Genomics of Terpene Biosynthesis in Dictyoceratid Sponges (Porifera) - What Do We (Not) Know?

Sponges are recognized as promising sources for novel bioactive metabolites. Among them are terpenoid metabolites that constitute key biochemical defense mechanisms in several sponge taxa. Despite their significance, the genetic basis for terpenoid biosynthesis in sponges remains poorly understood. Dictyoceratida comprise demosponges well-known for their bioactive terpenoids. In this study, we explored the currently available genomic data for insights into the metabolic pathways of dictyoceratid terpenoids. We first identified prenyltransferase (PT) and terpene cyclase (TC) enzymes essential for the terpenoid biosynthetic processes in the terrestrial realm by analyzing available transcriptomic and genomic data of Dictyoceratida sponges and 10 other sponge species. All Dictyoceratida sponges displayed various PTs involved in either sesqui- or diterpene, steroid and carotenoid production. Additionally, it was possible to identify a potential candidate for a dictyoceratid sesterterpene PT. However, analogs of common terrestrial TCs were absent, suggesting the existence of a distinct or convergently evolved sponge-specific TC. Our study aims to contribute to the foundational understanding of terpene biosynthesis in sponges, unveiling the currently evident genetic components for terpenoid production in species not previously studied. Simultaneously, it aims to identify the known and unknown factors, as a starting point for biochemical and genetic investigations in sponge terpenoid production.

Mono- to tetra-alkyl ether cardiolipins in a mesophilic, sulfate-reducing bacterium identified by UHPLC-HRMSn: a novel class of membrane lipids.

The composition of membrane lipids varies in a number of ways as adjustment to growth conditions. Variations in head group composition and carbon skeleton and degree of unsaturation of glycerol-bound acyl or alkyl chains results in a high structural complexity of the lipidome of bacterial cells. We studied the lipidome of the mesophilic, sulfate-reducing bacterium, Desulfatibacillum alkenivorans strain PF2803T by ultra-high-pressure liquid chromatography coupled with high-resolution tandem mass spectrometry (UHPLC-HRMSn). This anaerobic bacterium has been previously shown to produce high amounts of mono-and di-alkyl glycerol ethers as core membrane lipids. Our analyses revealed that these core lipids occur with phosphatidylethanomamine (PE) and phosphatidylglycerol (PG) head groups, representing each approximately one third of the phospholipids. The third class was a novel group of phospholipids, i.e., cardiolipins (CDLs) containing one (monoether/triester) to four (tetraether) ether-linked saturated straight-chain or methyl-branched alkyl chains. Tetraether CDLs have been shown to occur in archaea (with isoprenoid alkyl chains) but have not been previously reported in the bacterial Domain. Structurally related CDLs with one or two alkyl/acyl chains missing, so-called monolyso-and dilyso-CDLs, were also observed. The potential biosynthetic pathway of these novel CDLs was investigated by examining the genome of D. alkenivorans. Three CDL synthases were identified; one catalyzes the condensation of two PGs, the other two are probably involved in the condensation of a PE with a PG. A heterologous gene expression experiment showed the in vivo production of dialkylglycerols upon anaerobic expression of the glycerol ester reductase enzyme of D. alkenivorans in E. coli. Reduction of the ester bonds probably occurs first at the sn-1 and subsequently at the sn-2 position after the formation of PEs and PGs.

The development of a next-generation sequencing panel targeting cannabinoid synthase genes to distinguish between marijuana and hemp.

Hemp and marijuana, both derived from Cannabis sativa L. (C. sativa), are subject to divergent legal regulations due to their different Δ9-tetrahydrocannabinol (Δ9-THC) contents. Cannabinoid synthase genes are considered the key enzymes that determine the chemical composition or chemotype of a particular cultivar. However, existing methods for crop type differentiation based on previous synthase gene theories have limitations in terms of precision and specificity, and a wider range of cannabis varieties must be considered when examining cannabis-based genetic markers. A custom next-generation sequencing (NGS) panel was developed targeting all synthase genes, including Δ9-THC acid synthase, cannabidiolic acid synthase, and cannabichromenic acid synthase, as well as the pseudogenes across diverse C. sativa samples, spanning reference hemp and marijuana, commercial hemp derivatives, and seized marijuana extracts. Interpretation of NGS data revealed a relationship between genotypes and underlying chemotypes, with the principal component analysis indicating a clear distinction between hemp and marijuana clusters. This differentiation was attributed to variations in both synthase genes and pseudogene variants. Finally, this study proposes a genetic cannabis classification method using a differentiation flow chart with novel synthase markers. The flow chart successfully differentiated hemp from marijuana with a 1.3% error rate (n = 147).

THE ROLE OF HEREDITARY PREDISPOSITION (POLYMORPHIC MARKERS OF GLUTATHIONE-S-TRANSFERASE, CATALASE, ENDOTHELIAL NITROGEN OXIDE SYNTHASE GENES) AND SOME ADVERSE ENVIRONMENTAL FACTORS IN THE DEVELOPMENT OF BRONCHO-OBSTRUCTIVE PATHOLOGY IN CHILDREN LIVING IN RADIOACTIVELY CONTAMINATED AREAS. / РОЛЬ СПАДКОВОЇ СХИЛЬНОСТІ (ПОЛІМОРФНИХ МАРКЕРІВ ГЕНІВ ГЛУТАТІОН-S-ТРАНСФЕРАЗ, КАТАЛАЗИ, ЕНДОТЕЛІАЛЬНОЇ СИНТАЗИ ОКСИДУ АЗОТУ) ТА ДЕЯКИХ НЕСПРИЯТЛИВИХ ЧИННИКІВ ДОВКІЛЛЯ У ВИНИКНЕННІ БРОНХООБСТРУКТИВНОЇ ПАТОЛОГІЇ У ДІТЕЙ, МЕШКАНЦІВ РАДІОАКТИВНО ЗАБРУДНЕНИХ ТЕРИТОРІЙ.

OBJECTIVE: summarizing the results of many years of research by the authors on the influence of gene polymorphisms encoding xenobiotic biotransformation enzymes (GSTТ1, GSTM1, GSTР1), antioxidant protection (С^262Т of the catalase gene), endothelial nitric oxide synthase (4a/4b VNTR polymorphism of the eNOS gene), and some environmental factors on the occurrence of broncho-obstructive disorders and the development of bronchial asthma in children, residents of radioactively contaminated areas. MATERIALS AND METHODS: The examined school-aged children were residents of radioactively RCA who had no clinical signs of respiratory pathology. Deletion polymorphism of catalase gene (CAT C^262T), polymorphism of glutathione-S-transferase gene (GSTТ1, GSTM1, GSTР1) and the polymorphism in the 4th intron (4a/4b) of the eNOS gene were studied in the molecular genetics laboratory of the State Institution «Reference Center for Molecular Diagnostics of Public Health Ministry of Ukraine¼. Molecular genetic studies were performed by polymerase chain reaction. The study of the ventilation lung capacity was carried out by the method of computer spirometry based on the data of the «flow-volume¼ loop analysis. A pharmacological inhalation test with a bronchodilator drug which affects the ß2-adrenergic receptors of the lungs was used to detect early changes in the ventilatory lung capacity - bronchial hyperreactivity. RESULTS AND CONCLUSIONS: One of the leading mechanisms, due to which the implementation of hereditary predisposition to bronchial asthma in children living in radioactively contaminated areas is the polymorphism of certain genes of glutathione-S-transferase, catalase, endothelial nitric oxide synthase. With such polymorphic variants of the GST genes, isoforms of enzymes with reduced activity are produced, which limits their ability to effectively neutralize free radicals, which are formed in excess when free radical oxidation processes are activated due to the constant intake of radionuclides with a long half-life into the body of children. Unfavorable factors that increase the risk of developing broncho-obstructive disorders and the likelihood of their implementation in the form of bronchial asthma in children, residents of radioactively contaminated areas, have been identified. It has been established that among them the leading role is played by hereditary predisposition to this disease. On the part of the child, such negative factors were unfavorable conditions of intrauterine development, the presence of signs of exudative-catarrhal diathesis, manifestations of allergies and frequent respiratory diseases from the first months of life.

A haplotype-resolved chromosome-scale genome for Quercus rubra L. provides insights into the genetics of adaptive traits for red oak species.

Northern red oak (Quercus rubra L.) is an ecologically and economically important forest tree native to North America. We present a chromosome-scale genome of Q. rubra generated by the combination of PacBio sequences and chromatin conformation capture (Hi-C) scaffolding. This is the first reference genome from the red oak clade (section Lobatae). The Q. rubra assembly spans 739 Mb with 95.27% of the genome in 12 chromosomes and 33,333 protein-coding genes. Comparisons to the genomes of Quercus lobata and Quercus mongolica revealed high collinearity, with intrachromosomal structural variants present. Orthologous gene family analysis with other tree species revealed that gene families associated with defense response were expanding and contracting simultaneously across the Q. rubra genome. Quercus rubra had the most CC-NBS-LRR and TIR-NBS-LRR resistance genes out of the 9 species analyzed. Terpene synthase gene family comparisons further reveal tandem gene duplications in TPS-b subfamily, similar to Quercus robur. Phylogenetic analysis also identified 4 subfamilies of the IGT/LAZY gene family in Q. rubra important for plant structure. Single major QTL regions were identified for vegetative bud break and marcescence, which contain candidate genes for further research, including a putative ortholog of the circadian clock constituent cryptochrome (CRY2) and 8 tandemly duplicated genes for serine protease inhibitors, respectively. Genome-environment associations across natural populations identified candidate abiotic stress tolerance genes and predicted performance in a common garden. This high-quality red oak genome represents an essential resource to the oak genomic community, which will expedite comparative genomics and biological studies in Quercus species.

Changes in Metabolite Profiling and Expression Levels of Key Genes Involved in the Terpenoid Biosynthesis Pathway in Garden Sage (Salvia officinalis) under the Effect of Hydrazine Hydrate.

Mutagenesis is a highly efficient tool for establishing genetic variation and is widely used for genetic enhancement in various plants. The key benefit of mutation breeding is the prospect of enhancing one or several characteristics of a variety without altering the genetic background. In this study, we exposed the seeds of Salvia officinalis to four concentrations of hydrazine hydrate (HZ), i.e., (0%, 0.1%, 0.2%, and 0.3%) for 6 h. The contents of terpenoid compounds in the S. officinalis plantlets driven from the HZ-treated seeds were determined by GC-MS, which resulted in the identification of a total of 340 phytochemical compounds; 163 (87.48%), 145 (84.49%), 65 (97.45%), and 62 (98.32%), from the four concentrations of HZ (0%, 0.1%, 0.2%, and 0.3%), respectively. Furthermore, we used the qRT-PCR system to disclose the "transcriptional control" for twelve TPS genes related to terpenoid and terpene biosynthesis, namely, SoGPS, SoMYRS, SoNEOD, SoCINS, SoSABS, SoLINS, SoFPPS, SoHUMS, SoTPS6, SoSQUS, SoGGPS, and SoGA2. Altogether, results are likely to ensure some positive relationship between the concentrations of the chemical mutagen HZ used for treating the seeds, the type and amount of the produced terpenes, and the expression of their corresponding genes.

Characterization of chaetoglobosin producing Chaetomium globosum for the management of Fusarium-Meloidogyne wilt complex in tomato.

AIM: Simultaneous management of FOL and RKN causing wilt complex in tomato by chaetoglobosin-producing Chaetomium globosum. METHODS AND RESULTS: Random survey was carried out to isolate Fusarium and Chaetomium. Twelve Fusarium isolates were characterized, and FOL4 (virulent) was molecularly identified. Wilt complex by FOL, RKN was assessed individually and in combination under greenhouse. RKN (1000 juveniles ml-1) inoculation followed by FOL4 (5 × 105 spores ml-1) accounted for 90% incidence. The chaetoglobosin-producing Chaetomium was isolated, characterized morphologically and molecularly. Among 55 isolates, nine showed >50% inhibition against FOL, and crude culture filtrate showed a significant reduction in RKN egg hatching (15.66%) and juvenile mortality (100%). Chaetomium Cg 40 was confirmed as C. globosum using SCAR marker (OK032373). Among 40 volatile compounds, hexadecanoic acid and 1,2-epoxy-5,9-cyclododecadiene exhibited antifungal and nematicidal properties in GC-MS. High-performance liquid chromatography revealed chaetoglobosin A (0.767 µg µl-1), and the presence of bioactive molecules chaetoglobosin (528.25 m/z), chaetomin (710 m/z), chaetocin (692.8 m/z), chaetoviridin (432.85 m/z), and chaetomugilin (390 m/z) was confirmed by LC/MS/MS. Cg 40 and Cg 6 were able to synthesize the pks1a, b gene responsible for chaetoglobosin, sporulation, and melanin biosynthesis was confirmed by PCR. The application of an aqueous formulation as seed treatment, seedling dip, and soil drenching (application) recorded lowest wilt incidence (11.11%) and gall index (1) with the maximum growth parameter (plant height 51.9 cm), fruit yield (287.5 g), and lycopene content (11.46 mg/100 g). CONCLUSIONS: Cg 40 and Cg 6, containing polyketides, secondary metabolites, antibiotics, chaetoglobosin, and plant growth-promoting ability, showed antifungal and nematicidal properties against the FOL-RKN wilt complex in tomato in vitro and pot culture experiments.

Predicting functions of putative fungal sesquiterpene synthase genes based on multiomics data analysis.

Sesquiterpenes (STs) are secondary metabolites, which mediate biotic interactions between different organisms. Predicting the species-specific ST repertoires can contribute to deciphering the language of communication between organisms of the same or different species. High biochemical plasticity and catalytic promiscuity of sesquiterpene synthases (STSs), however, challenge the homology-based prediction of the STS functions. Using integrated analyses of genomic, transcriptomic, volatilomic, and metabolomic data, we predict product profiles for 116 out of 146 putative STS genes identified in the genomes of 30 fungal species from different trophic groups. Our prediction method is based on the observation that STSs encoded by genes closely related phylogenetically are likely to share the initial enzymatic reactions of the ST biosynthesis pathways and, therefore, produce STs via the same reaction route. The classification by reaction routes allows to assign STs known to be emitted by a particular species to the putative STS genes from this species. Gene expression information helps to further specify these ST-to-STS assignments. Validation of the computational predictions of the STS functions using both in silico and experimental approaches shows that integrated multiomic analyses are able to correctly link cyclic STs of non-cadalane type to genes. In the process of the experimental validation, we characterized catalytic properties of several putative STS genes from the mycorrhizal fungus Laccaria bicolor. We show that the STSs encoded by the L.bicolor mycorrhiza-induced genes emit either nerolidol or α-cuprenene and α-cuparene, and discuss the possible roles of these STs in the mycorrhiza formation.

Tissue specific expression of bacterial cellulose synthase (Bcs) genes improves cotton fiber length and strength.

Fiber growing inside the cotton bolls is a highly demandable product and its quality is key to the success of the textile industry. Despite the various efforts to improve cotton fiber staple length Pakistan has to import millions of bales to sustain its industrial needs. To improve cotton fiber quality Bacterial cellulose synthase (Bcs) genes (acsA, acsB) were expressed in a local cotton variety CEMB-00. In silico studies revealed a number of conserved domains both in the cotton-derived and bacterial cellulose synthases which are essential for the cellulose synthesis. Transformation efficiency of 1.27% was achieved by using Agrobacterium shoot apex cut method of transformation. The quantitative mRNA expression analysis of the Bcs genes in transgenic cotton fiber was found to be many folds higher during secondary cell wall synthesis stage (35 DPA) than the expression during elongation phase (10 DPA). Average fiber length of the transgenic cotton plant lines S-00-07, S-00-11, S-00-16 and S-00-23 was calculated to be 13.02% higher than that of the non-transgenic control plants. Likewise, the average fiber strength was found to be 20.92% higher with an enhanced cellulose content of 22.45%. The mutated indigenous cellulose synthase genes of cotton generated through application of CRISPR/Cas9 resulted in 6.03% and 12.10% decrease in fiber length and strength respectively. Furthermore, mature cotton fibers of transgenic cotton plants were found to have increased number of twists with smooth surface as compared to non-transgenic control when analyzed under scanning electron microscope. XRD analysis of cotton fibers revealed less cellulose crystallinity index in transgenic cotton fibers as compared to control fibers due to deposition of more amorphous cellulose in transgenic fibers as a result of Bcs gene expression. This study paved the way towards unraveling the fact that Bcs genes influence cellulose synthase activity and this enzyme helps in determining the fate of cotton fiber length and strength.

Integrated transcriptomic and metabolomic analysis reveals the changes in monoterpene compounds during the development of Muscat Hamburg (Vitis vinifera L.) grape berries.

Monoterpenes are important compounds that influence the aromas of grapes and wines. The molecular mechanisms underlying the changes in monoterpenes during the grape ripening period have not been thoroughly characterized. In this study, the free and bound monoterpene profiles in Muscat Hamburg grape berries at different phenological stages were investigated at the transcriptomic and metabolomic levels. Principal component analyses indicated that the free and bound monoterpene profiles were affected by the developmental stages. Most monoterpenes were produced slowly before veraison, but they accumulated rapidly during the veraison period, after which their contents decreased slightly in mature berries. The transcriptomic analysis revealed 35 differentially expressed genes involved in the monoterpene synthesis pathway. The VIT_04s0008g04970, VIT_03s0063g02030 and VIT_15s0024g00850 expression levels were consistent with the changes in the accumulation of monoterpene compounds. The quantitative real-time polymerase chain reaction analysis of eight key differentially expressed genes in the monoterpenoid pathway confirmed the RNA-seq data were reliable. Our findings provide new insights into Muscat Hamburg grape aroma development. Further research on the period with the highest aroma potential may lead to enhanced grape berry aroma qualities.

Genome-wide analysis of terpene synthase gene family to explore candidate genes related to disease resistance in Prunus persica.

In plants, a family of terpene synthases (TPSs) is responsible for the biosynthesis of terpenes and contributes to species-specific diversity of volatile organic compounds, which play essential roles in fitness of plants. However, little is known about the TPS gene family in peach and/or nectarine (Prunus persica L.). In this study, we identified 40 PpTPS genes in peach genome v2.0. Although these PpTPSs could be clustered into five classes, they distribute in several gene clusters of three chromosomes, share conserved exon-intron organizations, and code similar protein motifs. Thirty-five PpTPSs, especially PpTPS2, PpTPS23, PpTPS17, PpTPS18, and PpTPS19, altered their transcript levels after inoculation with Botryosphaeria dothidea, a cause of peach gummosis, compared to the mock treatments, which might further affect the contents of 133 terpenoids at 48 hours and/or 84 hours post inoculations in the current-year shoots of 'Huyou018', a highly susceptible nectarine cultivar. Moreover, about fifteen PpTPSs, such as PpTPS1, PpTPS2, PpTPS3, and PpTPS5, showed distinct expression patterns during fruit development and ripening in two peach cultivars, yellow-fleshed 'Jinchun' and white-fleshed 'Hikawa Hakuho'. Among them, the transcription level of chloroplast-localized PpTPS3 was obviously related to the content of linalool in fruit pulps. In addition, elevated concentrations (0.1 g/L to 1.0 g/L) of linalool showed antifungal activities in PDA medium. These results improve our understanding of peach PpTPS genes and their potential roles in defense responses against pathogens.

Liverwort oil bodies: diversity, biochemistry, and molecular cell biology of the earliest secretory structure of land plants.

Liverworts are known for their large chemical diversity. Much of this diversity is synthesized and enclosed within oil bodies (OBs), a synapomorphy of the lineage. OBs contain the enzymes to biosynthesize and store large quantities of sesquiterpenoids and other compounds while limiting their cytotoxicity. Recent important biochemical and molecular discoveries related to OB formation, diversity, and biochemistry allow comparison with other secretory structures of land plants from an evo-devo perspective. This review addresses and discusses the most recent advances in OB origin, development, and function towards understanding the importance of these organelles in liverwort physiology and adaptation to changing environments. Our mapping of OB types and chemical compounds to the current liverwort phylogeny suggests that OBs were present in the most recent common ancestor of liverworts, supporting that OBs evolved as the first secretory structures in land plants. Yet, we require better sampling to define the macroevolutionary pattern governing the ancestral type of OB. We conclude that current efforts to find molecular mechanisms responsible for the morphological and chemical diversity of secretory structures will help understand the evolution of each major group of land plants, and open new avenues in biochemical research on bioactive compounds in bryophytes and vascular plants.

Monoterpene Synthase Genes and Monoterpene Profiles in Pinus nigra subsp. laricio.

In the present study, we carried out a quantitative analysis of the monoterpenes composition in different tissues of the non-model conifer Pinus nigra J.F. Arnold subsp. laricio Palib. ex Maire (P. laricio, in short). All the P. laricio tissues examined showed the presence of the same fourteen monoterpenes, among which the most abundant were ß-phellandrene, α-pinene, and ß-pinene, whose distribution was markedly tissue-specific. In parallel, from the same plant tissues, we isolated seven full-length cDNA transcripts coding for as many monoterpene synthases, each of which was found to be attributable to one of the seven phylogenetic groups in which the d1-clade of the canonical classification of plants' terpene synthases can be subdivided. The amino acid sequences deduced from the above cDNA transcripts allowed to predict their putative involvement in the biosynthesis of five of the monoterpenes identified. Transcripts profiling revealed a differential gene expression across the different tissues examined, and was found to be consistent with the corresponding metabolites profiles. The genomic organization of the seven isolated monoterpene synthase genes was also determined.

Genome-wide bioinformatics analysis of Cellulose Synthase gene family in common bean (Phaseolus vulgaris L.) and the expression in the pod development.

BACKGROUND: CesA and Csl gene families, which belong to the cellulose synthase gene superfamily, plays an important role in the biosynthesis of the plant cell wall. Although researchers have investigated this gene superfamily in several model plants, to date, no comprehensive analysis has been conducted in the common bean. RESULTS: In this study, we identified 39 putative cellulose synthase genes from the common bean genome sequence. Then, we performed a bioinformatics analysis of this gene family involving sequence alignment, phylogenetic analysis, gene structure, collinearity analysis and chromosome location. We found all members possess a cellulose_synt domain. Phylogenetic analysis revealed that these cellulose synthase genes may be classified into five subfamilies, and that members in the same subfamily share conserved exon-intron distribution and motif compositions. Abundant and distinct cis-acting elements in the 2 k basepairs upstream regulatory regions indicate that the cellulose synthase gene family may plays a vital role in the growth and development of common bean. Moreover, the 39 cellulose synthase genes are distributed on 10 of the 11 chromosomes. Additionally expression analysis shows that all CesA/Csl genes selected are constitutively expressed in the pod development. CONCLUSIONS: This research reveals both the putative biochemical and physiological functions of cellulose synthase genes in common bean and implies the importance of studying non-model plants to understand the breadth and diversity of cellulose synthase genes.

Vitamin B12-auxotrophy in dinoflagellates caused by incomplete or absent cobalamin-independent methionine synthase genes (metE).

Dinoflagellates are responsible for most marine harmful algal blooms (HABs) and play vital roles in many ocean processes. More than 90% of dinoflagellates are vitamin B12 auxotrophs and that B12 availability can control dinoflagellate HABs, yet the genetic basis of B12 auxotrophy in dinoflagellates in the framework of the ecology of dinoflagellates and particularly HABs, which was the objective of this work. Here, we investigated the presence, phylogeny, and transcription of two methionine synthase genes (B12-dependent metH and B12-independent metE) via searching and assembling transcripts and genes from transcriptomic and genomic databases, cloning 38 cDNA isoforms of the two genes from 14 strains of dinoflagellates, measuring the expression at different scenarios of B12, and comprehensive phylogenetic analyses of more than 100 organisms. We found that 1) metH was present in all 58 dinoflagellates accessible and metE was present in 40 of 58 species, 2) all metE genes lacked N-terminal domains, 3) metE of dinoflagellates were phylogenetically distinct from other known metE genes, and 4) expression of metH in dinoflagellates was responsive to exogenous B12 levels while expression of metE was not responding as that of genuine metE genes. We conclude that most, hypothetically all, dinoflagellates have either non-functional metE genes lacking N-terminal domain for most species, or do not possess metE for other species, which provides the genetic basis for the widespread nature of B12 auxotrophy in dinoflagellates. The work elucidated a fundamental aspect of the nutritional ecology of dinoflagellates.

Carotenoid Biosynthetic Genes in Cabbage: Genome-Wide Identification, Evolution, and Expression Analysis.

Carotenoids are natural functional pigments produced by plants and microorganisms and play essential roles in human health. Cabbage (Brassica oleracea L. var. capitata L.) is an economically important vegetable in terms of production and consumption. It is highly nutritious and contains ß-carotene, lutein, and other antioxidant carotenoids. Here, we systematically analyzed carotenoid biosynthetic genes (CBGs) on the whole genome to understand the carotenoid biosynthetic pathway in cabbage. In total, 62 CBGs were identified in the cabbage genome, which are orthologs of 47 CBGs in Arabidopsis thaliana. Out of the 62 CBGs, 46 genes in cabbage were mapped to nine chromosomes. Evolutionary analysis of carotenoid biosynthetic orthologous gene pairs among B. oleracea, B. rapa, and A. thaliana revealed that orthologous genes of B. oleracea underwent a negative selection similar to that of B. rapa. Expression analysis of the CBGs showed functional differentiation of orthologous gene copies in B. oleracea and B. rapa. Exogenous phytohormone treatment suggested that ETH, ABA, and MeJA can promote some important CBGs expression in cabbage. Phylogenetic analysis showed that BoPSYs exhibit high conservatism. Subcellular localization analysis indicated that BoPSYs are located in the chloroplast. This study is the first to study carotenoid biosynthesis genes in cabbage and provides a basis for further research on carotenoid metabolic mechanisms in cabbage.

Delivery of Rice Gall Dwarf Virus Into Plant Phloem by Its Leafhopper Vectors Activates Callose Deposition to Enhance Viral Transmission.

Rice gall dwarf virus (RGDV) and its leafhopper vector Recilia dorsalis are plant phloem-inhabiting pests. Currently, how the delivery of plant viruses into plant phloem via piercing-sucking insects modulates callose deposition to promote viral transmission remains poorly understood. Here, we initially demonstrated that nonviruliferous R. dorsalis preferred feeding on RGDV-infected rice plants than viruliferous counterpart. Electrical penetration graph assay showed that viruliferous R. dorsalis encountered stronger physical barriers than nonviruliferous insects during feeding, finally prolonging salivary secretion and ingestion probing. Viruliferous R. dorsalis feeding induced more defense-associated callose deposition on sieve plates of rice phloem. Furthermore, RGDV infection significantly increased the cytosolic Ca2+ level in rice plants, triggering substantial callose deposition. Such a virus-mediated insect feeding behavior change potentially impedes insects from continuously ingesting phloem sap and promotes the secretion of more infectious virions from the salivary glands into rice phloem. This is the first study demonstrating that the delivery of a phloem-limited virus by piercing-sucking insects into the plant phloem activates the defense-associated callose deposition to enhance viral transmission.

The Draft Genome of a Flat Peach (Prunus persica L. cv. '124 Pan') Provides Insights into Its Good Fruit Flavor Traits.

The flat peach has become more and more popular worldwide for its fruit quality with relatively low acidity, high sugar content and rich flavor. However, the draft genome assembly of flat peach is still unavailable and the genetic basis for its fruit flavor remains unclear. In this study, the draft genome of a flat peach cultivar '124 Pan' was assembled by using a hybrid assembly algorithm. The final assembly resulted in a total size of 206 Mb with a N50 of 26.3 Mb containing eight chromosomes and seven scaffolds. Genome annotation revealed that a total of 25,233 protein-coding genes were predicted with comparable gene abundance among the sequenced peach species. The phylogenetic tree and divergence times inferred from 572 single copy genes of 13 plant species confirmed that Prunus ferganensis was the ancestor of the domesticated peach. By comparing with the genomes of Prunus persica (Lovell) and Prunus ferganensis, the expansion of genes encoding enzymes involved in terpene biosynthesis was found, which might contribute to the good fruit flavor traits of '124 Pan'. The flat peach draft genome assembly obtained in this study will provide a valuable genomic resource for peach improvement and molecular breeding.

Common Endothelial Nitric Oxide Synthase Single Nucleotide Polymorphisms are not Related With the Risk for Restless Legs Syndrome.

Because nitric oxide and endothelial dysfunction could play a role in the pathogenesis of idiopathic restless legs syndrome (RLS), as was suggested by some preliminary data, we investigated the possible association between the rs2070744 variants in the endothelial nitric oxide synthase (eNOS or NOS3) gene (chromosome 7q36.1) and the risk for RLS in a Caucasian Spanish population. We assessed the frequencies of NOS3 single nucleotide polymorphisms (SNPs) rs2070744, rs1799983, and rs79467411 genotypes and allelic variants in 273 patients with idiopathic RLS and 325 healthy controls using a TaqMan-based qPCR assay. We also analyzed the possible influence of genotype frequency on age at onset of RLS symptoms, gender, family history of RLS, and response to drugs commonly used in the treatment of RLS such as dopaminergic drugs, clonazepam, and GABAergic drugs. The frequencies of genotypes and allelic variants were not associated with the risk for RLS and were not influenced by gender, age, and positive family history of RLS. We identified weak statistical associations of the SNP rs1799983 with the response to dopamine agonists (Pc = 0.018 for the rs1799983 G/T genotype) and of the SNP rs79467411 with the response to clonazepam (Pc = 0.018 for the rs79467411 G allele), although these findings should be cautiously interpreted and require further confirmation. These associations aside, our findings suggest that common NOS3 SNPs are not associated with the risk for idiopathic RLS in Caucasian Spanish people.

The cellulose synthase (CesA) gene family in four Gossypium species: phylogenetics, sequence variation and gene expression in relation to fiber quality in Upland cotton.

Cellulose synthases (CesAs) are multi-subunit enzymes found on the plasma membrane of plant cells and play a pivotal role in cellulose production. The cotton fiber is mainly composed of cellulose, and the genetic relationships between CesA genes and cotton fiber yield and quality are not fully understood. Through a phylogenetic analysis, the CesA gene family in diploid Gossypium arboreum and Gossypium raimondii, as well as tetraploid Gossypium hirsutum ('TM-1') and Gossypium barbadense ('Hai-7124' and '3-79'), was divided into 6 groups and 15 sub-groups, with each group containing two to five homologous genes. Most CesA genes in the four species are highly collinear. Among the five cotton genomes, 440 and 1929 single nucleotide polymorphisms (SNPs) in the CesA gene family were identified in exons and introns, respectively, including 174 SNPs resulting in amino acid changes. In total, 484 homeologous SNPs between the A and D genomes were identified in diploids, while 142 SNPs were detected between the two tetraploids, with 32 and 82 SNPs existing within G. hirsutum and G. barbadense, respectively. Additionally, 74 quantitative trait loci near 18 GhCesA genes were associated with fiber quality. One to four GhCesA genes were differentially expressed (DE) in ovules at 0 and 3 days post anthesis (DPA) between two backcross inbred lines having different fiber lengths, but no DE genes were identified between these lines in developing fibers at 10 DPA. Twenty-seven SNPs in above DE CesA genes were detected among seven cotton lines, including one SNP in Ghi_A08G03061 that was detected in four G. hirsutum genotypes. This study provides the first comprehensive characterization of the cotton CesA gene family, which may play important roles in determining cotton fiber quality.