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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.

[Display omitted] • Six predominantly expressed vomeronasal receptor genes (OzVRs) were identified in the female muskrat. • OzVR genes were clustered into two clades: OzV1Rs and OzV2Rs. • OzV1R and OzV2R were predicted associate with testosterone and MUPs, respectively. • The expression levels of OzVRs were highest in the vomeronasal organ. • OzV1Rs were highly expressed in the breeding season, while OzV2Rs showed the opposite. Vomeronasal receptors (VRs) play a crucial role in recognizing pheromones, which are essential for social chemical communication. The male muskrat (Ondatra zibethicus) secretes musk, which contains pheromones as a reproductive signal, and the female can recognize it through the VNO to mediate social communication behavior. This study aimed to identify the genomic information of VRs (OzVRs) in the female muskrat and elucidate their physicochemical properties and evolutionary relationship. Six predominantly expressed OzVR genes were identified using the RACE technique, and a comprehensive analysis was conducted on their gene structure, subcellular distribution, functional predictions, and mRNA levels, revealed that all OzVRs were transmembrane proteins. Phylogenetic analysis clustered OzVR genes into two clades (V1Rs: OzV1R21 , OzV1R81 , OzV1R105 ; V2Rs: OzV2R33 , OzV2R44 , OzV2R60). Physiochemically, OzV1Rs were basic proteins, while OzV2Rs exhibited weakly acidic character. Among them, OzV1R81 and OzV2R44 were identified as hydrophobicitystable proteins, with the remainder categorized as hydrophobicity-unstable proteins. Promoters analysis revealed the involvement of transcription factors and complexes, including Ahr::Arnt , Runx1 , Arnt , and TFAP2A , in regulating the expression of the OzVR genes. Conserved domain and motif analyses demonstrated a high conservation of the VRs superfamily in rodents, with many conserved domains linked to pheromone binding. Functional predictions confirmed that OzVRs were associated with pheromones detection. Finally, the expression patterns of OzVR genes in different tissues and seasons indicated that OzVRs have the highest level of expression in the vomeronasal organ, and OzV1Rs notably higher in the breeding season than that in the non-breeding season, however the expression levels of OzV2Rs were higher in the non-breeding season. This study provided insights into the phylogenetic relationships, gene structure, physicochemical properties, promoter binding sites, functions and gene expression patterns of OzVRs , offering a theoretical reference for further examination of VR gene functions and a foundation for understanding chemical signaling mechanisms in the muskrat. [ABSTRACT FROM AUTHOR]

In this study, three members of the Bmp family were cloned and characterized in yellow catfish Pelteobagrus fulvidraco, including Bmp2a, Bmp4 and Bmp9. The predicted amino acid sequences of P. fulvidraco Bmp2a, Bmp4 and Bmp9 showed the characteristic domains of the Bmp family, including an N-terminal signal peptide, Arg-X-X-Arg site, TGF-β family signature and seven conserved cysteines, indicating that function is likely to have been conserved during evolution. mRNAs of the three Bmp genes had a variable level of expression in tissues. Compared to the control diet, a high fat diet tended to down-regulate the mRNA expression of Bmp2a, Bmp4 and Bmp9 in mesenteric fat, liver and ovary, while it tended to up-regulate their mRNA levels in muscle and kidney. The responses to dietary lipid status and the potential role in lipid metabolism have not previously been reported and reinforces the idea of their multiple functions. Our findings provide the first data about the potential role of the Bmp family in lipid metabolism in teleost.

Abstract Background Genetically modified cotton accounts for 64% of the world’s cotton growing area (22.3 million hectares). The genome sequencing of the diploid cotton progenitors Gossypium raimondii and Gossypium arboreum as well as the cultivated Gossypium hirsutum has provided a wealth of genetic information that could be exploited for crop improvement. Unfortunately, gene functional characterization in cotton is lagging behind other economically important crops due to the low efficiency, lengthiness and technical complexity of the available stable transformation methods. We present here a simple, fast and efficient method for the transient transformation of G. hirsutum that can be used for gene characterization studies. Results We developed a transient transformation system for gene characterization in upland cotton. Using β-glucuronidase as a reporter for Agrobacterium-mediated transformation assays, we evaluated multiple transformation parameters such as Agrobacterium strain, bacterial density, length of co-cultivation, chemicals and surfactants, which can affect transformation efficiency. After the initial characterization, the Agrobacterium EHA105 strain was selected and a number of binary constructs used to perform gene characterization studies. 7-days-old cotton seedlings were co-cultivated with Agrobacterium and transient gene expression was observed 5 days after infection of the plants. Transcript levels of two different transgenes under the control of the cauliflower mosaic virus (CaMV) 35S promoter were quantified by real-time reverse transcription PCR (qRT-PCR) showing a 3–10 times increase over the levels observed in non-infected controls. The expression patterns driven by the promoters of two G. hirsutum genes as well as the subcellular localization of their corresponding proteins were studied using the new transient expression system and our observations were consistent with previously published results using Arabidopsis as a heterologous system. Conclusions The Agrobacterium-mediated transient transformation method is a fast and easy transient expression system enabling high transient expression and transformation efficiency in upland cotton seedlings. Our method can be used for gene functional studies such as promoter characterization and protein subcellular localization in cotton, obviating the need to perform such studies in a heterologous system such as Arabidopsis.

• V instar larvae convert the substrate into biomass more efficiently than prepupae. • Hermetia illucens nutritional composition was dependent on the developmental stage. • V instar larvae and prepupae showed a different fatty acid profile. • Lipid metabolism genes were characterized from H. illucens for the first time. • Lipid metabolism related genes were differentially expressed in larvae and prepupae. The Black Soldier Fly (BSF) Hermetia illucens provides a promising strategy in the waste valorisation process and a sustainable alternative source of valuable nutrients, including lipids for food and feed. In the present study, the differences in growth performances and nutritional values of BSF V instar larvae and prepupae reared on vegetable waste were analyzed and compared focusing on fat content. V instar larvae showed higher capacity to bioconvert the substrate into biomass than prepupae. The nutritional composition and the fatty acid profiles were dependent on the developmental stage. The expression levels of acetyl-CoA carboxylase (acc), fatty acid synthase (fas), lipase (lip) and acyl-CoA dehydrogenase (acd) genes involved in the lipid metabolism pathway and herein characterized for the first time, were evaluated in order to understand the molecular basis underlying the observed differences in fatty acid profiles. Our results suggest that the different fatty acid profiles of BSF V instar larvae and prepupae may be related to the modulation of the lipid metabolism-related genes expression during larval development. Our study highlights substantial differences between H. illucens V instar larvae and prepupae giving important features regarding the opportunity to modulate the preferable fatty acid profile to meet the industrial requirements. [ABSTRACT FROM AUTHOR]

Cynomolgus macaques (Macaca fascicularis) are an established animal model of asthma, which exhibit different responses to allergen exposure that are clinically relevant. The chemokine ligand gene (CCL7) encodes Monocyte Chemotactic Protein-3, which has an important role in asthma pathogenesis. While CCL7 polymorphism in humans is associated with asthma phenotype, very little is known about CCL7 in nonhuman primate models of respiratory disease. The objective of this study was to isolate and characterize CCL7 gene in cynomolgus macaques of Indonesian origin. In this study, we used sequencing and bioinformatics technique for gene isolation, characterization, and protein 3D structure prediction. We isolated a 2253 base-pair (bp) sequence of CCL7 in cynomolgus macaques, which exhibited 95% similarity in coding sequence to human CCL7. The amino acid sequence was more closely clustered with human CCL7 than with that of rodents. Importantly, the predictive protein structure of CCL7 was similar to that in humans. These similarities in CCL7 suggests the potential of cynomolgus macaque as a translational model to study asthma, particularly in the context of genetics and role of chemokines such as CCL7.

The hypothesis of the present study is that apoptosis through an intrinsic mitochondrial pathway may mediate high fat diet (HFD)-induced changes in the metabolism of Pelteobagrus fulvidraco. To this end, we cloned the full-length cDNA sequences of Cycs, Apaf1, Casp9, Casp3a, and Casp3b involved in the mitochondria apoptotic pathway, and explored their mRNA tissue expressions and transcriptional responses to HFD. All of these members shared similar domains to their orthologous vertebrate genes. They were constitutively expressed in all analyzed tissues but varied from tissue to tissue. Compared to the control, HFD up-regulated the mRNA expression of partial genes among these five key genes (Cycs, Apaf1, Casp9, Casp3a, and Casp3b) in mesenteric fat, intestine, ovary and the kidney, indicating the induction of apoptosis in these tissues; in contrast, HFD down-regulated mRNA levels of partial genes among the five key genes (Cycs, Apaf1, Casp9, Casp3a, and Casp3b) in the heart, spleen and gill tissues, indicating the inhibition of apoptosis in these tissues. The present study will facilitate further exploration into the functions of these genes at the molecular level and disclose the critical involvement of these genes against nutrient changes, indicating that processes of apoptosis in various tissues may differentially be modified by HFD.

The hypothesis of the present study is that apoptosis through an intrinsic mitochondrial pathway may mediate high fat diet (HFD)-induced changes in the metabolism of Pelteobagrus fulvidraco. To this end, we cloned the full-length cDNA sequences of Cycs, Apaf1, Casp9, Casp3a, and Casp3b involved in the mitochondria apoptotic pathway, and explored their mRNA tissue expressions and transcriptional responses to HFD. All of these members shared similar domains to their orthologous vertebrate genes. They were constitutively expressed in all analyzed tissues but varied from tissue to tissue. Compared to the control, HFD up-regulated the mRNA expression of partial genes among these five key genes (Cycs, Apaf1, Casp9, Casp3a, and Casp3b) in mesenteric fat, intestine, ovary and the kidney, indicating the induction of apoptosis in these tissues; in contrast, HFD down-regulated mRNA levels of partial genes among the five key genes (Cycs, Apaf1, Casp9, Casp3a, and Casp3b) in the heart, spleen and gill tissues, indicating the inhibition of apoptosis in these tissues. The present study will facilitate further exploration into the functions of these genes at the molecular level and disclose the critical involvement of these genes against nutrient changes, indicating that processes of apoptosis in various tissues may differentially be modified by HFD. [ABSTRACT FROM AUTHOR]

Antimicrobial peptides have a wide range of antimicrobial activity and widely occur in different organisms including mollusks, crustaceans and vertebrates. Hepcidins are a group of cysteine-rich antimicrobial peptides that are active against a variety of pathogens including gram-positive and gram-negative bacteria, as well as viruses. In this study, the hepcidin gene of Caspian trout (CtHep) was identified and characterized. Our results showed that CtHep cDNA has a 267-bp Open Reading Frame (ORF), which is translated to 88 amino acids. The CtHep was classified in the HAMP1 class of hepcidins. Comparison of DNA and cDNA sequences showed that CtHep has 3 exons and 2 introns. The signal, prodomain and mature part of CtHep have 24, 39 and 25 amino acids, respectively. The mature peptide has a molecular weight of 2881.43 Da and a theoretical isoelectric point of 8.53. The expression of CtHep mRNA was detected in different tissues of healthy and infected fish. CtHep expression in the liver, head kidney, spleen and skin was significantly enhanced after bacterial challenge. Expression of CtHep in different embryonic development stages was also substantial. Antibacterial activity of synthetic CtHep peptides was investigated against a number of Gram-positive and Gram-negative bacteria. CtHep inhibited some pathogenic bacteria such as Streptococcus iniae and Aeromonas hydrophila. In the in vivo experiment, CtHep upregulated the cytokines IL-6 and TNF-α in both kidney and spleen tissues after 24 h of the peptide injection. In conclusion, our study showed that CtHep plays an important role in the immune system of Caspian trout and also in the embryonic stages. Moreover, CtHep peptide has a potential to be used as an antimicrobial therapeutic agent as well as an immunostimulant in aquaculture. • We have identified and characterized the hepcidin gene of endangered Caspian trout. • Synthetic CtHep showed inhibitory effects on several bacteria. • Synthetic CtHep exhibited in vivo immunomodulatory function in Caspian trout. • CtHep plays an important role in immune system of Caspian trout against pathogens. [ABSTRACT FROM AUTHOR]

Cynomolgus macaques (Macaca fascicularis) are an established animal model of asthma, which exhibit different responses to allergen exposure that are clinically relevant. The chemokine ligand gene (CCL7) encodes Monocyte Chemotactic Protein-3, which has an important role in asthma pathogenesis. While CCL7 polymorphism in humans is associated with asthma phenotype, very little is known about CCL7 in nonhuman primate models of respiratory disease. The objective of this study was to isolate and characterize CCL7 gene in cynomolgus macaques of Indonesian origin. In this study, we used sequencing and bioinformatics technique for gene isolation, characterization, and protein 3D structure prediction. We isolated a 2253 base-pair (bp) sequence of CCL7 in cynomolgus macaques, which exhibited 95% similarity in coding sequence to human CCL7. The amino acid sequence was more closely clustered with human CCL7 than with that of rodents. Importantly, the predictive protein structure of CCL7 was similar to that in humans. These similarities in CCL7 suggests the potential of cynomolgus macaque as a translational model to study asthma, particularly in the context of genetics and role of chemokines such as CCL7. [ABSTRACT FROM AUTHOR]

Mx and Viperin are important interferon‐stimulated genes that mediate the antiviral immune response. In this study, we cloned the Mx and viperin genes from Dabry's sturgeon (Acipenser dabryanus). The Mx cDNA sequence contained an open reading frame (ORF) of 1,449 nucleotides, encoding a putative protein of 392 aa, which is significantly shorter than other animal Mx proteins. Although the similarity and identity were low between sturgeon Mx and other animal Mx proteins, sturgeon Mx contains the conserved tripartite GTP binding motif and a dynamin family signature. The sturgeon Mx gene contains eight exons split by seven introns. The sturgeon viperin cDNA sequence contained an ORF of 1,047 bp encoding a putative protein of 349 aa, which is relatively well conserved among species. Sturgeon viperin proteins show 82% similarity with those of Xiphophorus maculatus platyfish and Poecilia formosa Amazon molly. The sturgeon viperin gene has a six exon/five intron structure with the same size of second, third, fourth, and fifth exons between different species. The expression of Mx and viperin was detectable in all tissues examined, with the highest expression in skin for Mx and in peripheral blood for viperin. After mock infection using polyinosine‐polycytidylic acid, Mx and viperin showed significantly upregulated expression in primary spleen leukocytes from 3 hr to 72 hr. Lipopolysaccharide could also induce their expression. These results suggested Mx and Viperin could play a vital antiviral role in the innate immune system of Dabry's sturgeon. [ABSTRACT FROM AUTHOR]

Insects have been recognized as sustainable alternative sources of nutrients for food and feed. The Black Soldier Fly (BSF), Hermetia illucens, is a particularly promising species for its great potential in the waste valorization to produce, during the bioconversion process, high-value fat and proteins that currently represent a valuable source for fish feed. The present study aims to evaluate the efficiency to use substrate proteins in two different BSF developmental stages as sustainable biotechnological tools for vegetable waste management. We provide insights into the nutritional values of both V instar larvae and prepupae in terms of valuable amino acids with special focus on taurine, a crucial nutrient for fish. Moreover, we cloned four key genes from BSF involved in the taurine biosynthesis pathway, 2-aminoethanethiol dioxygenase (Hiado), cysteine dioxygenase (Hicdo), cysteine sulfonate decarboxylase (Hicsad), and glutamate decarboxylase (Higad). The gene expression analysis in larvae and prepupae by qPCR showed development-specific profiles suggesting they influence the taurine content during BSF development. These findings showed peculiar phenotypes in larvae and prepupae that can be selected for different biotechnological applications as sustainable source of relevant amino acids and taurine to support the increasing demand for animal feed and aquafeed in the next decades.

Valsa mali, a parasitic fungus, is a destructive pathogen of apple tree that causes heavy economic losses in China. The pathogen secretes various cell wall-degrading enzymes (CWDEs) that degrade plant cell-wall components, and thus facilitate its entry into host cells. Therefore, functional analysis of the genes encoding CWDEs is necessary to understand virulence of V. mali toward apple tree. Here, we identified and cloned an endo-β-1,4-xylanase gene, VmXyl1 in V. mali. The full-length cDNA of VmXyl1 is 1626 bp containing 5′- and 3′-non-coding regions, as well an open reading frame of 1320 bp that encodes a protein with a calculated molecular mass and an isoelectric point of 43.8 kDa and 4.4, respectively. The predicted amino acid sequences showed significant homology to a family GH10 of glycosyl hydrolases. The apple branch extract and beechwood xylan, but not glucose, induced the expression of VmXyl1. Furthermore, VmXyl1 had high expression levels in the apple tree bark during the pathogen infection. The deletion of VmXyl1 did not affect mycelia growth; however, it significantly reduced pycnidia formation in V. mali. The deletion strains showed a reduced virulence toward apple leaves and twigs. Moreover, the mutant strains had reduced endo-β-1,4-xylanase activity and growth when cultured using beechwood xylan as the only carbon source. Reintroducing wild-type VmXyl1 into the mutant strains rescued the defect phenotype. We conclude that VmXyl1 determines the virulence of V. mali toward apple tree. These results provide valuable insight into the plant–pathogen molecular interactions.

The goal of this study was to clone and characterize complete cDNA sequences of three important development-relevant genes of yellow catfish Pelteobagrus fulvidraco , including lrp6 , sox9a1 and fgfr2c , and explore their transcriptional responses in several tissues of P . fulvidraco to high fat diet. The predicted amino acid sequences of P . fulvidraco Lrp6, Sox9a1 and Fgfr2c contained all of the conserved structural features that were characteristic of these genes in other species, including YWTD domains, EGF-like repeats, LDLR ligand binding repeats, PPSP repeats motifs, HMG box, TA-binding functional domain, Ig I-III and PTK I-II. The mRNAs of the three genes were expressed in various tissues, but their mRNA levels varied among tissues. Compared to the control, high fat diet tended to down-regulate the mRNA expression of sox9a1 and fgfr2c in mesenteric fat, liver and ovary, and up-regulate their mRNA levels in muscle and kidney; in contrast, high fat diet down-regulated lrp6 mRNA levels in the ovary and muscle, but had no significant effects on lrp6 mRNA expression in mesenteric fat, liver and kidney. Our findings provide the first data about their expression responses to dietary lipid in teleosts and reinforce the multiple functions at the molecular level. [ABSTRACT FROM AUTHOR]

The present study was conducted during the period from 10th of March 2017 until 31th of July 2017. The study designed tostudying gene characterization of Giardia lamblia among gastrointestinal disturbances patients. Two hundred and fifty stool specimens were collected from patients suffering from gastrointestinal disturbances with different age groups, who attending to various governmental hospitals in Baghdad city with the main clinical feature (abdominal pain, nausea and bloating). These patients had examined and diagnosed by specialist physicians as suspected H. pylori infection. The stool specimens were collected in sterile dry plastic cups with tight lids specially made for this purpose, each cup was given a unique number representing the patients. The results showed that there were 250 cases constituted of 132 male, which represent (52.8%) and (118) female, which characterize (47.2%) suspected as acute gastritis cases. The total infection rate with H. pylori was (98) positive samples, which stand for (39.2%) and (152) negative samples in the rate of (60.8%). The total infection rate with Giardia lamblia was (20) positive samples, which represent (8.0%) and (230) negative samples in the rate of 92.0%. Positive samples of G. lamblia examined by PCR techniques and from these 20 samples the result of PCR assay, which amplification of ß-giardin gene showed the presence of (11) positive results at 511bp PCR product size. Sequences analysis for ß- giardin gene of G. lamblia (three samples) was done by using Bio Edit Sequence Alignment Editor Software and the nucleotide sequence datasets(KY320577.1) from NCBI had used as references. [ABSTRACT FROM AUTHOR]

Genes in the ZIP family encode transcripts to store and transport bivalent metal micronutrient, particularly iron (Fe) and or zinc (Zn). These transcripts are important for a variety of functions involved in the developmental and physiological processes in many plant species, including most, if not all, Poaceae plant species and the model species Arabidopsis. Here, we present the report of a genome wide investigation of orthologous ZIP genes in Setaria italica and the identification of 7 single copy genes. RT-PCR shows 4 of them could be used to increase the bio-availability of zinc and iron content in grains. Of 36 ZIP members, 25 genes have traces of signal peptide based sub-cellular localization, as compared to those of plant species studied previously, yet translocation of ions remains unclear. In silico analysis of gene structure and protein nature suggests that these two were preeminent in shaping the functional diversity of the ZIP gene family in S. italica. NAC, bZIP and bHLH are the predominant Fe and Zn responsive transcription factors present in SiZIP genes. Together, our results provide new insights into the signal peptide based/independent iron and zinc translocation in the plant system and allowed identification of ZIP genes that may be involved in the zinc and iron absorption from the soil, and thus transporting it to the cereal grain underlying high micronutrient accumulation.

Lycium chinense is a shrub that has health benefits and is used as a source of medicines in Asia. In this study, a full-length cDNA clone encoding β-ring carotene hydroxylase (LcCHXB) and partial-length cDNA clones encoding phytoene synthase (LcPSY), phytoene desaturase (LcPDS), ξ-carotene desaturase (LcZDS), lycopene β-cyclase (LcLCYB), lycopene ε-cyclase (LcLCYE), ε-ring carotene hydroxylase (LcCHXE), zeaxanthin epoxidase (LcZEP), carotenoid cleavage dioxygenase (LcCCD1), and 9-cis epoxycarotenoid dioxygenase (LcNCED) were identified in L. chinense. The transcripts were constitutively expressed at high levels in leaves, flowers and red fruits, where the carotenoids are mostly distributed. In contrast, most of the carotenoid biosynthetic genes were weakly expressed in the roots and stems, which contained only small amounts of carotenoids. The level of LcLCYE transcripts was very high in leaves and correlated with the abundance of lutein in this plant tissue. During maturation, the levels of lutein and zeaxanthin in L. chinense fruits dramatically increased, concomitant with a rise in the level of β-cryptoxanthin. LcPSY, LcPDS, LcZDS, LcLCYB, and LcCHXE were highly expressed in red fruits, leading to their substantially higher total carotenoid content compared to that in green fruits. Total carotenoid content was high in both the leaves and red fruits of L. chinense. Our findings on the biosynthesis of carotenoids in L. chinense provide insights into the molecular mechanisms involved in carotenoid biosynthesis and may facilitate the optimization of carotenoid production in L. chinense.

Full-length cDNAs encoding ξ-carotene desaturase (CmZDS), lycopene ε-cyclase (CmLCYE), β-ring carotene hydroxylase (CmCHXB), and zeaxanthin epoxidase (CmZEP), and partial-length cDNA encoding ε-ring carotene hydroxylase (CmCHXE) were isolated in Chamoe (Cucumis melo L. var. makuwa), an important commercial fruit. Sequence analyses revealed that these proteins share high identity and common features with other orthologous genes. Expression levels of entire genes involved in the carotenoid biosynthetic pathway were investigated in the peel, pulp, and stalk of chamoe cultivars Ohbokggul and Gotgam. Most of the carotenoid biosynthetic genes were expressed at their highest levels in the stalk, whereas carotenoids were highly distributed in the peel. The expression levels of all carotenoid biosynthetic genes in fruits of the native cultivar Gotgam chamoe were higher than those in the cultivar Ohbokggul chamoe, consistent with the abundant carotenoid accumulation in Gotgam chamoe fruits and trace carotenoid content of Ohbokggul chamoe fruit. Lutein and β-carotene were the dominant carotenoids; high levels (278.05 μg g−1 and 112.02 μg g−1 dry weight, respectively) were found in the peel of Gotgam chamoe. Our findings may provide a foundation for elucidating the carotenoid biosynthetic mechanism in C. melo and inform strategies for developing new chamoe cultivars with improved characteristics.

Genes in the ZIP family encode transcripts to store and transport bivalent metal micronutrient, particularly iron (Fe) and or zinc (Zn). These transcripts are important for a variety of functions involved in the developmental and physiological processes in many plant species, including most, if not all, Poaceae plant species and the model species Arabidopsis. Here, we present the report of a genome wide investigation of orthologous ZIP genes in Setaria italica and the identification of 7 single copy genes. RT-PCR shows 4 of them could be used to increase the bio-availability of zinc and iron content in grains. Of 36 ZIP members, 25 genes have traces of signal peptide based sub-cellular localization, as compared to those of plant species studied previously, yet translocation of ions remains unclear. In silico analysis of gene structure and protein nature suggests that these two were preeminent in shaping the functional diversity of the ZIP gene family in S. italica. NAC, bZIP and bHLH are the predominant Fe and Zn responsive transcription factors present in SiZIP genes. Together, our results provide new insights into the signal peptide based/independent iron and zinc translocation in the plant system and allowed identification of ZIP genes that may be involved in the zinc and iron absorption from the soil, and thus transporting it to the cereal grain underlying high micronutrient accumulation. [ABSTRACT FROM AUTHOR]

Salinity is a severe abiotic stress limiting agricultural yield and productivity. Plants have evolved various strategies to cope with salt stress. Chloroplasts are important photosynthesis organelles, which are sensitive to salinity. An understanding of molecular mechanisms in chloroplast tolerance to salinity is of great importance for genetic modification and plant breeding. Previous studies have characterized more than 53 salt-responsive genes encoding important chloroplast-localized proteins, which imply multiple vital pathways in chloroplasts in response to salt stress, such as thylakoid membrane organization, the modulation of photosystem II (PS II) activity, carbon dioxide (CO2) assimilation, photorespiration, reactive oxygen species (ROS) scavenging, osmotic and ion homeostasis, abscisic acid (ABA) biosynthesis and signaling, and gene expression regulation, as well as protein synthesis and turnover. This review presents an overview of salt response in chloroplasts revealed by gene characterization efforts. [ABSTRACT FROM AUTHOR]

Nicotine is the major alkaloid compound in cultivated tobacco (Nicotiana tabacum) that could potentially be converted into carcinogenic compound (nor-nicotine). The PMT gene encoding putrescine N-methyltransferase (PMT) is one of the two key genes that play a prominent role in nicotine biosynthesis. The aimed of this study was to isolate and characterize the cDNA sequence originated from Indonesian local tobacco cv. Sindoro1 (Ntpmt_Sindoro1). The results showed that the Ntpmt_Sindoro1 was 1124 bp in length. This cDNA fragment encodes for 374 amino acid residues. The predicted polypeptide from the cDNA is a hidrophilic protein, and has a predicted molecular weight of 40.95 kDa. The predicted amino acids sequence also showed high similarity to the PMT gene product Nicotiana sp. available in the GenBank data base. The amino acid sequences also exert conserved residues specifically exhibited only by PMT gene originated from N. tabacum. Clustering analysis revealed that Ntpmt_Sindoro1 belongs to the same clade as the PMT3 gene, a member of the N. tabacum PMT gene family. The Ntpmt_Sindoro1 cDNA sequence covering exon1-exon8 of the PMT gene fragment has been registered in the GenBank data base, under the accession number JX978277.

Musa acuminata cultivar pisang ambon lumut is a native climacteric fruit from Indonesia. Climacteric fruit ripening process is triggered by the gaseous plant hormone ethylene. The rate limiting enzyme involved in ethylene biosynthesis is ACC synthase (ACS) which is encoded by ACS gene family. The objective of this study is to identify MA-ACS gene family in M. acuminata cultivar pisang ambon lumut and to study the MA-ACS1 gene expression. The result showed that there were nine M. acuminata ACS gene family members called MA-ACS1–9. Two of them (MA-ACS1 and MA-ACS2) were assessed using reverse transcriptase PCR (RT-PCR) for gene expression study and it was only MA-ACS1 correlated with fruit ripening. The MA-ACS1 gene fragment has been successfully isolated and characterized and it has three introns, four exons, and one stop codon. It also shows highest homology with MACS1 gene from M. acuminata cultivar Hsian Jien Chiao (GenBank accession number AF056164). Expression analysis of MA-ACS1 using quantitative PCR (qPCR) showed that MA-ACS1 gene expression increased significantly in the third day, reached maximum at the fifth day, and then decreased in the seventh day after harvesting. The qPCR expression analysis result correlated with the result of physical analysis during fruit ripening.

Two isoforms of Cu transporter (CTR1 and CTR2) and metallothionein (MT1 and MT2), and divalent metal ion transporter 1 (DMT1) were cloned and characterized in Synechogobius hasta , respectively. The protein sequences of S. hasta CTRs possessed two methionine-rich regions (MxM and MxxxM) and three transmembrane regions. At the C-terminus, CTR1 contained a sequence of conserved cysteine and histidine residues (HCH), while CTR2 did not contain the conserved sequence. The protein sequence of S. hasta DMT1 possessed all the characteristic features of DMT1, including twelve conserved hydrophobic cores of transmembrane domains. The protein sequences of S. hasta MTs were highly conserved in the total number of cysteine residues and their locations. mRNA of the five genes were expressed in a wide range of tissues but the levels were relatively higher in the liver. Cu exposure tended to up-regulate the mRNA expressions of CTR2, DMT1, MT1 and MT2. However, Fe down-regulated the Cu-induced increase of CTR2 and DMT1 mRNA levels. For the first time, our study cloned and characterized CTR1, CTR2, DMT1, MT1 and MT2 genes in S. hasta and determined their tissue-specific expression, and also the transcriptional change by Cu and Fe exposure, which shed new light on the Cu Fe relationship and help to understand the basic mechanisms of Cu and Fe homeostasis in fish. [ABSTRACT FROM AUTHOR]

Ammonium is the primarily nitrogen source for plant growth, but the molecular basis of ammonium acquisition in fruit species remains poorly understood. In this study, we report on the characterization of two new ammonium transporters (AMT) in the perennial tree Pyrus betulaefolia. In silico analyses and yeast complementation assays revealed that both PbAMT1;3 and PbAMT1;5 can be classified in the AMT1 sub-family. The specific expression of PbAMT1;3 in roots and of PbAMT1;5 in leaves indicates that they have diverse functions in ammonium uptake or transport in P. betulaefolia. Their expression was strongly influenced by ammonium availability. In addition, the transcript level of PbAMT1;5 was significantly affected by the diurnal cycle and senescence hormones. They conferred the ability to uptake nitrogen to the yeast strain 31019b; however, the NH uptake kinetics of PbAMT1;3 were different from those of PbAMT1;5. Indeed, PbAMT1;3 had a higher affinity for NH, and pH changes were associated with this substrates' transport in yeast. The present study provides basic gene features and transcriptional information for the two new members of the AMT1 sub-family in P. betulaefolia and will aid in decoding the precise roles of AMTs in P. betulaefolia physiology. [ABSTRACT FROM AUTHOR]

The enzyme Δ6-fatty acid desaturase regulates the rate of highly unsaturated fatty acid (HUFA) biosynthesis. We first obtained the cDNA sequences and structures of Fads6 in Coilia nasus and investigated the mRNA expression patterns in tissue, and in juveniles under different dietary regulation. The Fads6 cDNA was 2032 bp, specifying a protein of 445 amino acids. A high expression was observed in the brain and intestine, relatively high expression in muscle and liver, and a weak expression was exhibited in the heart, kidney and gill. The effects of three different diets (diet 1-soft pellet; diet 2-slow-sinking pellet; diet 3- Daphnia) were studied on lipid metabolism enzyme activities and gene expression levels in different tissues of juveniles of C. nasus for 60 d. The differential expression of Fads6 genes in liver, brain and intestine changed with different diets, respectively. We detected lipid metabolism enzyme-specific activities such as lipase enzyme, lipoprotein lipase enzyme and lipid peroxides in liver, and found that the lipase activity in liver of diet 2 group was significantly (P<0.05) higher than the other diets. The mechanism of HUFAs synthesis in C. nasus is described in the future. [ABSTRACT FROM AUTHOR]

Dystrophinopathies are X-linked recessive diseases caused by mutations in the DMD gene. Our objective was to identify mutations in this gene by Multiplex Ligation Probe Amplification (MLPA), to confirm the clinical diagnosis and determine the carrier status of at-risk relatives. Also, we aimed to characterize the Dystrophinopathies argentine population and the DMD gene. We analyzed a cohort of 121 individuals (70 affected boys, 11 symptomatic women, 37 at-risk women and 3 male villus samples). The MLPA technique identified 56 mutations (45 deletions, 9 duplications and 2 point mutations). These results allowed confirming the clinical diagnosis in 63% (51/81) of patients and symptomatic females. We established the carrier status of 54% (20/37) of females at-risk and 3 male villus samples. We could establish an association between the most frequent deletion intron breakpoints and the abundance of dinucleotide microsatellites loci, despite the underlying mutational molecular mechanism remains to be elucidated. The MLPA demonstrate, again, to be the appropriate first mutation screening methodology for molecular diagnosis of Dystrophinopathies. The reported results permitted to characterize the Dystrophinopathies argentine population and lead to better understanding of the genetic and molecular basis of rearrangements in the DMD gene, useful information for the gene therapies being developed. [ABSTRACT FROM AUTHOR]

Soil pollution caused by heavy metals is one of the major problems throughout the world. To maintain a safe and healthy environment for human beings, there is a dire need to identify hyperaccumulator plants and the underlying genes involved in heavy metals stress tolerance and accumulation. The goal of this research is to explore the potential of hemp as a decontaminator of heavy metals by identifying the two important heavy metals responsive genes, glutathione- disulfidereductase ( GSR) and phospholipase D- α ( PLDα). The results revealed heavy metals accumulation; Cu (1530 mg kg−1), Cd (151 mg kg−1), and Ni (123 mg kg−1) in hemp plants' leaves collected from the contaminated site. This shows the ability of the hemp plant to tolerate heavy metals, perhaps due to the presence of stress tolerance genes. In this study, partial sequences of putative GSR (215 bp) and PLDα (517 bp) genes were identified, responsive to heavy metals stress in hemp leaves. Both genes exhibited 40-60% sequence identity to previously reported genes from other plant species. Glutathione binding residues and conserved arginine residues were found identical in a putative GSR gene to those of other plant species, while the phospholipids binding domain and catalytic domain were found in the PLDα gene. These results will help to improve our understanding about the phytoremediation potential of hemp as well as in manipulating GSR and PLDα genes in breeding programs to produce transgenic heavy-metals-tolerant varieties. [ABSTRACT FROM AUTHOR]

Geranylgeranyl-diphosphate synthases (GGDPS) catalyze branch point enzymatic reactions producing isoprenoid-derived products which are necessary for plant growth and responses to a wide range of biotic and abiotic stresses. In our study, full length geranylgeranyl-diphosphate synthase 1 ( PgGGDPS1) and 2 ( PgGGDPS2) cDNA were isolated and characterized from the flower of Panax ginseng and 4-year old P. ginseng cv. Gumpoong. The cDNA had open reading frame of 1032 and 1116 bp with a deduced amino acid sequence of 343 and 371 residues for GGDPS1 and GGDPS2, respectively. The calculated molecular mass of GGDPS1 and GGDPS2 were approximately 37.66 and 40.21 kDa with a predicated isoelectric point of 5.32 and 6.23 and predicted localization of plastid. A GenBank Blast X search revealed that the deduced amino acid of PgGGDPS1 shared a high degree of homology with GGDPS from Panax notoginseng. The transcription pattern of GGDPS genes was different at various developmental stages. Both GGDPS genes were highly expressed in aerial parts of the plant, especially in rapidly growing tissues such as 4-year old flower and stem tissues. Transcript level of PgGGDPS1 was differentially induced in ginseng not only during Pseudomonas syringae pv tomato infection but also after exposure to abiotic stresses. Our results suggested that the induction of GGDPS genes specifically PgGGDPS1 by drought stress may affect chlorophyll levels, intracellular GA content and accumulation of carotenoids as the precursor for higher production of ABA and possibly stomatal closure as the barrier for water loss. [ABSTRACT FROM AUTHOR]

Elovl5 elongase is a critical enzyme involved in the highly unsaturated fatty acid (HUFA) biosynthesis. There is very little information on the evolution and functional characterization of Elovl5-a and Elovl5-b genes in common carp ( Cyprinus carpio var. Jian). In the present study, the genomic sequences and structures of two putative Elovl5-like elongase genes in the common carp genome were obtained. The mRNA expression patterns of Elovl5-a and Elovl5-b in tissues, hatching carp embryos, and juveniles under nutritional regulation were investigated. The results show that the two Elovl5 elongase genes have similar organization, coding 8 exons of high identity and introns of distinct size and sequence composition. They are not allelic variants of a single gene. Both Elovl5 elongase genes are highly expressed in liver, intestine (pyloric caeca) and brain. Elovl5-a and Elovl5-b mRNAs showed increased expression from newly hatched to 20 days after hatching. The regulation of Elovl5-a and Elovl5-b in response to dietary fatty acid composition was determined in liver, brain and intestine ( pyloric caeca) of common carp fed with diets: (i) fish oil (FO) rich in n-3 HUFA, (ii) corn oil (CO, 18:2n-6) or (iii) linseed oil (LO, 18:3n-3). Also the differential expression of Elovl5-a and Elovl5-b genes in liver, brain and intestine in common carps fed with different oil sources was studied. Further work aimed at the determination of the mechanisms of differential expression of the Elovl5-a and Elovl5-b in different tissues and the roles of transcription factors in regulating HUFA synthesis is in progress. [ABSTRACT FROM AUTHOR]

Scutellaria baicalensis has a wide range of biological activities and has been considered as an important traditional drug in Asia and North America for centuries. A partial-length cDNA clone encoding phytoene synthase (SbPSY) and full-length cDNA clones encoding phytoene desaturase (SbPDS), ξ-carotene desaturase (SbZDS), ß-ring carotene hydroxylase (SbCHXB), and zeaxanthin epoxidase (SbZEP) were identified in S. baicalensis. Sequence analyses revealed that these proteins share high identity and conserved domains with their orthologous genes. SbPSY, SbPDS, SbZDS, SbCHXB, and SbZEP were constitutively expressed in the roots, stems, leaves, and flowers of S. baicalensis. SbPSY, SbPDS, and SbZDS were highly expressed in the stems, leaves, and flowers and showed low expression in the roots, where only trace amounts of carotenoids were detected. SbCHXB and SbZEP transcripts were expressed at relatively high levels in the roots, stems, and flowers and were expressed at low levels in the leaves, where carotenoids were mostly distributed. The predominant carotenoids in S. baicalensis were lutein and ß-carotene, with abundant amounts found in the leaves (517.19 and 228.37 µg g-1 dry weight, respectively). Our study on the biosynthesis of carotenoids in S. baicalensis will provide basic data for elucidating the contribution of carotenoids to the considerable medicinal properties of S. baicalensis. [ABSTRACT FROM AUTHOR]

Oil palm (( Elaeis guineensis Jacq) is one of the most productive oil crops in the world. It can produce oil up to 90% of its dry weight and has the highest oil content reported among other plant tissues. WRI1 gene is one of many contributing genes that control oil content in oil palm fruit. Despite its obvious scientific and economic interest, literature and molecular resources about WRI1 gene in oil palm are still limited. The objective of this research was to isolate sequence and characterize the WRI1 gene from oil palm genome. WRI1 gene was successfully amplified from oil palm cDNA library. The amplification produced a single DNA fragment of 1 000 bp and which was cloned into pJET cloning vector for sequencing. The sequencing result showed two clones that were identified as WRI1 transcription factor. [ABSTRACT FROM AUTHOR]

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]

Highlights: [•] Petunia has two DAHP synthase isoforms. [•] PhDAHP2 may have a general function throughout the plant. [•] PhDAHP1 is highly expressed in floral limb tissue during open flower stages. [•] Upon reduction of PhDAPH1 transcript, floral volatiles are greatly reduced. [•] PhDAHP1 has a specific function in floral volatile biosynthesis. [Copyright &y& Elsevier]

Grain yield potential in cereals results from the contributions of three main components: inflorescence number per plant, grain number per inflorescence and mean grain weight. In rice, the Dense and erect panicle (DEP1) gene affects three important quantitative traits of the inflorescence and DEP1 homologs have been reported in barley and wheat. In this work, we have performed a detailed characterization of the barley DEP1 ( HvDEP1) gene. We obtained a full-length sequence of its transcript, examined its expression in various tissues, genetically mapped it to chromosome 5H and measured its nucleotide diversity in a collection of barley cultivars from Canada. This gene has an exceptionally long 5′ UTR (297 bp) that contains an upstream open reading frame (uORF) coding for a predicted peptide of 70 amino acids. A similarly long 5′ UTR containing a putative uORF was found in all six grass species that we examined. Although HvDEP1 transcripts could be detected in all tissues tested, it was highest in meristematic tissues. In a collection of 167 barley cultivars, a low level of polymorphism was observed ( π = 0.001) and the 37 SNPs/indels detected, none of which result in changes in the amino acid sequence of the HvDEP1 protein, defined 8 haplotypes. Diversity was especially low among 83 six-row types, all but one of which carried the exact same haplotype. We suggest that HvDEP1 is involved in the control of cellular growth and differentiation, that the conserved uORF may play a role in its post-transcriptional regulation and that this gene has undergone a very different history of selection within the two-row and six-row Canadian elite germplasm. [ABSTRACT FROM AUTHOR]

Eugenol- O-methyltransferase (E OMT) catalyzes the conversion of eugenol to methyleugenol in one of the final steps of phenylpropanoid pathway. There are no comprehensive reports on comparative EOMT gene expression and developmental stage specific accumulation of phenylpropenes in Ocimum tenuiflorum. Seven chemotypes, rich in eugenol and methyleugenol, were selected by assessment of volatile metabolites through multivariate data analysis. Isoeugenol accumulated in higher levels during juvenile stage (36.86 ng g), but reduced sharply during preflowering (8.04 ng g), flowering (2.29 ng g) and postflowering stages (0.17 ng g), whereas methyleugenol content gradually increased from juvenile (12.25 ng g) up to preflowering (16.35 ng g) and then decreased at flowering (7.13 ng g) and post flowering (5.95 ng g) from fresh tissue. Extreme variations of free intracellular and alkali hydrolysable cell wall released phenylpropanoid compounds were observed at different developmental stages. Analyses of EOMT genomic and cDNA sequences revealed a 843 bp open reading frame and the presence of a 90 bp intron. The translated proteins had eight catalytic domains, the major two being dimerisation superfamily and methyltransferase_2 superfamily. A validated 3D structure of E OMT protein was also determined. The chemotype Ot7 had a reduced reading frame that lacked both dimerisation domains and one of the two protein-kinase-phosphorylation sites; this was also reflected in reduced accumulation of methyleugenol compared to other chemotypes. EOMT transcripts showed enhanced expression in juvenile stage that increased further during preflowering but decreased at flowering and further at postflowering. The expression patterns may possibly be compared and correlated to the amounts of eugenol/isoeugenol and methyleugenol in different developmental stages of all chemotypes. [ABSTRACT FROM AUTHOR]