Genome-Wide Identification, Characterization and Expression Analysis of Soybean CHYR Gene Family.
Ontology highlight
ABSTRACT:
SUBMITTER: Jia B
PROVIDER: S-EPMC8625759 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Trihelix transcription factors play multiple roles in plant growth, development and various stress responses. In this study, we identified 71 trihelix family genes in the soybean genome. These trihelix genes were located at 19 out of 20 soybean chromosomes unevenly and were classified into six distinct subfamilies: GT-1, GT-2, GTγ, SIP1, SH4 and GTδ. The gene structure and conserved functional domain of these trihelix genes were similar in the same subfamily but diverged between different subfamilies. Thirteen segmental duplicated gene pairs were identified and all of them experienced a strong purifying selective pressure during evolution. Various stress-responsive cis-elements presented in the promoters of soybean trihelix genes, suggesting that the trihelix genes might respond to the environmental stresses in soybean. The expression analysis suggests that trihelix genes are involved in diverse functions during soybean development, flood or salinity tolerance, and plant immunity. Our results provide genomic information of the soybean trihelix genes and a basis for further characterizing their roles in response to environmental stresses.
| S-EPMC7075366 | biostudies-literature
Project description:Sucrose nonfermenting 2 (Snf2) family proteins are the core component of chromatin remodeling complexes that can alter chromatin structure and nucleosome position by utilizing the energy of ATP, playing a vital role in transcription regulation, DNA replication, and DNA damage repair. Snf2 family proteins have been characterized in various species including plants, and they have been found to regulate development and stress responses in Arabidopsis. Soybean (Glycine max) is an important food and economic crop worldwide, unlike other non-leguminous crops, soybeans can form a symbiotic relationship with rhizobia for biological nitrogen fixation. However, little is known about Snf2 family proteins in soybean. In this study, we identified 66 Snf2 family genes in soybean that could be classified into six groups like Arabidopsis, unevenly distributed on 20 soybean chromosomes. Phylogenetic analysis with Arabidopsis revealed that these 66 Snf2 family genes could be divided into 18 subfamilies. Collinear analysis showed that segmental duplication was the main mechanism for expansion of Snf2 genes rather than tandem repeats. Further evolutionary analysis indicated that the duplicated gene pairs had undergone purifying selection. All Snf2 proteins contained seven domains, and each Snf2 protein had at least one SNF2_N domain and one Helicase_C domain. Promoter analysis revealed that most Snf2 genes had cis-elements associated with jasmonic acid, abscisic acid, and nodule specificity in their promoter regions. Microarray data and real-time quantitative PCR (qPCR) analysis revealed that the expression profiles of most Snf2 family genes were detected in both root and nodule tissues, and some of them were found to be significantly downregulated after rhizobial infection. In this study, we conducted a comprehensive analysis of the soybean Snf2 family genes and demonstrated their responsiveness to Rhizobia infection. This provides insight into the potential roles of Snf2 family genes in soybean symbiotic nodulation.
| S-EPMC10138738 | biostudies-literature
Project description:The VILLIN (VLN) protein is an important regulator of the actin cytoskeleton, which orchestrates many developmental processes and participates in various biotic and abiotic responses in plants. Although the VLN gene family and their potential functions have been analyzed in several plants, knowledge of VLN genes in soybeans and legumes remains rather limited. In this study, a total of 35 VLNs were characterized from soybean and five related legumes. Combining with the VLN sequences from other nine land plants, we categorized the VLN gene family into three groups according to phylogenetic relationships. Further detailed analysis of the soybean VLNs indicated that the ten GmVLNs were distributed on 10 of the 20 chromosomes, and their gene structures and protein motifs showed high group specificities. The expression pattern analysis suggested that most GmVLNs are widely expressed in various tissues, but three members have a very high level in seeds. Moreover, we observed that the cis-elements enriched in the promoters of GmVLNs are mainly related to abiotic stresses, hormone signals, and developmental processes. The largest number of cis-elements were associated with light responses, and two GmVLNs, GmVLN5a, and GmVLN5b were significantly increased under the long light condition. This study not only provides some basic information about the VLN gene family but also provides a good reference for further characterizing the diverse functions of VLN genes in soybeans.
| S-EPMC10255930 | biostudies-literature
Project description:The LOR (LURP-one related) family genes encode proteins containing a conserved LOR domain. Several members of the LOR family genes are required for defense against Hyaloperonospora parasitica (Hpa) in Arabidopsis. However, there are few reports of LOR genes in response to abiotic stresses in plants. In this study, a genome-wide survey and expression levels in response to abiotic stresses of 36 LOR genes from Glycine max were conducted. The results indicated that the GmLOR gene family was divided into eight subgroups, distributed on 14 chromosomes. A majority of members contained three extremely conservative motifs. There were four pairs of tandem duplicated GmLORs and nineteen pairs of segmental duplicated genes identified, which led to the expansion of the number of GmLOR genes. The expansion patterns of the GmLOR family were mainly segmental duplication. A heatmap of soybean LOR family genes showed that 36 GmLOR genes exhibited various expression patterns in different tissues. The cis-acting elements in promoter regions of GmLORs include abiotic stress-responsive elements, such as dehydration-responsive elements and drought-inducible elements. Real-time quantitative PCR was used to detect the expression level of GmLOR genes, and most of them were expressed in the leaf or root except that GmLOR6 was induced by osmotic and salt stresses. Moreover, GmLOR4/10/14/19 were significantly upregulated after PEG and salt treatments, indicating important roles in the improvement of plant tolerance to abiotic stress. Overall, our study provides a foundation for future investigations of GmLOR gene functions in soybean.
| S-EPMC8624885 | biostudies-literature
Project description:DEAD-box proteins are a large family of RNA helicases that play important roles in almost all cellular RNA processes in model plants. However, little is known about this family of proteins in crops such as soybean. Here, we identified 80 DEAD-box family genes in the Glycine max (soybean) genome. These DEAD-box genes were distributed on 19 chromosomes, and some genes were clustered together. The majority of DEAD-box family proteins were highly conserved in Arabidopsis and soybean, but Glyma.08G231300 and Glyma.14G115100 were specific to soybean. The promoters of these DEAD-box genes share cis-acting elements involved in plant responses to MeJA, salicylic acid (SA), low temperature and biotic as well as abiotic stresses; interestingly, half of the genes contain nodulation-related cis elements in their promoters. Microarray data analysis revealed that the DEAD-box genes were differentially expressed in the root and nodule. Notably, 31 genes were induced by rhizobia and/or were highly expressed in the nodule. Real-time quantitative PCR analysis validated the expression patterns of some DEAD-box genes, and among them, Glyma.08G231300 and Glyma.14G115100 were induced by rhizobia in root hair. Thus, we provide a comprehensive view of the DEAD-box family genes in soybean and highlight the crucial role of these genes in symbiotic nodulation.
| S-EPMC8835661 | biostudies-literature
Project description:The glabrous-enhancer-binding protein (GeBP) family is a family of plant-specific transcription factors, whose members share a central DNA-binding domain. Previous studies have already proven that GeBP genes are involved in the control of cell expansion but not cell proliferation in Arabidopsis. However, there has not yet been a versatile analysis of the GeBP genes' function in soybean (Glycine max L.). Here, we identified and named 9 GmGeBP genes in the soybean genome. These genes were distributed on 7 of the 20 chromosomes and the intron numbers ranged from zero to one. According to the phylogenetic tree, 52 GeBP genes obtained from four plant species were clustered into major four groups. Through the RNA-seq analysis of the nine GmGeBP genes, 8 of 9 GmGeBP genes were be found to expressed differentially across the 14 tissues. Additionally, among nine GmGeBP genes, only GeBP4 were highly expressed in abnormal trichome soybeans, which was predicted to be involved in trichome development. This genome-wide analysis of GmGeBP genes helps to provide an overview of the evolution and functions of two kinds of soybean plants. These results will help to clarify the potential functions and characteristics of GmGeBP genes in the soybean life cycle.
| S-EPMC9318833 | biostudies-literature
Project description:BackgroundAs the key regulators in BR signaling, BES1 family genes regulate thousands of target genes involved in various development processes. So far, the functions of BES1 family are poorly understood in tomato, and a comprehensive genomic and expressional analysis is worth to conduct for this family.ResultsHere, nine SlBES1 family members were identified in tomato and classified into five groups based on the conserved motif, gene structure and phylogenetic analysis. Synteny among tomato, Arabidopsis, pepper and rice were further analyzed to obtain insights into evolutionary characteristics. Several cis-elements related to hormone, stress and plant development were exhibited in the promoter regions of SlBES1 family genes. Subcellular localization showed seven members localized both in the nucleus and cytoplasm, implying the presence of dephosphorylated and phosphorylated form of these seven proteins, furthermore, five of them possessed transcription activation activity whereas the left two functioned as transcriptional repressors. Another two members, however, neither localized in the nucleus nor had transactivation activity. Besides, SlBES1.8 showed flower-specific expression while other members expressed ubiquitously in all organs. Moreover, SlBES1 genes exhibited variational expression in response to nine principal plant hormones. Notably, the expression levels of SlBES1 genes presented a dominant downregulated trend in response to stresses.ConclusionsIn this study, we systematically analyzed the genomic characterization of SlBES1 family, together with the analyses of protein functional features and expression patterns, our results lay a foundation for the functional research of SlBES1 family.
| S-EPMC8010994 | biostudies-literature
Project description:Soybean is one of the most important legumes, providing high-quality protein for humans. The caffeic acid O-methyltransferase (COMT) gene has previously been demonstrated to be a critical gene that regulates lignin production in plant cell walls and plays an important function in plant growth and development. However, the COMT gene family has not been studied in soybeans. In this study, 55 COMT family genes in soybean were identified by phylogenetic analysis and divided into two groups, I and II. The analysis of conserved domains showed that all GmCOMTs genes contained Methyltransferase-2 domains. Further prediction of cis-acting elements showed that GmCOMTs genes were associated with growth, light, stress, and hormonal responses. Eventually, based on the genomic data of soybean under different stresses, the results showed that the expression of GmCOMTs genes was different under different stresses, such as salt and drought stress. This study has identified and characterized the COMT gene family in soybean, which provides an important theoretical basis for further research on the biological functions of COMT genes and promotes revealing the role of GmCOMTs genes under stress resistance.
| S-EPMC8703356 | biostudies-literature
Project description: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 ? and non-? 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.
| S-EPMC6901008 | biostudies-literature
Project description:BackgroundSoybean is an important legume crop and has significant agricultural and economic value. Previous research has shown that the AT-Hook Motif Nuclear Localized (AHL) gene family is highly conserved in land plants, playing crucial roles in plant growth and development. To date, however, the AHL gene family has not been studied in soybean.ResultsTo investigate the roles played by the AHL gene family in soybean, genome-wide identification, expression patterns and gene structures were performed to analyze. We identified a total of 63 AT-hook motif genes, which were characterized by the presence of the AT-hook motif and PPC domain in soybean. The AT-hook motif genes were distributed on 18 chromosomes and formed two distinct clades (A and B), as shown by phylogenetic analysis. All the AHL proteins were further classified into three types (I, II and III) based on the AT-hook motif. Type-I was belonged to Clade-A, while Type-II and Type-III were belonged to Clade-B. Our results also showed that the main type of duplication in the soybean AHL gene family was segmented duplication event. To discern whether the AHL gene family was involved in stress response in soybean, we performed cis-acting elements analysis and found that AHL genes were associated with light responsiveness, anaerobic induction, MYB and gibberellin-responsiveness elements. This suggest that AHL genes may participate in plant development and mediate stress response. Moreover, a co-expression network analysis showed that the AHL genes were also involved in energy transduction, and the associated with the gibberellin pathway and nuclear entry signal pathways in soybean. Transcription analysis revealed that AHL genes in Jack and Williams82 have a common expression pattern and are mostly expressed in roots, showing greater sensitivity under drought and submergence stress. Hence, the AHL gene family mainly reacts on mediating stress responses in the roots and provide comprehensive information for further understanding of the AT-hook motif gene family-mediated stress response in soybean.ConclusionSixty-three AT-hook motif genes were identified in the soybean genome. These genes formed into two distinct phylogenetic clades and belonged to three different types. Cis-acting elements and co-expression network analyses suggested that AHL genes participated in significant biological processes. This work provides important theoretical basis for the understanding of AHLs biological functions in soybean.
| S-EPMC8132359 | biostudies-literature