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The organization of chromatin into self-interacting domains is universal among eukaryotic genomes, though how and why they form varies considerably. Here we report a chromosome-scale reference genome assembly of pepper ( Capsicum annuum ) and explore its 3D organization through integrating high-resolution Hi-C maps with epigenomic, transcriptomic, and genetic variation data. Chromatin folding domains in pepper are as prominent as TADs in mammals but exhibit unique characteristics. They tend to coincide with heterochromatic regions enriched with retrotransposons and are frequently embedded in loops, which may correlate with transcription factories. Their boundaries are hotspots for chromosome rearrangements but are otherwise depleted for genetic variation. While chromatin conformation broadly affects transcription variance, it does not predict differential gene expression between tissues. Our results suggest that pepper genome organization is explained by a model of heterochromatin-driven folding promoted by transcription factories and that such spatial architecture is under structural and functional constraints. The organization of chromatin into self-interacting domains is universal among eukaryotic genomes. Here, the authors report a reference-grade pepper genome assembly and use this reference to help describe the relationship among 3D chromatin conformation, chromatin function, and gene expression.

Information encryption technique has broad applications in individual privacy, military confidentiality, and national security, but traditional electronic encryption approaches are increasingly unable to satisfy the demands of strong safety and large bandwidth of high-speed data transmission over network. Optical encryption technology could be more flexible and effective in parallel programming and multiple degree-of-freedom data transmitting application. Here, we show a dual-layer optical encryption fluorescent polymer waveguide chip based on optical pulse-code modulation technique. Fluorescent oligomers were doped into epoxy cross-linking SU-8 polymer as a gain medium. Through modifying both the external pumping wavelength and operating frequency of the pulse-code modulation, the sender could ensure the transmission of vital information is secure. If the plaintext transmission is eavesdropped, the external pumping light will be switched, and the receiver will get warning commands of ciphertext information in the standby network. This technique is suitable for high-integration and high-scalability optical information encryption communications. Data security of internet is increasingly more demanding in the current era, yet the traditional electronic approach is limited in speed and efficiency. Here, the authors proposed a dual-layer optical encryption fluorescent polymer waveguide chip based on optical pulse-code modulation to mitigate the limitations.

The capsaicinoids are a group of compounds produced by chili pepper fruits and are used widely in many fields, especially in medical purposes. The capsaicinoid biosynthetic pathway has not yet been established clearly. To understand more knowledge in biosynthesis of capsaicinoids, we applied RNA-seq for the mixture of placenta and pericarp of pungent pepper (Capsicum frutescens L.). We have assessed the effect of various assembly parameters using different assembly software, and obtained one of the best strategies for de novo assembly of transcriptome data. We obtained a total 54,045 high-quality unigenes (transcripts) using Trinity software. About 92.65% of unigenes showed similarity to the public protein sequences, genome of potato and tomato and pepper (C. annuum) ESTs databases. Our results predicted 3 new structural genes (DHAD, TD, PAT), which filled gaps of the capsaicinoid biosynthetic pathway predicted by Mazourek, and revealed new candidate genes involved in capsaicinoid biosynthesis based on KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis. A significant number of SSR (Simple Sequence Repeat) and SNP (Single Nucleotide Polymorphism) markers were predicted in C. frutescens and C. annuum sequences, which will be helpful in the identification of polymorphisms within chili pepper populations. These data will provide new insights to the pathway of capsaicinoid biosynthesis and subsequent research of chili peppers. In addition, our strategy of de novo transcriptome assembly is applicable to a wide range of similar studies.

Background The basic helix–loop–helix (bHLH) transcription factors (TFs) serve crucial roles in regulating plant growth and development and typically participate in biological processes by interacting with other TFs. Capsorubin and capsaicinoids are found only in Capsicum , which has high nutritional and economic value. However, whether bHLH family genes regulate capsorubin and capsaicinoid biosynthesis and participate in these processes by interacting with other TFs remains unknown. Results In this study, a total of 107 CabHLHs were identified from the Capsicum annuum genome. Phylogenetic tree analysis revealed that these CabHLH proteins were classified into 15 groups by comparing the CabHLH proteins with Arabidopsis thaliana bHLH proteins. The analysis showed that the expression profiles of CabHLH009 , CabHLH032 , CabHLH048 , CabHLH095 and CabHLH100 found in clusters C1, C2, and C3 were similar to the profile of carotenoid biosynthesis in pericarp, including zeaxanthin, lutein and capsorubin, whereas the expression profiles of CabHLH007 , CabHLH009 , CabHLH026 , CabHLH063 and CabHLH086 found in clusters L5, L6 and L9 were consistent with the profile of capsaicinoid accumulation in the placenta. Moreover, CabHLH007 , CabHLH009 , CabHLH026 and CabHLH086 also might be involved in temperature-mediated capsaicinoid biosynthesis. Yeast two-hybrid (Y2H) assays demonstrated that CabHLH007 , CabHLH009 , CabHLH026 , CabHLH063 and CabHLH086 could interact with MYB31, a master regulator of capsaicinoid biosynthesis. Conclusions The comprehensive and systematic analysis of CabHLH TFs provides useful information that contributes to further investigation of CabHLHs in carotenoid and capsaicinoid biosynthesis.

Human gut microbiota is believed to be directly or indirectly involved in cardiovascular diseases and hypertension. However, the identification and functional status of the hypertension-related gut microbe(s) have not yet been surveyed in a comprehensive manner. Here we characterized the gut microbiome in hypertension status by comparing fecal samples of 60 patients with primary hypertension and 60 gender-, age-, and body weight-matched healthy controls based on whole-metagenome shotgun sequencing. Hypertension implicated a remarkable gut dysbiosis with significant reduction in within-sample diversity and shift in microbial composition. Metagenome-wide association study (MGWAS) revealed 53,953 microbial genes that differ in distribution between the patients and healthy controls (false discovery rate, 0.05) and can be grouped into 68 clusters representing bacterial species. Opportunistic pathogenic taxa, such as, spp., spp., and were frequently distributed in hypertensive gut microbiome, whereas the short-chain fatty acid producer, such as, spp. and , were higher in controls. The number of hypertension-associated species also showed stronger correlation to the severity of disease. Functionally, the hypertensive gut microbiome exhibited higher membrane transport, lipopolysaccharide biosynthesis and steroid degradation, while in controls the metabolism of amino acid, cofactors and vitamins was found to be higher. We further provided the microbial markers for disease discrimination and achieved an area under the receiver operator characteristic curve (AUC) of 0.78, demonstrating the potential of gut microbiota in prediction of hypertension. These findings represent specific alterations in microbial diversity, genes, species and functions of the hypertensive gut microbiome. Further studies on the causality relationship between hypertension and gut microbiota will offer new prospects for treating and preventing the hypertension and its associated diseases.

Background ERF transcription factors (TFs) belong to the Apetala2/Ethylene responsive Factor (AP2/ERF) TF family and play a vital role in plant growth and development processes. Capsorubin and capsaicinoids have relatively high economic and nutritional value, and they are specifically found in Capsicum . However, there is little understanding of how ERFs participate in the regulatory networks of capsorubin and capsaicinoids biosynthesis. Results In this study, a total of 142 ERFs were identified in the Capsicum annuum genome. Subsequent phylogenetic analysis allowed us to divide ERFs into DREB (dehydration responsive element binding proteins) and ERF subfamilies, and further classify them into 11 groups with several subgroups. Expression analysis of biosynthetic pathway genes and CaERFs facilitated the identification of candidate genes related to the regulation of capsorubin and capsaicinoids biosynthesis; the candidates were focused in cluster C9 and cluster C10, as well as cluster L3 and cluster L4, respectively. The expression patterns of CaERF82 , CaERF97 , CaERF66 , CaERF107 and CaERF101 , which were found in cluster C9 and cluster C10, were consistent with those of accumulating of carotenoids (β-carotene, zeaxanthin and capsorubin) in the pericarp. In cluster L3 and cluster L4, the expression patterns of CaERF102 , CaERF53 , CaERF111 and CaERF92 were similar to those of the accumulating capsaicinoids. Furthermore, CaERF92 , CaERF102 and CaERF111 were found to be potentially involved in temperature-mediated capsaicinoids biosynthesis. Conclusion This study will provide an extremely useful foundation for the study of candidate ERFs in the regulation of carotenoids and capsaicinoids biosynthesis in peppers.

Purple foliage always appears in Camellia sinensis families; however, the transcriptional regulation of anthocyanin biosynthesis is unknown. The tea bud sport cultivar ‘Zijuan’ confers an abnormal pattern of anthocyanin accumulation, resulting in a mutant phenotype that has a striking purple color in young foliage and in the stem. In this study, we aimed to unravel the underlying molecular mechanism of anthocyanin biosynthetic regulation in C. sinensis . Our results revealed that activation of the R2R3-MYB transcription factor (TF) anthocyanin1 (CsAN1) specifically upregulated the bHLH TF CsGL3 and anthocyanin late biosynthetic genes (LBGs) to confer ectopic accumulation of pigment in purple tea. We found CsAN1 interacts with bHLH TFs (CsGL3 and CsEGL3) and recruits a WD-repeat protein CsTTG1 to form the MYB-bHLH-WDR (MBW) complex that regulates anthocyanin accumulation. We determined that the hypomethylation of a CpG island in the CsAN1 promoter is associated with the purple phenotype. Furthermore, we demonstrated that low temperature and long illumination induced CsAN1 promoter demethylation, resulting in upregulated expression to promote anthocyanin accumulation in the foliage. The successful isolation of CsAN1 provides important information on the regulatory control of anthocyanin biosynthesis in C. sinensis and offers a genetic resource for the development of new varieties with enhanced anthocyanin content.

Background Centromeres are chromosomal loci epigenetically specified by the histone variant CENH3, where kinetochores assemble to ensure accurate chromosome segregation during cell division. Their repetitive and rapidly evolving DNA has long impeded large-scale characterization. Advances in long-read sequencing now enable complete genome assemblies across species and within populations, providing opportunities to investigate how centromeres evolve and diversify over timescales from thousands to millions of years. Results Here, we generate near-telomere-to-telomere genome assemblies for eggplant, African eggplant, and wild pepper. Using CENH3 ChIP–seq, we delineate functional centromeric chromatin in these assemblies and in the cultivated pepper ‘CA59’, tomato ‘Heinz 1706’, and a wild tomato accession. These genomes harbor satellite-free centromeres across all chromosomes except chromosome 3 in tomato and its wild progenitor. Instead, centromeres are primarily composed of Ty3/Gypsy LTR retrotransposons, whose clade composition, abundance, recent activity, and spatial distribution differ among species. Centromere size scales with genome size in Solanaceae crops. Comparisons of closely related genomes reveal frequent centromere positional shifts driven by pericentromeric inversions and centromere repositioning. Synteny decays more rapidly around centromeres, consistent with elevated breakage within CENH3-binding regions. Finally, centromere haplotypes vary within species, exemplified by multiple haplotypes on four African eggplant chromosomes. Conclusions These findings highlight the remarkable evolutionary dynamics and within-species variation of centromeres in Solanaceae crops, revealing distinct species-specific organizational patterns. This study positions Solanaceae as a promising model for comparative analyses of plant centromere evolution and provides a foundation for future research exploring how centromere variation contributes to phenotypic diversity.

Diagnostic and therapeutic illumination on internal organs and tissues with high controllability and adaptability in terms of spectrum, area, depth, and intensity remains a major challenge. Here, we present a flexible, biodegradable photonic device called iCarP with a micrometer scale air gap between a refractive polyester patch and the embedded removable tapered optical fiber. ICarP combines the advantages of light diffraction by the tapered optical fiber, dual refractions in the air gap, and reflection inside the patch to obtain a bulb-like illumination, guiding light towards target tissue. We show that iCarP achieves large area, high intensity, wide spectrum, continuous or pulsatile, deeply penetrating illumination without puncturing the target tissues and demonstrate that it supports phototherapies with different photosensitizers. We find that the photonic device is compatible with thoracoscopy-based minimally invasive implantation onto beating hearts. These initial results show that iCarP could be a safe, precise and widely applicable device suitable for internal organs and tissue illumination and associated diagnosis and therapy. Illuminating internal organs and tissues with high controllability and adaptability remains challenging. Here the authors present a flexible, biodegradable photonic device called iCarP for large area, high intensity, wide spectrum, deeply penetrating, continuous or pulsatile illumination.

•The cortisol awakening response (CAR) has been associated with emotion-related psychiatric disorders and is theorized to proactively provide an allostatic boost.•Suppressed CAR in the morning can result in an impairment in discrimination performance for negative facial expressions in the afternoon.•Suppressed CAR can lead to an increase in functional connectivity between the amygdala and the right dorsolateral prefrontal cortex during negative emotion processing.•These findings suggest a causal role of the CAR in anticipating upcoming emotional task demands and support its proactive role in brain preparedness. The cortisol awakening response (CAR) has been linked to a variety of emotion-related psychiatric conditions and is proposed to prepare the brain for upcoming stress and challenges. Yet, the underlying neurobiological mechanisms of such proactive effects on emotional processing remain elusive. In the current double-blinded, pharmacologically-manipulated study, 36 male adults (DXM group) received cortisol-repressive dexamethasone on the previous night, then performed the Emotional Face Matching Task (EFMT) during fMRI scanning the next afternoon. Relative to the placebo group (31 male adults), the DXM group exhibited lower accuracy in the emotion matching condition, but not in the sensorimotor control condition. Psychophysiological interaction (PPI) analyses revealed significant task-by-group interaction involving the right and left amygdala, but not the medial orbitofrontal cortex (MOFC) or hippocampus. Specifically, the DXM group exhibited stronger functional connectivity between the right amygdala and left dorsolateral prefrontal cortex (lDLPFC) during emotion condition but reduced connectivity in the same network during control condition, as compared to the placebo group. Meanwhile, the DXM group exhibited weaker left amygdala–right posterior middle temporal gyrus (rMTG) connectivity than the placebo group during control condition, but there was no group effect in the connectivity during emotion condition. These results indicate that the CAR proactively modulates fronto-limbic functional organization for emotion processing in male adults. Our findings support a causal link between CAR and its proactive effects on emotional processing, and suggest a model of CAR-mediated brain preparedness where CAR sets a tonic tone for the upcoming day to actively regulate neuroendocrinological responses to emotionally charged stimuli on a moment-to-moment basis.