Dataset Information

Genome-wide identification and characterization of the soybean SOD family during alkaline stress.

ABSTRACT: Background:Superoxide dismutase (SOD) proteins, as one kind of the antioxidant enzymes, play critical roles in plant response to various environment stresses. Even though its functions in the oxidative stress were very well characterized, the roles of SOD family genes in regulating alkaline stress response are not fully reported. Methods:We identified the potential family members by using Hidden Markov model and soybean genome database. The neighbor-joining phylogenetic tree and exon-intron structures were generated by using software MEGA 5.0 and GSDS online server, respectively. Furthermore, the conserved motifs were analyzed by MEME online server. The syntenic analysis was conducted using Circos-0.69. Additionally, the expression levels of soybean SOD genes under alkaline stress were identified by qRT-PCR. Results:In this study, we identified 13 potential SOD genes in soybean genome. Phylogenetic analysis suggested that SOD genes could be classified into three subfamilies, including MnSODs (GmMSD1-2), FeSODs (GmFSD1-5) and Cu/ZnSODs (GmCSD1-6). We further investigated the gene structure, chromosomal locations and gene-duplication, conserved domains and promoter cis-elements of the soybean SOD genes. We also explored the expression profiles of soybean SOD genes in different tissues and alkaline, salt and cold stresses, based on the transcriptome data. In addition, we detected their expression patterns in roots and leaves by qRT-PCR under alkaline stress, and found that different SOD subfamily genes may play different roles in response to alkaline stress. These results also confirmed the hypothesis that the great evolutionary divergence may contribute to the potential functional diversity in soybean SOD genes. Taken together, we established a foundation for further functional characterization of soybean SOD genes in response to alkaline stress in the future.

SUBMITTER: Lu W

PROVIDER: S-EPMC7007734 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Genome-wide identification and characterization of the soybean SOD family during alkaline stress.

Lu Wenxiu W Duanmu Huizi H Qiao Yanhua Y Jin Xiaoxia X Yu Yang Y Yu Lijie L Chen Chao C

PeerJ 20200205

<h4>Background</h4>Superoxide dismutase (SOD) proteins, as one kind of the antioxidant enzymes, play critical roles in plant response to various environment stresses. Even though its functions in the oxidative stress were very well characterized, the roles of <i>SOD</i> family genes in regulating alkaline stress response are not fully reported.<h4>Methods</h4>We identified the potential family members by using Hidden Markov model and soybean genome database. The neighbor-joining phylogenetic tre ...[more]

PMID: 32071807

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Project description:BackgroundNDR1/HIN1-like (NHL) family genes are known to be involved in pathogen induced plant responses to biotic stress. Even though the NHL family genes have been identified and characterized in plant defense responses in some plants, the roles of these genes associated with the plant abiotic stress tolerance in wild soybean is not fully established yet, especially in response to alkaline stress.MethodsWe identified the potential NHL family genes by using the Hidden Markov model and wild soybean genome. The maximum-likelihood phylogenetic tree and conserved motifs were generated by using the MEME online server and MEGA 7.0 software, respectively. Furthermore, the syntenic analysis was generated with Circos-0.69. Then we used the PlantCARE online software to predict and analyze the regulatory cis-acting elements in promoter regions. Hierarchical clustering trees was generated using TM4: MeV4.9 software. Additionally, the expression levels of NHL family genes under alkaline stress, ABA and MEJA treatment were identified by qRT-PCR.ResultsIn this study, we identified 59 potential NHL family genes in wild soybean. We identified that wild soybean NHL family genes could be mainly classified into five groups as well as exist with conserved motifs. Syntenic analysis of NHL family genes revealed genes location on 18 chromosomes and presence of 65 pairs of duplication genes. Moreover, NHL family genes consisted of a variety of putative hormone-related and abiotic stress responsive elements, where numbers of methyl jasmonate (MeJA) and abscisic acid (ABA) responsive elements were significantly larger than other elements. We confirmed the regulatory roles of NHL family genes in response to alkaline stress, ABA and MEJA treatment. In conclusion, we identified and provided valuable information on the wild soybean NHL family genes, and established a foundation to further explore the potential roles of NHL family genes in crosstalk with MeJA or ABA signal transduction mechanisms under alkaline stress.

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.

Dataset Information

Genome-wide identification and characterization of the soybean SOD family during alkaline stress.

Publications

Genome-wide identification and characterization of the soybean SOD family during alkaline stress.

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