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Heat map of top 50 differentially expressed genes between early-and late-stages of seed development in S. tora. Heatmap showing differentially expressed genes between early and late stages of seed development in S. tora. Color scale representing normalized expression values is shown at the bottom. https://doi.org/10.1371/journal.pone.0225564.g003
Source publication
Senna tora is an annual herb with rich source of anthraquinones that have tremendous pharmacological properties. However, there is little mention of genetic information for this species, especially regarding the biosynthetic pathways of anthraquinones. To understand the key genes and regulatory mechanism of anthraquinone biosynthesis pathways, we p...
Context in source publication
Context 1
... genes belong to diverse functional groups including glycosyl hydrolases, dehydrogenases, transferases, kinases, phosphatases, cytochrome P450, oxygenases, and hormone-responsive proteins. A heat map was constructed to cluster the top 50 DEGs based on the similarity and diversity of expression profiles using normalized FPKM values within a range of 6 to 16 (Fig 3). Specifically, transcripts of various proteins are expressed differently depending on the tissue and stage of seed. ...
Citations
... Senna species have been used for various economic and medicinal applications such as treating diabetes, microbial infections, skin diseases, gastrointestinal disorders, and inflammation (Oliur Rahman et al., 2013;Ongchai et al., 2019;Kang et al., 2020b). They contain a diverse range of important metabolites (alkaloids, anthraquinones, flavonoids, tannins, glycosides, steroids, terpenoids, and saponins) and display a wide range of in vitro and in vivo pharmacological activities (antidiabetic, anti-gonorrhea, antimicrobial, antioxidant, antipyretic, antinociceptive, antidepressant, and anti-inflammatory effects) (Puri, 2018;Kang et al., 2020a;Oladeji et al., 2021). However, the genus Senna presents challenges for cytogenetic studies owing to the diverse morphological and ecological characteristics of its members (Cordeiro and Felix, 2017;Nguyen et al., 2021;Ta et al., 2021;Waminal et al., 2021). ...
... Notably, Senna tora L. (Roxb) (syn. Cassia tora L.) emerges as a widespread and representative species within the genus, subject to comprehensive genome sequencing to enhance our understanding of its biological evolution and relationship with other Senna species (Puri, 2018;Kang et al., 2020a;Waminal et al., 2021). Moreover, TRs are discerned to actively mediate the significantly rearranged descending dysploid karyotype of S. tora. ...
Introduction
Tandem repeats (TRs) occur abundantly in plant genomes. They play essential roles that affect genome organization and evolution by inducing or generating chromosomal rearrangements such as duplications, deletions, inversions, and translocations. These impact gene expression and chromosome structure and even contribute to the emergence of new species.
Method
We investigated the effects of TRs on speciation in Senna genus by performing a comparative analysis using fluorescence in situ hybridization (FISH) with S. tora-specific TR probes. We examined the chromosomal distribution of these TRs and compared the genome sizes of seven Senna species (estimated using flow cytometry) to better understand their evolutionary relationships.
Results
Two (StoTR03_159 and StoTR04_55) of the nine studied TRs were not detected in any of the seven Senna species, whereas the remaining seven were found in all or some species with patterns that were similar to or contrasted with those of S. tora. Of these studies species, only S. angulata showed significant genome rearrangements and dysploid karyotypes resembling those of S. tora. The genome sizes varied among these species and did not positively correlate with chromosome number. Notably, S. angulata had the fewest chromosomes (2n = 22) but a relatively large genome size.
Discussion
These findings reveal the dynamics of TRs and provide a cytogenetic depiction of chromosomal rearrangements during speciation in Senna. To further elucidate the dynamics of repeat sequences in Senna, future studies must include related species and extensive repeatomic studies, including those on transposable elements.
... The authors analyzed the tandem duplicated genes S. tora. The study [38] will provide helpful information for the further functional analysis of the CHS-L genes in the regulation of anthraquinone biosynthesis in S. tora [39]. ...
The study of gene expression regulation raises the challenge of developing bioinformatics tools and algorithms, demanding data integration [...]
... S. tora is a widely cultivated and used medicinal and food crop in subtropical and tropical countries, especially India, China, Sri Lanka, Nepal, and the Korean Peninsula [12]. The medicinal value of S. tora is attributed to the presence of secondary metabolites, especially flavonoids and anthraquinones. ...
... Senna_tora2, accessed on 22 September 2022), according to Kang et al. [15]. The RNA-Seq data of Senna (S. tora) leaves, young seeds, and mature seeds were downloaded from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (accession number SRP159435), as described by Kang et al. [12]. The RNA-Seq data of Senna (S. obtusifolia) leaves and seeds were also obtained from the SRA database (accession number SRP144670) of NCBI [1]. ...
... To unravel the expression profile of the type III polyketide synthase genes in the leaves and seeds, the transcriptome data of Senna (S. tora and S. obtusifolia) were reanalyzed, and the genomic assembly was used as a reference [1,12,15]. Clean data were obtained by removing the adaptor and low-quality reads using the fastp (version 0.12.4) software with -q 20 -u 30 -n 15 parameters. For transcript abundance calculation, the sequencing reads were mapped onto the genomic sequences using hisat2 (version 2.1.0) ...
Senna tora is one of the homologous crops used as a medicinal food containing an abundance of anthraquinones. Type III polyketide synthases (PKSs) are key enzymes that catalyze polyketide formation; in particular, the chalcone synthase-like (CHS-L) genes are involved in anthraquinone production. Tandem duplication is a fundamental mechanism for gene family expansion. However, the analysis of the tandem duplicated genes (TDGs) and the identification and characterization of PKSs have not been reported for S. tora. Herein, we identified 3087 TDGs in the S. tora genome; the synonymous substitution rates (Ks) analysis indicated that the TDGs had recently undergone duplication. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the type III PKSs were the most enriched TDGs involved in the biosynthesis of the secondary metabolite pathways, as evidenced by 14 tandem duplicated CHS-L genes. Subsequently, we identified 30 type III PKSs with complete sequences in the S. tora genome. Based on the phylogenetic analysis, the type III PKSs were classified into three groups. The protein conserved motifs and key active residues showed similar patterns in the same group. The transcriptome analysis showed that the chalcone synthase (CHS) genes were more highly expressed in the leaves than in the seeds in S. tora. The transcriptome and qRT-PCR analysis showed that the CHS-L genes had a higher expression in the seeds than in other tissues, particularly seven tandem duplicated CHS-L2/3/5/6/9/10/13 genes. The key active-site residues and three-dimensional models of the CHS-L2/3/5/6/9/10/13 proteins showed slight variation. These results indicated that the rich anthraquinones in S. tora seeds might be ascribed to the PKSs’ expansion from tandem duplication, and the seven key CHS-L2/3/5/6/9/10/13 genes provide candidate genes for further research. Our study provides an important basis for further research on the regulation of anthraquinones’ biosynthesis in S. tora.
... De novo transcriptome excavation is a helpful tool for generating an organism's overall genetic information in the absence of a genome sequence [6]. Even with the availability of a reference genome, gene expression studies using a de novo transcriptome are still recommended to uncover the transcripts missed during the genome assembly operation [7]. ...
A high-quality transcriptome is required to advance numerous bioinformatics workflows. Nevertheless, the effectuality of tools for de novo assembly and real precision assembled transcriptomes looks somewhat unexplored, particularly for non-model organisms with complicated (very long, heterozygous, polyploid) genomes. To disclose the performance of various transcriptome assembly programs, this study built 11 single assemblies and analyzed their performance on some significant reference-free and reference-based criteria. As well as to reconfirm the outputs of benchmarks, 55 BLAST were performed and compared using 11 constructed transcriptomes. Concisely, normalized benchmarking demonstrated that Velvet–Oases suffer from the worst results, while the EvidentialGene strategy can provide the most comprehensive and accurate transcriptome of Lilium ledebourii (Baker) Boiss. The BLAST results also confirmed the superiority of EvidentialGene, so it could capture even up to 59% more (than Velvet–Oases) unique gene hits. To promote assembly optimization, with the help of normalized benchmarking, PCA and AHC, it is emphasized that each metric can only provide part of the transcriptome status, and one should never settle for just a few evaluation criteria. This study supplies a framework for benchmarking and optimizing the efficiency of assembly approaches to analyze RNA-Seq data and reveals that selecting an inefficient assembly strategy might result in less identification of unique gene hits.
... During the past ten years, the transcriptome was widely used to study the gene expression of secondary metabolites [79]. While plant secondary metabolites are thought to be the readouts of plant defense activation, usually PSM quantity increase can be detected around 20 days or more after treatment (defense activation). ...
Plant secondary metabolites (PSM) are small molecules of organic compounds produced in plant metabolism that have various ecological functions, such as defense against pathogens, herbivores, and neighboring plants. They can also help to reduce abiotic stresses, such as drought, salinity, temperature, and UV. This chapter reviewed the ecological functions of the PSM and how people utilize these metabolites to reduce crop biotic and abiotic stresses in agriculture. Specific topics covered in this review are (1) extraction of PSM from plant parts and its application on crops; (2) screening of crop/cover crop germplasms for high PSM content and with resistance to pathogens, herbivores, and/or neighboring plants; (3) regulation of PSM biosynthesis (including plant hormones and defense activators) to increase plant readiness for defense; (4) transcriptome and genome technology improvements in the last decade leading to valuable tools to characterize differential gene expression and gene composition in a genome, and lineage-specific gene family expansion and contraction. In addition, there is a critical need to understand how the biosynthesis and release of allelochemicals occur. Filling this knowledge gap will help us to improve and encourage sustainable weed control practices in agriculture.
... To analyze anthraquinone biosynthesis, we determined the levels of seven derivatives of the anthraquinone biosynthesis pathway in the young-and mature-stage seeds and compared them with those identified in S. tora in previous studies ( Table 2; Kang et al., 2020a). Three of the derivatives (obtusin, chryso-obtusin, and obtusifolin) isolated from S. tora could not be isolated from S. occidentalis or were present only in trace amounts. ...
... based on the log 2 (FPKM + 1) value ( Figure 5). In our study, 582 RNA-Seq unigenes were involved in the S. occidentalis secondary metabolite pathways, which were classified into five groups (the MEP/DOXP, MEV, shikimate, carotenoid, and flavonoid/polyketide pathways) based on the anthraquinone biosynthesis pathway of S. tora (Figure 5 and Supplementary Table 5; Kang et al., 2020a). For the MEP/DOXP pathway, which led to the production of the precursor dimethylallyl diphosphate, 28 and 32 unigenes from the RNA-Seq and Iso-Seq datasets, respectively, were identified. ...
... Based on previous studies, many researchers predicted that anthraquinone might be biosynthesized in plants through the polyketide biosynthesis pathway, the most important enzyme of which is CHS, a type III PKS (Pandith et al., 2016). It was also suggested that PKS could form an anthraquinone precursor, octaketide, using acetyl-CoA and malonyl-CoA, which would then be cyclized by PKC-encoding polyketide cyclase to form (Kang et al., 2020a). N/D, Not detected; N/A, Not assayed. ...
Senna occidentalis is an annual leguminous herb that is rich in anthraquinones, which have various pharmacological activities. However, little is known about the genetics of S. occidentalis, particularly its anthraquinone biosynthesis pathway. To broaden our understanding of the key genes and regulatory mechanisms involved in the anthraquinone biosynthesis pathway, we used short RNA sequencing (RNA-Seq) and long-read isoform sequencing (Iso-Seq) to perform a spatial and temporal transcriptomic analysis of S. occidentalis. This generated 121,592 RNA-Seq unigenes and 38,440 Iso-Seq unigenes. Comprehensive functional annotation and classification of these datasets using public databases identified unigene sequences related to major secondary metabolite biosynthesis pathways and critical transcription factor families (bHLH, WRKY, MYB, and bZIP). A tissue-specific differential expression analysis of S. occidentalis and measurement of the amount of anthraquinones revealed that anthraquinone accumulation was related to the gene expression levels in the different tissues. In addition, the amounts and types of anthraquinones produced differ between S. occidentalis and S. tora. In conclusion, these results provide a broader understanding of the anthraquinone metabolic pathway in S. occidentalis.
... The 20-kb SMRTbell library was constructed using the SMRTbell TM Template Prep Kit (version 1.0) [36]. The 350-bp small, fragmented library was constructed using the NEBNext ® Ultra TM DNA Library Prep Kit (NEB, Ipswich, MA, USA) [37]. ...
Naematelia aurantialba is a rare edible fungus with both nutritional and medicinal values and especially rich in bioactive polysaccharides. However, due to the lack of genomic information, researches on the mining of active compounds, artificial breeding and cultivation, genetics, and molecular biology are limited. To facilitate the medicinal and food applications of N. aurantialba, we sequenced and analyzed the whole genome of N. aurantialba for the first time. The 21-Mb genome contained 15 contigs, and a total of 5860 protein-coding genes were predicted. The genome sequence shows that 296 genes are related to polysaccharide synthesis, including 15 genes related to nucleoside-activated sugar synthesis and 11 genes related to glucan synthesis. The genome also contains genes and gene clusters for the synthesis of other active substances, including terpenoids, unsaturated fatty acids, and bioactive proteins. In addition, it was also found that N. aurantialba was more closely related to Naematelia encephala than to Tremella fuciformis. In short, this study provides a reference for molecular cognition of N. aurantialba and related researches.
... Senna tora is an annual shrub belonging to the Caesalpinioideae, a subfamily of the Leguminosae, and is mainly used as medicinal food source in India, China, Sri Lanka, Nepal, and Korea [26]. However, our understanding of the defense mechanisms of this species is limited. ...
Wounds in tissues provide a pathway of entry for pathogenic fungi and bacteria in plants. Plants respond to wounding by regulating the expression of genes involved in their defense mechanisms. To analyze this response, we investigated the defense-related genes induced by wounding in the leaves of Senna tora using RNA sequencing. The genes involved in jasmonate and ethylene biosynthesis were strongly induced by wounding, as were a large number of genes encoding transcription factors such as ERFs, WRKYs, MYBs, bHLHs, and NACs. Wounding induced the expression of genes encoding pathogenesis-related (PR) proteins, such as PR-1, chitinase, thaumatin-like protein, cysteine proteinase inhibitor, PR-10, and plant defensin. Furthermore, wounding led to the induction of genes involved in flavonoid biosynthesis and the accumulation of kaempferol and quercetin in S. tora leaves. All these genes were expressed systemically in leaves distant from the wound site. These results demonstrate that mechanical wounding can lead to a systemic defense response in the Caesalpinioideae, a subfamily of the Leguminosae. In addition, a co-expression analysis of genes induced by wounding provides important information about the interactions between genes involved in plant defense responses.
... Most genes encoding enzymes involved in the isochorismate and MVA/MEP pathways were present in the transcriptome of P. cuspidatum in our study. 2-Succinylbenzoate was formed from isochorismate through a series of enzymatic reactions, but only one enzyme (Men D) was identified in our transcriptome data, similar to the findings in Cassia angustifolia [34] and Senna tora [35]. ...
Background
Polygonum cuspidatum Sieb. et Zucc. is a well-known medicinal plant whose pharmacological effects derive mainly from its stilbenes, anthraquinones, and flavonoids. These compounds accumulate differentially in the root, stem, and leaf; however, the molecular basis of such tissue-specific accumulation remains poorly understood. Because tissue-specific accumulation of compounds is usually associated with tissue-specific expression of the related biosynthetic enzyme genes and regulators, we aimed to clarify and compare the transcripts expressed in different tissues of P. cuspidatum in this study.
Results
High-throughput RNA sequencing was performed using three different tissues (the leaf, stem, and root) of P. cuspidatum . In total, 80,981 unigenes were obtained, of which 40,729 were annotated, and 21,235 differentially expressed genes were identified. Fifty-four candidate synthetase genes and 12 transcription factors associated with stilbene, flavonoid, and anthraquinone biosynthetic pathways were identified, and their expression levels in the three different tissues were analyzed. Phylogenetic analysis of polyketide synthase gene families revealed two novel CHS genes in P. cuspidatum . Most phenylpropanoid pathway genes were predominantly expressed in the root and stem, while methylerythritol 4-phosphate and isochorismate pathways for anthraquinone biosynthesis were dominant in the leaf. The expression patterns of synthase genes were almost in accordance with metabolite profiling in different tissues of P. cuspidatum as measured by high-performance liquid chromatography or ultraviolet spectrophotometry. All predicted transcription factors associated with regulation of the phenylpropanoid pathway were expressed at lower levels in the stem than in the leaf and root, but no consistent trend in their expression was observed between the leaf and the root.
Conclusions
The molecular knowledge of key genes involved in the biosynthesis of P. cuspidatum stilbenes, flavonoids, and anthraquinones is poor. This study offers some novel insights into the biosynthetic regulation of bioactive compounds in different P. cuspidatum tissues and provides valuable resources for the potential metabolic engineering of this important medicinal plant.
... The genus Senna (Family Leguminosae, Subfamily Caesalpiniaceae) comprises many anthraquinone-producing medicinal plants (Jang et al., 2007;Puri, 2018;Kang et al., 2020b). Specifically, Senna tora L. (Roxb) (syn. ...
Tandem repeats can occupy a large portion of plant genomes and can either cause or result from chromosomal rearrangements, which are important drivers of dysploidy-mediated karyotype evolution and speciation. To understand the contribution of tandem repeats in shaping the extant Senna tora dysploid karyotype, we analyzed the composition and abundance of tandem repeats in the S. tora genome and compared the chromosomal distribution of these repeats between S. tora and a closely related euploid, Senna occidentalis. Using a read clustering algorithm, we identified the major S. tora tandem repeats and visualized their chromosomal distribution by fluorescence in situ hybridization. We identified eight independent repeats covering ~85 Mb or ~12% of the S. tora genome. The unit lengths and copy numbers had ranges of 7–5,833 bp and 325–2.89 × 10⁶, respectively. Three short duplicated sequences were found in the 45S rDNA intergenic spacer, one of which was also detected at an extra-NOR locus. The canonical plant telomeric repeat (TTTAGGG)n was also detected as very intense signals in numerous pericentromeric and interstitial loci. StoTR05_180, which showed subtelomeric distribution in Senna occidentalis, was predominantly pericentromeric in S. tora. The unusual chromosomal distribution of tandem repeats in S. tora not only enabled easy identification of individual chromosomes but also revealed the massive chromosomal rearrangements that have likely played important roles in shaping its dysploid karyotype.
