Identification and expression analysis of expansin gene family in Salvia miltiorrhiza
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ABSTRACT:
SUBMITTER: Li Y
PROVIDER: S-EPMC10838462 | biostudies-literature | 2024 Jan
REPOSITORIES: biostudies-literature
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Project description:In response to abiotic stresses, transcription factors are essential. Heat shock transcription factors (HSFs), which control gene expression, serve as essential regulators of plant growth, development, and stress response. As a model medicinal plant, Salvia miltiorrhiza is a crucial component in the treatment of cardiovascular illnesses. But throughout its growth cycle, S.miltiorrhiza is exposed to a series of abiotic challenges, including heat and drought. In this study, 35 HSF genes were identified based on genome sequencing of Salvia miltiorrhiza utilizing bioinformatics techniques. Additionally, 35 genes were classified into three groups by phylogeny and gene structural analysis, comprising 22 HSFA, 11 HSFB, and two HSFC. The distribution and sequence analysis of motif showed that SmHSFs were relatively conservative. In SmHSF genes, analysis of the promoter region revealed the presence of many cis-acting elements linked to stress, hormones, and growth and development, suggesting that these factors have regulatory roles. The majority of SmHSFs were expressed in response to heat and drought stress, according to combined transcriptome and real-time quantitative PCR (qRT-PCR) analyses. In conclusion, this study looked at the SmHSF gene family using genome-wide identification, evolutionary analysis, sequence characterization, and expression analysis. This research serves as a foundation for further investigations into the role of HSF genes and their molecular mechanisms in plant stress responses.
| S-EPMC9745953 | biostudies-literature
Project description:The pentatricopeptide repeat (PPR) gene family is one of the largest gene families in plants and plays important roles in posttranscriptional regulation. In this study, we combined whole genome sequencing and transcriptomes to systematically investigate PPRs in Salvia miltiorrhiza, which is a well-known material of traditional Chinese medicine and an emerging model system for medicinal plant studies. Among 562 identified SmPPRs, 299 belong to the P subfamily while the others belong to the PLS subfamily. The majority of SmPPRs have only one exon and are localized in the mitochondrion or chloroplast. As many as 546 SmPPRs were expressed in at least one tissue and exhibited differential expression patterns, which indicates they likely play a variety of functions in S. miltiorrhiza. Up to 349 SmPPRs were salicylic acid-responsive and 183 SmPPRs were yeast extract and Ag⁺-responsive, which indicates these genes might be involved in S. miltiorrhiza defense stresses and secondary metabolism. Furthermore, 23 salicylic acid-responsive SmPPRs were co-expressed with phenolic acid biosynthetic enzyme genes only while 16 yeast extract and Ag⁺-responsive SmPPRs were co-expressed with tanshinone biosynthetic enzyme genes only. Two SmPPRs were co-expressed with both phenolic acid and tanshinone biosynthetic enzyme genes. The results provide a useful platform for further investigating the roles of PPRs in S. miltiorrhiza.
| S-EPMC6099403 | biostudies-literature
Project description:Late embryogenesis abundant (LEA) proteins play important roles in plant defense response to drought stress. However, genome-wide identification of the LEA gene family was not revealed in Salvia miltiorrhiza. In this study, 61 SmLEA genes were identified from S. miltiorrhiza and divided into 7 subfamilies according to their conserved domains and phylogenetic relationships. SmLEA genes contained the LEA conserved motifs and few introns. SmLEA genes of the same subfamilies had similar gene structures and predicted subcellular locations. Our results indicated that the promoters of SmLEA genes contained various cis-acting elements associated with abiotic stress response. In addition, RNA-seq and real-time PCR results suggested that SmLEA genes are specifically expressed in different tissue, and most SmLEA genes can be induced by drought stress. These results provide a valuable foundation for future functional investigations of SmLEA genes and drought stress-resistant breeding of S. miltiorrhiza.
| S-EPMC8078505 | biostudies-literature
Project description:The auxin/indole-3-acetic acid (Aux/IAA) gene family serves as a principal group of genes responsible for modulating plant growth and development through the auxin signaling pathway. Despite the significance of this gene family, the identification and characterization of members within the well-known Chinese medicinal herb Salvia miltiorrhiza (S. miltiorrhiza) have not been thoroughly investigated. In this study, we employed bioinformatics methods to identify 23 Aux/IAA genes within the genome of S. miltiorrhiza. These genes were classified into typical IAA and atypical IAA based on their domain structure. Our analysis of the promoter regions revealed that the expression of these genes is regulated not only by auxins, but also by other hormones and environmental factors. Furthermore, we found that the expression patterns of these genes varied across various tissues of S. miltiorrhiza. While our initial hypothesis suggested that the primary function of these genes was the interaction between SmIAA and ARF, gene co-expression network analysis revealed that they are also influenced by various other transcription factors, such as WRKY and ERF. The findings establish a sturdy basis for future investigations into the function of the Aux/IAA gene family and exhibit promising prospects for enhancing the genetics of this medicinal flora and its associated species.
| S-EPMC10117383 | biostudies-literature
Project description:Cytosine DNA methylation is highly conserved epigenetic modification involved in a wide range of biological processes in eukaryotes. It was established and maintained by cytosine-5 DNA methyltransferases (C5-MTases) in plants. Through genome-wide identification, eight putative SmC5-MTase genes were identified from the genome of Salvia miltiorrhiza, a well-known traditional Chinese medicine material and an emerging model medicinal plant. Based on conserved domains and phylogenetic analysis, eight SmC5-MTase genes were divided into four subfamilies, including MET, CMT, DRM and DNMT2. Genome-wide comparative analysis of the C5-MTase gene family in S. miltiorrhiza and Arabidopsis thaliana, including gene structure, sequence features, sequence alignment and conserved motifs, was carried out. The results showed conservation and divergence of the members of each subfamily in plants. The length of SmC5-MTase open reading frames ranges widely from 1,152 (SmDNMT2) to 5,034 bp (SmMET1). The intron number of SmC5-MTases varies between 7 (SmDRM1) and 20 (SmCMT1 and SmCMT2b). These features were similar to their counterparts from Arabidopsis. Sequence alignment and conserved motif analysis showed the existence of highly conserved and subfamily-specific motifs in the C5-MTases analyzed. Differential transcript abundance was detected for SmC5-MTases, implying genome-wide variance of DNA methylation in different organs and tissues. Transcriptome-wide analysis showed that the transcript levels of all SmC5-MTase genes was slightly changed under yeast extract and methyl jasmonate treatments. Six SmC5-MTases, including SmMET1, SmCMT1, SmCMT2a, SmCMT2b, SmCMT3 and SmDRM1, were salicylic acid-responsive, suggesting the involvement of SmC5-MTases in salicylic acid-dependent immunity. These results provide useful information for demonstrating the role of DNA methylation in bioactive compound biosynthesis and Dao-di herb formation in medicinal plants.
| S-EPMC5842782 | biostudies-literature
Project description:BackgroundArgonaute (AGO) is the core component of RNA-induced silencing complex. The AGO gene family has been analyzed in various plant species; however, there is no report about AGOs in the well-known Traditional Chinese Medicine (TCM) plant, Salvia miltiorrhiza.ResultsThrough a genome-wide analysis, we identified ten SmAGO genes in S. miltiorrhiza. Full-length cDNAs of all SmAGOs were subsequently cloned and sequenced. These SmAGOs were characterized using a comprehensive approach. Sequence features, gene structures and conserved domains were analyzed by the comparison of SmAGOs and AtAGOs. Phylogenetic relationships among AGO proteins from S. miltiorrhiza, Arabidopsis and rice were revealed. The expression levels of SmAGO genes in various tissues of S. miltiorrhiza were investigated. The results implied that some SmAGOs, such as SmAGO1, SmAGO2, SmAGO3, SmAGO7 and SmAGO10, probably played similar roles as their counterparts in Arabidopsis; whereas the others could be more species-specialized. It suggests the conservation and diversity of AGOs in plants. Additionally, we identified a total of 24 hairpin structures, representing six miRNA gene families, to be miRNA precursors. Using the modified 5'-RACE method, we confirmed that SmAGO1 and SmAGO2 were targeted by S. miltiorrhiza miR168a/b and miR403, respectively. It suggests the conservation of AGO1-miR168 and AGO2-miR403 regulatory modules in S. miltiorrhiza and Arabidopsis.ConclusionsThis is the first attempt to explore SmAGOs and miRNAs in S. miltiorrhiza. The results provide useful information for further elucidation of gene silencing pathways in S. miltiorrhiza.
| S-EPMC3750313 | biostudies-literature
Project description:The plant SABATH gene family is a group of O-methyltransferases (O-MTs), which belongs to the S-adenosyl-l-methionine-dependent methyltransferases (SAM-MTs). The resulting reaction products of SABATH genes play an important role in various processes of plant development. In this study, a total of 30 SABATH genes were detected in Salvia miltiorrhiza, which is an important medicinal plant, widely used to treat cardiovascular disease. Multiple sequence alignment and phylogenetic analyses showed that SmSABATH genes could be classified into three groups. The ratios of non-synonymous (Ka) and synonymous (Ks) substitution rates of 11 pairs paralogous of SmSABATH genes revealed that the SmSABATH genes had gone through purifying selection. Positive selection analyses using site models and branch-site models indicated that SmSABATH genes had undergone selective pressure for adaptive evolution. Functional divergence analyses suggested that the SmSABATH subgroup genes were divergent in terms of functions and positive selection sites that contributed to a functional divergence among the subgroups that were detected. Tissue-specific expression showed that the SABATH gene family in S. miltiorrhiza was primarily expressed in stems and leaves.
| S-EPMC5748683 | biostudies-literature
Project description:BackgroundExpansin loosens plant cell walls and involves in cell enlargement and various abiotic stresses. Plant expansin superfamily contains four subfamilies: α-expansin (EXPA), β-expansin (EXPB), expansin-like A (EXLA), and expansin-like B (EXLB). In this work, we performed a comprehensive study on the molecular characterization, phylogenetic relationship and expression profiling of common wheat (Triticum aestivum) expansin gene family using the recently released wheat genome database (IWGSC RefSeq v1.1 with a coverage rate of 94%).ResultsGenome-wide analysis identified 241 expansin genes in the wheat genome, which were grouped into three subfamilies (EXPA, EXPB and EXLA) by phylogenetic tree. Molecular structure analysis showed that wheat expansin gene family showed high evolutionary conservation although some differences were present in different subfamilies. Some key amino acid sites that contribute to functional divergence, positive selection, and coevolution were detected. Evolutionary analysis revealed that wheat expansin gene superfamily underwent strong positive selection. The transcriptome map and qRT-PCR analysis found that wheat expansin genes had tissue/organ expression specificity and preference, and generally highly expressed in the roots. The expression levels of some expansin genes were significantly induced by NaCl and polyethylene glycol stresses, which was consistent with the differential distribution of the cis-elements in the promoter region.ConclusionsWheat expansin gene family showed high evolutionary conservation and wide range of functional divergence. Different selection constraints may influence the evolution of the three expansin subfamilies. The different expression patterns demonstrated that expansin genes could play important roles in plant growth and abiotic stress responses. This study provides new insights into the structures, evolution and functions of wheat expansin gene family.
| S-EPMC6359794 | biostudies-literature
Project description:MADS-box genes constitute a large family of transcription factors that play important roles in plant growth and development. However, our understanding of MADS-box genes involved in anther development and male sterility in Salvia miltiorrhiza is still limited. In this study, 63 MADS-box genes were identified from the genome of the male sterility ecotype Sichuan S. miltiorrhiza (S. miltiorrhiza_SC) unevenly distributed among eight chromosomes. Phylogenetic analysis classified them into two types and 17 subfamilies. They contained 1 to 12 exons and 10 conserved motifs. Evolution analysis showed that segmental duplication was the main force for the expansion of the SmMADS gene family, and duplication gene pairs were under purifying selection. Cis-acting elements analysis demonstrated that the promoter of SmMADS genes contain numerous elements associated with plant growth and development, plant hormones, and stress response. RNA-seq showed that the expression levels of B-class and C-class SmMADS genes were highly expressed during anther development, with SmMADS11 likely playing an important role in regulating anther development and male fertility in S. miltiorrhiza_SC. Overall, this study provides a comprehensive analysis of the MADS-box gene family in S. miltiorrhiza, shedding light on their potential role in anther development and male sterility.
| S-EPMC10341755 | biostudies-literature
Project description:Auxin response factors (ARFs) can function as transcriptional activators or repressors to regulate the expression of auxin response genes by specifically binding to auxin response elements (AuxREs) during plant development. Based on a genome-wide strategy using the medicinal model plant Salvia miltiorrhiza, 25 S. miltiorrhiza ARF (SmARF) gene family members in four classes (class Ia, IIa, IIb and III) were comprehensively analyzed to identify characteristics including gene structures, conserved domains, phylogenetic relationships and expression patterns. In a hybrid analysis of the phylogenetic tree, microRNA targets, and expression patterns of SmARFs in different organs, root tissues, and methyl jasmonate or indole-3-acetic acid treatment conditions, we screened for candidate SmARFs involved in various developmental processes of S. miltiorrhiza Based on this analysis, we predicted that SmARF25, SmARF7, SmARF16 and SmARF20 are involved in flower, leaf, stem and root development, respectively. With the further insight into the targets of miR160 and miR167, specific SmARF genes in S. miltiorrhiza might encode products that participate in biological processes as described for ARF genes in Arabidopsis Our results provide a foundation for understanding the molecular basis and regulatory mechanisms of SmARFs in S. miltiorrhiza.
| S-EPMC4920185 | biostudies-literature