Genome-wide analysis of the SBT gene family involved in drought tolerance in cotton

Mei, Dai; Zhou, Na; Zhang, Yue; Zhang, Yuexin; Ni, Kesong; Wu, Zhongjie; Liu, Liying; Wang, Xiaoge; Chen, Quanjia

doi:10.3389/fpls.2022.1097732

Cited by 14 publications

(6 citation statements)

References 45 publications

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“…The gene sequences in cotton underwent duplication through repeated occurrences, leading to the selective loss or recombination of some redundant genes [ 64 ]. The total number of SBT genes of G. hirsutum , was less than the sum of the genes of G. raimondii and G. arboreum , [ 65 ], and after polyploidization, the gene number in G. hirsutum SAC gene family members decreased [ 66 ]. In our research findings, the CER gene number in G. hirsutum and G. barbadense was lower than the combined total in G. raimondii and G. arboreum .…”

Section: Discussionmentioning

confidence: 99%

Decoding drought resilience: a comprehensive exploration of the cotton Eceriferum (CER) gene family and its role in stress adaptation

Hamid,

Ghorbanzadeh,

Jacob

et al. 2024

BMC Plant Biol

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Background The cuticular wax serves as a primary barrier that protects plants from environmental stresses. The Eceriferum (CER) gene family is associated with wax production and stress resistance. Results In a genome-wide identification study, a total of 52 members of the CER family were discovered in four Gossypium species: G. arboreum, G. barbadense, G. raimondii, and G. hirsutum. There were variations in the physicochemical characteristics of the Gossypium CER (GCER) proteins. Evolutionary analysis classified the identified GCERs into five groups, with purifying selection emerging as the primary evolutionary force. Gene structure analysis revealed that the number of conserved motifs ranged from 1 to 15, and the number of exons varied from 3 to 13. Closely related GCERs exhibited similar conserved motifs and gene structures. Analyses of chromosomal positions, selection pressure, and collinearity revealed numerous fragment duplications in the GCER genes. Additionally, nine putative ghr-miRNAs targeting seven G. hirsutum CER (GhCER) genes were identified. Among them, three miRNAs, including ghr-miR394, ghr-miR414d, and ghr-miR414f, targeted GhCER09A, representing the most targeted gene. The prediction of transcription factors (TFs) and the visualization of the regulatory TF network revealed interactions with GhCER genes involving ERF, MYB, Dof, bHLH, and bZIP. Analysis of cis-regulatory elements suggests potential associations between the CER gene family of cotton and responses to abiotic stress, light, and other biological processes. Enrichment analysis demonstrated a robust correlation between GhCER genes and pathways associated with cutin biosynthesis, fatty acid biosynthesis, wax production, and stress response. Localization analysis showed that most GCER proteins are localized in the plasma membrane. Transcriptome and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) expression assessments demonstrated that several GhCER genes, including GhCER15D, GhCER04A, GhCER06A, and GhCER12D, exhibited elevated expression levels in response to water deficiency stress compared to control conditions. The functional identification through virus-induced gene silencing (VIGS) highlighted the pivotal role of the GhCER04A gene in enhancing drought resistance by promoting increased tissue water retention. Conclusions This investigation not only provides valuable evidence but also offers novel insights that contribute to a deeper understanding of the roles of GhCER genes in cotton, their role in adaptation to drought and other abiotic stress and their potential applications for cotton improvement.

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Section: Discussionmentioning

confidence: 99%

Decoding drought resilience: a comprehensive exploration of the cotton Eceriferum (CER) gene family and its role in stress adaptation

Hamid,

Ghorbanzadeh,

Jacob

et al. 2024

BMC Plant Biol

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“…In addition, we also predicted the cis-acting elements of SOT genes in G. barbadense, including some cis-acting elements involved in drought induction with MYB binding sites, and plant hormonerelated cis-acting elements including abscisic acid response elements, salicylic acid response elements, MeJA response elements, auxin-responsive elements, etc. The results suggest that SOT genes not only participate in a variety of signaling pathways but also participate in plant growth and development and defense responses [40]. We know that the predicted cis-acting elements in the promoters using upstream activating promoter sequences are only speculative hypothesis, and none are known to be functional as predicted until tested experimentally.…”

Section: Basic Analysis Of Sot Family Members Of G Barbadensementioning

confidence: 98%

GBSOT4 Enhances the Resistance of Gossypium barbadense to Fusarium oxysporum f. sp. vasinfectum (FOV) by Regulating the Content of Flavonoid

Su,

Jiao,

Jiang

et al. 2023

Plants

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Sulfotransferases (SOTs) (EC 2.8.2.-) are sulfate regulatory proteins in a variety of organisms that have been previously shown to be involved in regulating a variety of physiological and biological processes, such as growth, development, adaptation to land, stomatal closure, drought tolerance, and response to pathogen infection. However, there is a lack of comprehensive identification and systematic analysis of SOT in cotton, especially in G. barbadense. In this study, we used bioinformatics methods to analyze the structural characteristics, phylogenetic relationships, gene structure, expression patterns, evolutionary relationships, selection pressure and stress response of SOT gene family members in G. barbadense. In this study, a total of 241 SOT genes were identified in four cotton species, among which 74 SOT gene members were found in G. barbadense. According to the phylogenetic tree, 241 SOT protein sequences were divided into five distinct subfamilies. We also mapped the physical locations of these genes on chromosomes and visualized the structural information of SOT genes in G. barbadense. We also predicted the cis-acting elements of the SOT gene in G. barbadense, and we identified the repetitive types and collinearity analysis of SOT genes in four cotton species. We calculated the Ka/Ks ratio between homologous gene pairs to elucidate the selective pressure between SOT genes. Transcriptome data were used to explore the expression patterns of SOT genes, and then qRT-PCR was used to detect the expression patterns of GBSOT4, GBSOT17 and GBSOT33 under FOV stress. WGCNA (weighted gene co-expression network analysis) showed that GB_A01G0479 (GBSOT4) belonged to the MEblue module, which may regulate the resistance mechanism of G. barbadense to FOV through plant hormones, signal transduction and glutathione metabolism. In addition, we conducted a VIGS (virus-induced gene silencing) experiment on GBSOT4, and the results showed that after FOV inoculation, the plants with a silenced target gene had more serious leaf wilting, drying and cracking than the control group, and the disease index of the plants with the silenced target gene was significantly higher than that of the control group. This suggests that GBSOT4 may be involved in protecting the production of G. barbadense from FOV infection. Subsequent metabolomics analysis showed that some flavonoid metabolites, such as Eupatorin-5-methylether (3′-hydroxy-5,6,7,4′-tetramethoxyflavone, were accumulated in cotton plants in response to FOV infection.

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“…Most plants underwent an ancient genome-wide replication event, or polyploidy, resulting in the duplication of all genes in a region [26]. This large-scale chromosomal doubling event resulted in the retention of a large number of chromosomal doubling fragments in the genome [27]. Tandem repeats occur on the same chromosome and are adjacent to each other, often with similar sequences and similar functional clusters [28].…”

Section: Conserved Motifs Of the Oat Dmp Gene And Analysis Of Gene St...mentioning

confidence: 99%

Genome-wide identification of the oat DMP gene family and its expression analysis in response to seed aging

Ma,

Liu,

Wang

et al. 2024

Preprint

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Background: The Domain of unknown function 679 membrane proteins (DMPs) family, as a green plant-specific membrane protein, plays an important role in plant reproductive development, stress response and aging. To identify the DMP gene members of oat (AsDMP) and to investigate their family structural features and tissue expression profile characteristics, a study was conducted. Based on the whole genome and transcriptome data, in this investigation, we have scrutinized the physicochemical properties, gene structure, cisacting elements, phylogenetic relationships, conserved structural (CS) domains, CS motifs and expression patterns of the AsDMP family of oat. Results The DMP family genes of oat were found distributed across 17 chromosomal scaffolds with 33 members. We could divide the AsDMP genes into five subfamilies based on phylogenetic relationships. The gene structure suggests that oats may have also undergone an intron loss event during evolution. Covariance analysis suggests that genome-wide duplication/segmental duplication may be the major contributor to the expansion of the AsDMP gene family. Ka/Ks selective pressure analysis of oat DMP gene family, suggests that DMP gene pairs tend to be conserved over evolutionary time. The upstream promoter of these genes containing several cis-acting elements indicates a plausible role in abiotic stress and hormone induction. Gene expression pattern according to transcriptome data revealed participation of the DMP genes in tissue and organ development. In this study, AsDMP genes (AsDMP1, AsDMP19, and AsDMP22) were identified as potentially regulating oat seed senescence, and can be used as candidate genes for seed longevity and anti-aging germplasm breeding studies in oat. The study provides valuable information on the regulatory mechanism of the AsDMP gene family in the aging process of oat germplasm, and also provides theoretical support for further function investigation in the oat DMP gene and the molecular mechanism of seed anti-aging. Conclusions In this study, we found that the AsDMP gene is involved in the aging process of oat seeds, which is the first report on the potential role of DMP genes in oat seeds.

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Genome-wide analysis of the SBT gene family involved in drought tolerance in cotton

Cited by 14 publications

References 45 publications

Decoding drought resilience: a comprehensive exploration of the cotton Eceriferum (CER) gene family and its role in stress adaptation

Decoding drought resilience: a comprehensive exploration of the cotton Eceriferum (CER) gene family and its role in stress adaptation

GBSOT4 Enhances the Resistance of Gossypium barbadense to Fusarium oxysporum f. sp. vasinfectum (FOV) by Regulating the Content of Flavonoid

Genome-wide identification of the oat DMP gene family and its expression analysis in response to seed aging

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