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This document is an editorial published in the journal Frontiers in Plant Science. It discusses recent advancements in the understanding of plant secondary metabolites (PSM) and their biosynthesis. The editorial highlights the use of genomics, transcriptomics, and metabolomics technologies in studying PSM biosynthesis. It also emphasizes the importance of sustainable production and utilization of PSM and introduces a research topic on the subject. The document includes summaries of several research articles that explore the identification and characterization of genes involved in PSM biosynthesis and the development of biotechnological techniques to improve PSM yield. [Extracted from the article]

Kisspeptin (Kiss) and kisspeptin receptor (Kissr) system is a key regulator of GnRH expression in several vertebrates. The Indian catfish, Clarias magur, is popular in the Indian sub-continent, and a neo-type of the Asian catfish, C. batrachus. Catfish breeding is constrained as males do not release milt captivity with/without stimulation. Magur Kiss/Kissr system comprising of kiss1, kiss2, kissr1, and kissr2 genes was characterized for the first time. Full-length mRNA was sequenced using RACE PCR. Neighbor-joining tree of predicted proteins shows one clade of teleost orthologs. Magur whole genome (NCBI GenBank) has single copies of each gene, though yet unannotated/misannotated. Anomalies in the nomenclature of earlier sequences in GenBank were noted. Relative gene expression was profiled during various ontogenic stages, in six tissues including brain and gonads at maturity, and also in brains and gonads of premature and spent fish. Expression of gnrh1, gnrhr1, and gnrhr2 was estimated concomitantly. The kiss1 was the first to be twofold upregulated (P < 0.05) at 12 h post fertilization. Kiss/Kissr genes expressed primarily in the brain, ovary, and testis. Though kiss2 was 10 times higher than kiss1, only kiss1 showed significant modulation across stages and appears to be the active isotype that regulates GnRH in magur. [ABSTRACT FROM AUTHOR]

This study was aimed at understanding the role of the NAC transcription factor (TF) gene family in the development and stress responses of Drimia indica, a medicinal plant with immense therapeutic potential, to enhance its medicinal and agronomic traits. We identified and characterized 61 nonredundant putative NAC TF genes, and analyzed their physicochemical properties. The putative proteins encoded by these genes varied in their amino acid composition, molecular weight, and isoelectric point. The proteins were predicted to localize to different subcellular regions, mainly to the nucleus. The NAC genes were classified into 17 phylogenetic subgroups, which differed between D. indica and Arabidopsis thaliana. Gene structure analysis revealed a conserved CDS organization within each subfamily. The identified genes contained 10 conserved motifs, with "Motif 5" being the most prevalent. Promoter analysis revealed cis-elements responsive to light, abscisic acid, methyl jasmonate, and MYB transcription factors. Additionally, TF-binding site analysis revealed several protein families potentially regulating the expression of NAC genes. miRNA target analysis highlighted the potential role of miRNAs in the post-transcriptional regulation of NAC genes. Our findings offer valuable insights into the structural characteristics, regulatory mechanisms, and potential functions of the NAC TF gene family in D. indica, and advance our understanding of plant stress responses. These findings should provide future research avenues for modulating stress tolerance and secondary metabolite production. [ABSTRACT FROM AUTHOR]

Abstract Background The domain of unknown function 247 (DUF247) proteins is involved in plant development and stress response. Rice is an important worldwide cereal crop, although an increasing number of DUF proteins have been identified, the understanding of DUF proteins is still very limited in rice. Results In this study, we identified 69 genes that encode DUF247 proteins in the rice (Oryza sativa) genome by homology searches and domain prediction. All the OsDUF247 proteins were classified into four major groups (I, II, III and IV) by phylogenetic analysis. Remarkably, OsDUF247 genes clustered on the chromosomes solely show close phylogenetic relationships, suggesting that gene duplications have driven the expansion of the DUF247 gene family in the rice genome. Tissue profile analysis showed that most DUF247 genes expressed at constitutive levels in seedlings, roots, stems, and leaves, except for seven genes (LOC_Os01g21670, LOC_Os03g19700, LOC_Os05g04060, LOC_Os08g26820, LOC_Os08g26840, LOC_Os08g26850 and LOC_Os09g13410) in panicles. These seven genes were induced by various abiotic stress, including cold, drought, heat, hormone treatment, and especially salt, as demonstrated by further experimental analysis. DUF247 proteins contain transmembrane domains located on the membrane, suggesting their significant roles in rice development and adaptation to the environment. Conclusions These findings lay the foundation for functional characterizations of DUF247 genes to unravel their exact role in rice cultivars.

Background: The domain of unknown function 247 (DUF247) proteins is involved in plant development and stress response. Rice is an important worldwide cereal crop, although an increasing number of DUF proteins have been identified, the understanding of DUF proteins is still very limited in rice. Results: In this study, we identified 69 genes that encode DUF247 proteins in the rice (Oryza sativa) genome by homology searches and domain prediction. All the OsDUF247 proteins were classified into four major groups (I, II, III and IV) by phylogenetic analysis. Remarkably, OsDUF247 genes clustered on the chromosomes solely show close phylogenetic relationships, suggesting that gene duplications have driven the expansion of the DUF247 gene family in the rice genome. Tissue profile analysis showed that most DUF247 genes expressed at constitutive levels in seedlings, roots, stems, and leaves, except for seven genes (LOC_Os01g21670, LOC_Os03g19700, LOC_Os05g04060, LOC_Os08g26820, LOC_Os08g26840, LOC_Os08g26850 and LOC_Os09g13410) in panicles. These seven genes were induced by various abiotic stress, including cold, drought, heat, hormone treatment, and especially salt, as demonstrated by further experimental analysis. DUF247 proteins contain transmembrane domains located on the membrane, suggesting their significant roles in rice development and adaptation to the environment. Conclusions: These findings lay the foundation for functional characterizations of DUF247 genes to unravel their exact role in rice cultivars. [ABSTRACT FROM AUTHOR]

Carotenoid cleavage oxygenases can cleave carotenoids into a range of biologically important products. Carotenoid isomerooxygenase (NinaB) and β, β-carotene 15, 15′-monooxygenase (BCO1) are two important oxygenases. In order to understand the roles that both oxygenases exert in crustaceans, we first investigated NinaB-like (EsNinaBl) and BCO1-like (EsBCO1l) within the genome of Chinese mitten crab (Eriocheir sinensis). Their functions were then deciphered through an analysis of their expression patterns, an in vitro β-carotene degradation assay, and RNA interference. The results showed that both EsNinaBl and EsBCO1l contain an RPE65 domain and exhibit high levels of expression in the hepatopancreas. During the molting stage, EsNinaBl exhibited significant upregulation in stage C, whereas EsBCO1l showed significantly higher expression levels at stage AB. Moreover, dietary supplementation with β-carotene resulted in a notable increase in the expression of EsNinaBl and EsBCO1l in the hepatopancreas. Further functional assays showed that the EsNinaBl expressed in E. coli underwent significant changes in its color, from orange to light; in addition, its β-carotene cleavage was higher than that of EsBCO1l. After the knockdown of EsNinaBl or EsBCO1l in juvenile E. sinensis, the expression levels of both genes were significantly decreased in the hepatopancreas, accompanied by a notable increase in the redness (a*) values. Furthermore, a significant increase in the β-carotene content was observed in the hepatopancreas when EsNinaBl-mRNA was suppressed, which suggests that EsNinaBl plays an important role in carotenoid cleavage, specifically β-carotene. In conclusion, our findings suggest that EsNinaBl and EsBCO1l may exhibit functional co-expression and play a crucial role in carotenoid cleavage in crabs. [ABSTRACT FROM AUTHOR]

[Objective]The identification and analyses of heat shock proteins（HSP20s/sHSPs）in kiwifruit would lay foundation for the functional studies of AcHSP20 genes and resistance breeding of kiwifruit.[Method]Based on the genome-wide data of kiwifruit, the AcHSP20 gene family was identified, and the physicochemical properties, phyletic evolution, chromosome distribution, gene structure, subcellular localization as well as promoters were analyzed by bioinformatics.[Result]The 34 members of AcHSP20 gene family were identified. They encoded proteins with 85-371 amino acids, 9.93-40.18 kD molecular weight（Mw）and 4.4-9.3 isoelectric points（pI）. Meanwhile, most AcHSP20 proteins were predicted to be located in cytoplasm and chloroplast. The 34 AcHSP20 genes were distributed on 17 chromosomes, and there were no or only one intron, mostly. Promoters of AcHSP20 genes had phytohormone and abiotic stress response elements. All the detected AcHSP20 genes expressed ubiquitously in the roots, stems and leaves of kiwifruit and the expressions changed significantly under abiotic stresses and phytohormone treatments.[Conclusion]The AcHSP20 gene family plays important roles in high temperature, ABA, MeJA, NaCl stress responses in kiwifruit. [ABSTRACT FROM AUTHOR]

Main conclusion: Two trans-isopentenyl diphosphate synthase and one squalene synthase genes were identified and proved to be involved in the triterpenoid biosynthesis in Platycodon grandiflorus. Platycodon grandiflorus is a commonly used traditional Chinese medicine. The main bioactive compounds of P. grandiflorus are triterpenoid saponins. The biosynthetic pathway of triterpenoid saponins in P. grandiflorus has been preliminarily explored. However, limited functional information on related genes has been reported. A total of three trans-isopentenyl diphosphate synthases (trans-IDSs) genes (PgFPPS, PgGGPPS1 and PgGGPPS2) and one squalene synthase (SQS) gene (PgSQS) in P. grandiflorus were screened and identified from transcriptome dataset. Subcellular localization of the proteins was defined based on the analysis of GFP-tagged. The activity of genes was verified in Escherichia coli, demonstrating that recombinant PgFPPS catalysed the production of farnesyl diphosphate. PgGGPPS1 produced geranylgeranyl diphosphate, whereas PgGGPPS2 did not exhibit catalytic activity. By structural identification of encoding genes, a transmembrane region was found at the C-terminus of the PgSQS gene, which produced an insoluble protein when expressed in E. coli but showed no apparent effect on the enzyme function. Furthermore, some triterpenoid saponin synthesis-related genes were discovered by combining the component content and the gene expression assays at the five growth stages of P. grandiflorus seedlings. The accumulation of active components in P. grandiflorus was closely associated with the expression level of genes related to the synthesis pathway. [ABSTRACT FROM AUTHOR]

BackgroundIn the past few decades, heat waves and seasonal variation linked with global warming are causing frequent fluctuations of water temperature in aquatic environments, resulting in further challenges for marine organisms. As a poikilothermic marine animal and a temperate species, sea cucumber A. japonicus is also very sensitive to temperature variation and shows a limited ability to adapt to environmental temperature changes. However, the molecular mechanisms by which A. japonicus perceives signals from such a diverse environment including the trigger of aestivation still remain unclear. TRP (transient receptor potential) superfamily, as the great potential “sentinel” of the organism in response to the changes of the external environment signals, perceived little attention and will be the future great candidates for sensory function research in echinoderm.MethodsBLAST program was applied to identify the AjTRPs based on A. japonicus transcriptome database. Gene structure analysis of AjTRPs and phylogenetic analysis of TRPs were performed. The expression profiles of AjTRPs in different tissues and in response to different heat stress treatments (chronic/ acute) were measured using qRT-PCR.ResultsA total of 54 TRPs were identified in A. japonicus. Gene structure analysis showed that the exon numbers and the domains of AjTRPs varied greatly. Phylogenetic analysis indicated that AjTPRs were mainly grouped into six subfamilies: TRPA, TRPM, TRPC, TRPV, TRPML, and TRPP. Copy numbers of each TRP member in marine invertebrates including A. japonicus were more than those in vertebrates, however some TRP channel members were lost in invertebrates. Expression profile detection suggested that the representative 15 AjTRP genes belonging to 6 subfamilies were expressed in all tissues examined.ConclusionOur findings indicate that the plastic evolutionary history of TRP channel genes and suggest that TRPM2-1, TRPM2-2, TRPM3, and TRPC3-1 are potential thermo-TRP proteins involved in thermal regulation in A. japonicus. This work facilitates the knowledge of TRP-mediated sensory systems in echinoderms, provides new insights into the mechanisms of aestivation and global warming adaptation in marine invertebrates.

Background: The basidiomycete fungus, Ganoderma boninense is the main contributor to oil palm Basal Stem Rot (BSR) in Malaysia and Indonesia. Lanosterol 14α-Demethylase (ERG11) is a key enzyme involved in biosynthesis of ergosterol, which is an important component in the fungal cell membrane. The Azole group fungicides are effective against pathogenic fungi including G. boninense by inhibiting the ERG11 activity. However, the work on molecular characterization of G. boninense ERG11 is still unavailable today. Methods and results: This study aimed to isolate and characterize the full-length cDNA encoding ERG11 from G. boninense. The G. boninense ERG11 gene expression during interaction with oil palm was also studied. A full-length 1860 bp cDNA encoding ERG11 was successfully isolated from G. boninense. The G. boninense ERG11 shared 91% similarity to ERG11 from other basidiomycete fungi. The protein structure homology modeling of GbERG11 was analyzed using the SWISS-MODEL workspace. Southern blot and genome data analyses showed that there is only a single copy of ERG11 gene in the G. boninense genome. Based on the in-vitro inoculation study, the ERG11 gene expression in G. boninense has shown almost 2-fold upregulation with the presence of oil palm. Conclusion: This study provided molecular information and characterization study on the G. boninense ERG11 and this knowledge could be used to design effective control measures to tackle the BSR disease of oil palm. [ABSTRACT FROM AUTHOR]

Background and Aim: Newcastle disease (ND) is a viral infectious disease that affects commercial and native chickens, resulting in economic losses to the poultry industry. This study aimed to examine the viral strains circulating in commercial and native chickens by genetic characterization and observe the distribution of Newcastle disease virus (NDV) in chicken embryonic tissue. Materials and Methods: ND was detected using a quantitative reverse transcription-polymerase chain reaction. Genetic characterization of the fusion (F) and hemagglutinin-neuraminidase (HN) genes from the eight NDVs was performed using specific primers. The sequence was compared with that of other NDVs from GenBank and analyzed using the MEGA-X software. The distribution of NDV in chicken embryos was analyzed based on lesions and the immunopositivity in immunohistochemistry staining. Results: Based on F gene characterization, velogenic NDV strains circulating in commercial and native chickens that showed varying clinical symptoms belonged to genotype VII.2. Lentogenic strains found in chickens without clinical symptoms were grouped into genotype II (unvaccinated native chickens) and genotype I (vaccinated commercial chickens). Amino acid variations in the HN gene, namely, the neutralization epitope and antigenic sites at positions 263 and 494, respectively, occurred in lentogenic strains. The NDV reaches the digestive and respiratory organs, but in lentogenic NDV does not cause significant damage, and hence embryo death does not occur. Conclusion: This study showed that velogenic and lentogenic NDV strains circulated in both commercial and native chickens with varying genotypes. The virus was distributed in almost all organs, especially digestive and respiratory. Organ damage in lentogenic infection is not as severe as in velogenic NDV. Further research is needed to observe the distribution of NDV with varying pathogenicity in chickens.

The study of transcriptional regulation through protein-DNA binding exploring methods can provide an outline of the roles a transcription factor (TF) may carry out based on what coding genes are bound in their promoter regions. In non-model plant species, TFs can be now examined in their genome-wide DNA-binding profiles (cistromes) by the in vitro technique DAP-seq, which involves expressing a tagged TF and then immobilizing it for subsequent exposure to genomic DNA fragments. The technique offers important advantages with respect to ChIP-seq (no need to develop a TFspecific antibody or generate transgenic organisms expressing a tagged TF). This is of particular benefit when working on slow-growing non-model organisms, where genetic transformation is timeconsuming. Our group has implemented the DAP-seq method in grapevine to identify all the sites in the genome where transcription factors bind. Depending on each case we have been able to obtain thousands of binding events assigned to genes, with important TF family-specific differences of peak location distributions. The possibility of performing stable or transient over-expression experiments constitutes a second step in gene target discovery, as shown in the validation of MYB15/MYB14, HY5, MYBA7/A1 and MYBPA1 high confidence targets, or in the characterization of the main regulator of the onset of fruit ripening CARPO. In addition, to TF function discovery, DAP-seq also helped us to hypothesize and explore TF-TF interactions and to identify novel pathway genes that can later be characterized. To visualize the cistromes of different TFs we have created 'DAPBrowse', currently displayed in the Vitis Visualization platform, a publicly available resource with a range of analytical and visualization tools for grapevine. For the initial inspection of TF targets we demonstrate how bound genes can be overlapped with co-expression networks to look for potential targets. Finally, applying DAP-seq in grape calls for species-specific experimental considerations which are being gathered in a set of guidelines currently under preparation in the frame of the Integrape COST Action. The main aim of the guidelines is to provide a standardised framework for DAP-seq experiments in grapevine as well as to help the community in the preparation and analysis of experiments. [ABSTRACT FROM AUTHOR]

Background and Aim: Newcastle disease (ND) is a viral infectious disease that affects commercial and native chickens, resulting in economic losses to the poultry industry. This study aimed to examine the viral strains circulating in commercial and native chickens by genetic characterization and observe the distribution of Newcastle disease virus (NDV) in chicken embryonic tissue., Materials and Methods: ND was detected using a quantitative reverse transcription-polymerase chain reaction. Genetic characterization of the fusion (F) and hemagglutinin-neuraminidase (HN) genes from the eight NDVs was performed using specific primers. The sequence was compared with that of other NDVs from GenBank and analyzed using the MEGA-X software. The distribution of NDV in chicken embryos was analyzed based on lesions and the immunopositivity in immunohistochemistry staining., Results: Based on F gene characterization, velogenic NDV strains circulating in commercial and native chickens that showed varying clinical symptoms belonged to genotype VII.2. Lentogenic strains found in chickens without clinical symptoms were grouped into genotype II (unvaccinated native chickens) and genotype I (vaccinated commercial chickens). Amino acid variations in the HN gene, namely, the neutralization epitope and antigenic sites at positions 263 and 494, respectively, occurred in lentogenic strains. The NDV reaches the digestive and respiratory organs, but in lentogenic NDV does not cause significant damage, and hence embryo death does not occur., Conclusion: This study showed that velogenic and lentogenic NDV strains circulated in both commercial and native chickens with varying genotypes. The virus was distributed in almost all organs, especially digestive and respiratory. Organ damage in lentogenic infection is not as severe as in velogenic NDV. Further research is needed to observe the distribution of NDV with varying pathogenicity in chickens., Competing Interests: The authors declare that they have no competing interests., (Copyright: © Angeliya, et al.)