s participate in plant growth and can response to various environmental stresses. These results provide important information for further understanding of the functions of 14-3-3 genes in soybean.

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Genome-Wide Analysis of Members of the WRKY Gene Family and Their Cold Stress Response in Prunus mume

Genes ◽

10.3390/genes10110911 ◽

2019 ◽

Vol 10 (11) ◽

pp. 911 ◽

Cited By ~ 1

Author(s):

Bao ◽

Ding ◽

Cheng ◽

Wang ◽

Zhang

Keyword(s):

Gene Family ◽

Stress Responses ◽

Expression Patterns ◽

Wrky Transcription Factor ◽

Segmental Duplications ◽

Wrky Gene ◽

Prunus Mume ◽

Spatiotemporal Expression ◽

Genome Wide ◽

Transcription Factor Genes

Prunus mume, which is a rosaceous arbor with very high ornamental, edible and medical values, has a distribution that is mainly restricted by low temperature. WRKY transcription factor genes play crucial roles in the growth, development, and stress responses of plants. However, the WRKY gene family has not been characterised in P. mume. There were 58 PmWRKYs identified from genome of P. mume. They were anchored onto eight link groups and categorised into three broad groups. The gene structure and motif composition were reasonably conservative in each group. Investigation of gene duplication indicated that nine and seven PmWRKYs were arranged in tandem and segmental duplications, respectively. PmWRKYs were discriminately expressed in different tissues (i.e., roots, stems, leaves, ﬂowers and fruits) in P. mume. The 17 cold-related candidate genes were selected based on RNA-seq data. Further, to investigate the function of PmWRKYs in low temperatures, the expression patterns under artificial cold treatments were analysed. The results showed that the expression levels of the 12 PmWRKYs genes significantly and 5 genes slightly changed in stems. In particular, the expression level of PmWRKY18 was up-regulated after ABA treatment. In addition, the spatiotemporal expression patterns of 17 PmWRKYs were analysed in winter. These results indicated that 17 PmWRKYs were potential transcription factors regulating cold resistance in P. mume.

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