Genome-Wide Analysis of the TCP Transcription Factor Gene Family in Pepper (Capsicum annuum L.).

TCP transcription factors play a key role in regulating various developmental processes, particularly in shoot branching, flower development, and leaf development, and these factors are exclusively found in plants. However, comprehensive studies investigating TCP transcription factors in pepper (Capsicum annuum L.) are lacking. In this study, we identified 27 CaTCP members in the pepper genome, which were classified into Class I and Class II through phylogenetic analysis. The motif analysis revealed that CaTCPs in the same class exhibit similar numbers and distributions of motifs. We predicted that 37 previously reported miRNAs target 19 CaTCPs. The expression levels of CaTCPs varied in various tissues and growth stages. Specifically, CaTCP16, a member of Class II (CIN), exhibited significantly high expression in flowers. Class I CaTCPs exhibited high expression levels in leaves, while Class II CaTCPs showed high expression in lateral branches, especially in the CYC/TB1 subclass. The expression profile suggests that CaTCPs play specific roles in the developmental processes of pepper. We provide a theoretical basis that will assist in further functional validation of the CaTCPs.

Identification and expression analysis of LEA gene family members in pepper (Capsicum annuum L.).

Pepper (Capsicum annuum L.) is an economically important crop containing capsaicinoids in the seed and placenta, which has various culinary, medical, and industrial applications. Late embryogenesis abundant (LEA) proteins are a large group of hydrophilic proteins participating in the plant stress response and seed development. However, to date there have been no genome-wide analyses of the LEA gene family in pepper. In the present study, 82 LEA genes were identified in the C. annuum genome and classified into nine subfamilies. Most CaLEA genes contain few introns (≤ 2) and are unevenly distributed across 10 chromosomes. Eight pairs of tandem duplication genes and two pairs of segmental duplication genes were identified in the LEA gene family; these duplicated genes were highly conserved and may have performed similar functions during evolution. Expression profile analysis indicated that CaLEA genes exhibited different tissue expression patterns, especially during embryonic development and stress response, particularly in cold stress. Three out of five CaLEA genes showed induced expression upon cold treatment. In summary, we have comprehensively reviewed the LEA gene family in pepper, offering a new perspective on the evolution of this family.

Association of C-reactive protein with mortality in Covid-19 patients: a secondary analysis of a cohort study.

Our study aimed to explore the association between serum C-reactive protein (CRP) and COVID-19 mortality. This is a retrospective cohort study of all patients admitted to 4 hospitals within the Montefiore Health System between March 1 and April 16, 2020, with SARS-CoV-2 infection. All-cause mortality were collected in 7 May 2020. The mortality risk was estimated using Cox proportional hazards models. Of the 3545 patients with a median age of 63.7 years, 918 (25.9%) died within the time of cohort data collection after admission. When the CRP was < 15.6 mg/L, the mortality rate increased with an adjusted HR of 1.57 (95% CI 1.30-1.91, P < 0.0001) for every 10 mg/L increment in the CRP. When the CRP was ≥ 15.6 mg/L, the mortality rate increased with an adjusted HR of 1.11 (95% CI 0.99-1.24, P = 0.0819) for every 10 mg/L increment in the CRP. For patients with COVID-19, the association between the CRP and the mortality risk was curve and had a saturation effect. When the CRP was small, the mortality rate increased significantly with the increase of CRP. When CRP > 15.6 mg/L, with the increase of CRP, the mortality rate increases relatively flat.

Genome-wide analysis and identification of stress-responsive genes of the CCCH zinc finger family in Capsicum annuum L.

The CCCH zinc finger gene family encodes a class of proteins that can bind to both DNA and RNA, and an increasing number of studies have demonstrated that the CCCH gene family plays a key role in growth and development and responses to environmental stress. Here, we identified 57 CCCH genes in the pepper (Capsicum annuum L.) genome and explored the evolution and function of the CCCH gene family in C. annuum. Substantial variation was observed in the structure of these CCCH genes, and the number of exons ranged from one to fourteen. Analysis of gene duplication events revealed that segmental duplication was the main driver of gene expansion in the CCCH gene family in pepper. We found that the expression of CCCH genes was significantly up-regulated during the response to biotic and abiotic stress, especially cold and heat stress, indicating that CCCH genes play key roles in stress responses. Our results provide new information on CCCH genes in pepper and will aid future studies of the evolution, inheritance, and function of CCCH zinc finger genes in pepper.

Phylogenomic analysis of cytochrome P450 multigene family and its differential expression analysis in pepper (Capsicum annuum L.).

Plant cytochrome P450 is a multifamily enzyme widely involved in biochemical reactions for the synthesis of antioxidants, pigments, structural polymers, and defense-related compounds. Pepper (Capsicum annuum L.) is an economically important plant. A comprehensive identification and characterization of P450 genes would provide valuable information on the evolutionary relationships of genes and their functional characteristics. In this study, we identified P450 genes in pepper with the aid of bioinformatics methods to investigate the phylogenetic relation, gene structure, chromosomal localization, duplicated events, and collinearity among Solanaceae species. We identified and classified 478 genes of P450 from the pepper genome into two major clades and nine subfamilies through phylogenetic analysis. Massive duplication events were found in the P450 gene family, which may explain the expansion of the P450 gene family. In addition, we also found that these duplication genes may have undergone strict purification selection during evolution. Gene expression analysis showed that some P450 genes that belong to clan 71 in pepper may play an important role in placenta and pericarp development. Through quantitative real-time polymerase chain reaction and transcriptome analysis, we also found that many P450 genes were related to defensive and phytohormone response in pepper. These findings provide insight for further studies to identify the biological functions of the P450 genes in pepper.

Expression analysis and functional characterization of tomato Tubby-like protein family.

Tubby-like protein (TLP) plays an important role in plant growth and development. In this investigation, the characteristics of 11 members in the SlTLP family were studied. SlTLP genes were classified into two subgroups, and the members containing the F-box domain were renamed SlTLFPs. Subcellular localization indicated that most of the SlTLPs were localized in the nucleus. Expression pattern analysis revealed that eight genes (SlTLFP1, 3, 5, 7-10, and SlTLP11) showed differential expression across various tissues, while SlTLFP2, 4, and 6 were widely expressed in all the organs tested. Most SlTLP genes were induced by biotic and abiotic stress treatments such as Botrytis cinerea, temperature, MeJA, and ABA. TLP proteins in tomato have no transcriptional activation activity, and most members with an F-box domain could interact with SUPPRESSOR OF KINETOCHORE PROTEIN 1 (SlSkp1) or Cullin1 (Cul1) or both. Experiments on CRISPR edited SlTLFP8 showed that the N-terminal F-box domain was necessary for its function such as DNA ploidy and stomata size regulation. Our findings suggested that the F-box domain interacts with Skp1 and Cul1 to form the SCF complex, suggesting that SlTLFPs, at least SlTLFP8, function mainly through the F-box domain as an E3 ligase.

The transcription factor SlWRKY37 positively regulates jasmonic acid- and dark-induced leaf senescence in tomato.

Initiation and progression of leaf senescence are triggered by various environmental stressors and phytohormones. Jasmonic acid (JA) and darkness accelerate leaf senescence in plants. However, the mechanisms that integrate these two factors to initiate and regulate leaf senescence have not been identified. Here, we report a transcriptional regulatory module centred on a novel tomato WRKY transcription factor, SlWRKY37, responsible for both JA- and dark-induced leaf senescence. The expression of SlWRKY37, together with SlMYC2, encoding a master transcription factor in JA signalling, was significantly induced by both methyl jasmonate (MeJA) and dark treatments. SlMYC2 binds directly to the promoter of SlWRKY37 to activate its expression. Knock out of SlWRKY37 inhibited JA- and dark-induced leaf senescence. Transcriptome analysis and biochemical experiments revealed SlWRKY53 and SlSGR1 (S. lycopersicum senescence-inducible chloroplast stay-green protein 1) as direct transcriptional targets of SlWRKY37 to control leaf senescence. Moreover, SlWRKY37 interacted with a VQ motif-containing protein SlVQ7, and the interaction improved the stability of SlWRKY37 and the transcriptional activation of downstream target genes. Our results reveal the physiological and molecular functions of SlWRKY37 in leaf senescence, and offer a target gene to retard leaf yellowing by reducing sensitivity to external senescence signals, such as JA and darkness.

The complete chloroplast genome sequence of Oxalis corniculata (L.).

Oxalis corniculata L. is a perennial herb with a world-wide distribution. In this study, we sequenced the complete chloroplast genome of O. corniculata, which exhibited a circular genome of 155,182 bp in length with 37.5% GC content. The chloroplast genome contained a canonical quadripartite structure with a large single copy (LSC) region of 83,936 bp, a small single copy (SSC) region of 17,048 bp and a pair of 25,581 bp inverted repeats (IRs). A total of 108 unique genes, including 76 protein-coding genes (PCGs), 28 tRNA genes and four rRNA genes were found in this chloroplast genome. The phylogenetic tree was constructed based on O. corniculata and other 11 chloroplast genome sequences, which showed that O. corniculata was closely grouped with of O. corymbosa and O. drummondii.

Whole-genome sequencing provides insights into the genetic diversity and domestication of bitter gourd (Momordica spp.).

Bitter gourd (Momordica charantia) is a popular cultivated vegetable in Asian and African countries. To reveal the characteristics of the genomic structure, evolutionary trajectory, and genetic basis underlying the domestication of bitter gourd, we performed whole-genome sequencing of the cultivar Dali-11 and the wild small-fruited line TR and resequencing of 187 bitter gourd germplasms from 16 countries. The major gene clusters (Bi clusters) for the biosynthesis of cucurbitane triterpenoids, which confer a bitter taste, are highly conserved in cucumber, melon, and watermelon. Comparative analysis among cucurbit genomes revealed that the Bi cluster involved in cucurbitane triterpenoid biosynthesis is absent in bitter gourd. Phylogenetic analysis revealed that the TR group, including 21 bitter gourd germplasms, may belong to a new species or subspecies independent from M. charantia. Furthermore, we found that the remaining 166 M. charantia germplasms are geographically differentiated, and we identified 710, 412, and 290 candidate domestication genes in the South Asia, Southeast Asia, and China populations, respectively. This study provides new insights into bitter gourd genetic diversity and domestication and will facilitate the future genomics-enabled improvement of bitter gourd.

Controllable Two-dimensional Perovskite Crystallization via Water Additive for High-performance Solar Cells.

Steering the crystallization of two-dimensional (2D) perovskite film is an important strategy to improve the power conversion efficiency (PCE) of 2D perovskite solar cells (PVSCs). In this paper, the deionized water (H2O) additive is introduced into the perovskite precursor solution to prepare high-quality 2D perovskite films. The 2D perovskite film treated with 3% H2O shows a good surface morphology, increased crystal size, enhanced crystallinity, preferred orientation, and low defect density. The fabricated 2D PVSC with 3% H2O exhibits a higher PCE compared with that without H2O (12.15% vs 2.29%). Furthermore, the shelf stability of unsealed devices with 3% H2O under ambient environment is significantly improved. This work provides a simple method to prepare high-quality 2D perovskite films for efficient and stable 2D PVSCs.

Gene expression and metabolic changes of Momordica charantia L. seedlings in response to low temperature stress.

Low temperature is one of the abiotic factors limiting germination, growth and distribution of the plant in current plant-products industry, especially for the tropical vegetables in non-tropical area or other fields under cold temperature. Screening the plant with ability against cold temperature captured worldwide attention and exerted great importance. In our previous work, the anti-cold specie of Momordica Charantia L. seedlings was screened out. Yet, the molecular and physiological mechanisms underlying this adaptive process still remain unknown. This study was aimed to investigate adaption mechanism of anti-cold species of Momordica Charantia L. seedlings in genetical and metabolomics levels. Two species, cold-susceptible group (Y17) and cold-resistant group (Y54), were evaluated containing the indexes of malondialdehyde (MDA), hydrogen peroxide (H2O2), proline content, activities of antioxidant enzymes, metabolites changes and genes differentiation in plant tissues after cold treatment. It found that low temperature stress resulted in increased accumulation of MDA, H2O2 and proline content in two species, but less expressions in cold-resistant species Y54. As compared to Y17, cold-resistant species Y54 presented significantly enhanced antioxidant enzyme activities of POD (peroxidase), CAT (cataalase) and SOD (superoxide dismutase). Meanwhile, higher expressed genes encoded antioxidant enzymes and transcription factors when exposure to the low temperature were found in cold-resistant species Y54, and core genes were explored by Q-PCR validation, including McSOD1, McPDC1 and McCHS1. Moreover, plant metabolites containing amino acid, sugar, fatty acid and organic acid in Y54 were higher than Y17, indicating their important roles in cold acclimation. Meanwhile, initial metabolites, including amimo acids, polypeptides, sugars, organic acids and nucleobases, were apparently increased in cold resistant species Y54 than cold susceptible species Y17. Our results demonstrated that the Momordica Charantia L. seedlings achieved cold tolerance might be went through mobilization of antioxidant systems, adjustment of the transcription factors and accumulation of osmoregulation substance. This work presented meaning information for revealing the anti-cold mechanism of the Momordica Charantia L. seedlings and newsight for further screening of anti-cold species in other plant.

Enhanced Crystallinity of Triple-Cation Perovskite Film via Doping NH4SCN.

The trap-state density in perovskite films largely determines the photovoltaic performance of perovskite solar cells (PSCs). Increasing the crystal grain size in perovskite films is an effective method to reduce the trap-state density. Here, we have added NH4SCN into perovskite precursor solution to obtain perovskite films with an increased crystal grain size. The perovskite with increased crystal grain size shows a much lower trap-state density compared with reference perovskite films, resulting in an improved photovoltaic performance in PSCs. The champion photovoltaic device has achieved a power conversion efficiency of 19.36%. The proposed method may also impact other optoelectronic devices based on perovskite films.

Solution-Processed Inorganic Perovskite Flexible Photodetectors with High Performance.

All inorganic CsPbI3-xBrx perovskites have been widely used in photodetectors due to their excellent optoelectronic properties and simple preparation processes. Here, high-performance flexible photodetectors based on inorganic CsPbI3-xBrx perovskites are demonstrated, which are achieved by a modified solution-processed method. When biased at a low voltage of 10 mV, the device yielded fast response speeds (90 µs /110 µs for CsPbI2Br PDs and 100 µs/140 µs for CsPbIBr2 PDs), a high on/off ratio of 104, and a high detectivity about 1012 Jones. Meanwhile, the devices showed outstanding environmental stability and mechanical flexibility. The periodic I-t curves had negligible fluctuation (< 5%) after storing in air atmosphere for 30 days or bending for 100 times. The results indicate that CsPbI3-xBrx perovskites have great potential in photodetection areas and pave the way to achieve high-performance flexible PDs.

Genome-Wide Analysis, Expression Profile, and Characterization of the Acid Invertase Gene Family in Pepper.

Catalytic decomposition of sucrose by acid invertases (AINVs) under acidic conditions plays an important role in the development of sink organs in plants. To reveal the function of AINVs in the development of pepper fruits, nine AINV genes of pepper were identified. Protein sequencing and phylogenetic analysis revealed that the CaAINV family may be divided into cell wall invertases (CaCWINV1⁻7) and vacuolar invertases (CaVINV1⁻2). CaAINVs contain conserved regions and protein structures typical of the AINVs in other plants. Gene expression profiling indicated that CaCWINV2 and CaVINV1 were highly expressed in reproductive organs but differed in expression pattern. CaCWINV2 was mainly expressed in buds and flowers, while CaVINV1 was expressed in developmental stages, such as the post-breaker stage. Furthermore, invertase activity of CaCWINV2 and CaVINV1 was identified via functional complementation in an invertase-deficient yeast. Optimum pH for CaCWINV2 and CaVINV1 was found to be 4.0 and 4.5, respectively. Gene expression and enzymatic activity of CaCWINV2 and CaVINV1 indicate that these AINV enzymes may be pivotal for sucrose hydrolysis in the reproductive organs of pepper.

Genome-Wide Identification, Expression, and Functional Analysis of the Alkaline/Neutral Invertase Gene Family in Pepper.

Alkaline/neutral invertase (NINV) proteins irreversibly cleave sucrose into fructose and glucose, and play important roles in carbohydrate metabolism and plant development. To investigate the role of NINVs in the development of pepper fruits, seven NINV genes (CaNINV1-7) were identified. Phylogenetic analysis revealed that the CaNINV family could be divided into α and ß groups. CaNINV1-6 had typical conserved regions and similar protein structures to the NINVs of other plants, while CaNINV7 lacked amino acid sequences at the C-terminus and N-terminus ends. An expression analysis of the CaNINV genes in different tissues demonstrated that CaNINV5 is the dominant NINV in all the examined tissues (root, stem, leaf, bud, flower, and developmental pepper fruits stage). Notably, the expression of CaNINV5 was found to gradually increase at the pre-breaker stages, followed by a decrease at the breaker stages, while it maintained a low level at the post-breaker stages. Furthermore, the invertase activity of CaNINV5 was identified by functional complementation of the invertase-deficient yeast strain SEY2102, and the optimum pH of CaNINV5 was found to be ~7.5. The gene expression and enzymatic activity of CaNINV5 suggest that it might be the main NINV enzyme for hydrolysis of sucrose during pepper fruit development.

Motion deblurring with temporally coded illumination in an LED array microscope.

Motion blur, which results from time-averaging an image over the camera's exposure time, is a common problem in microscopy of moving samples. Here, we demonstrate linear motion deblurring using temporally coded illumination in an LED array microscope. By illuminating moving objects with a well-designed temporal coded sequence that varies during each single camera exposure, the resulting motion blur is invertible and can be computationally removed. This scheme is implemented in an existing LED array microscope, providing benefits of being grayscale, fast, and adaptive, which leads to high-quality deblur performance and a flexible implementation with no moving parts. The proposed method is demonstrated experimentally for fast moving targets in a microfluidic environment.

Dynamic evolution of resistance gene analogs in the orthologous genomic regions of powdery mildew resistance gene MlIW170 in Triticum dicoccoides and Aegilops tauschii.

KEY MESSAGE: Rapid evolution of powdery mildew resistance gene MlIW170 orthologous genomic regions in wheat subgenomes. Wheat is one of the most important staple grain crops in the world and also an excellent model for plant ploidy evolution research with different ploidy levels from diploid to hexaploid. Powdery mildew disease caused by Blumeria graminis f.sp. tritici can result in significant loss in both grain yield and quality in wheat. In this study, the wheat powdery mildew resistance gene MlIW170 locus located at the Triticum dicoccoides chromosome 2B short arm was further characterized by constructing and sequencing a BAC-based physical map contig covering a 0.3 cM genetic distance region (880 kb) and developing additional markers to delineate the resistance gene within a 0.16 cM genetic interval (372 kb). Comparative analyses of the T. dicoccoides 2BS region with the orthologous Aegilops tauschii 2DS region showed great gene colinearity, including the structure organization of both types of RGA1/2-like and RPS2-like resistance genes. Comparative analyses with the orthologous regions from Brachypodium and rice genomes revealed considerable dynamic evolutionary changes that have re-shaped this MlIW170 region in the wheat genome, resulting in a high number of non-syntenic genes including resistance-related genes. This result might reflect the rapid evolution in R-gene regions. Phylogenetic analysis on these resistance-related gene sequences indicated the duplication of these genes in the MlIW170 region, occurred before the separation of the wheat B and D genomes.

Real-time brightfield, darkfield, and phase contrast imaging in a light-emitting diode array microscope.

We demonstrate a single-camera imaging system that can simultaneously acquire brightfield, darkfield, and phase contrast images in real time. Our method uses computational illumination via a programmable light-emitting diode (LED) array at the source plane, providing flexible patterning of illumination angles. Brightfield, darkfield, and differential phase contrast images are obtained by changing the LED patterns, without any moving parts. Previous work with LED array illumination was only valid for static samples because the hardware speed was not fast enough to meet real-time acquisition and processing requirements. Here, we time multiplex patterns for each of the three contrast modes in order to image dynamic biological processes in all three contrast modes simultaneously. We demonstrate multicontrast operation at the maximum frame rate of our camera (50 Hz with 2160 × 2560 pixels).

Identification and comparative mapping of a powdery mildew resistance gene derived from wild emmer (Triticum turgidum var. dicoccoides) on chromosome 2BS.

Powdery mildew, caused by Blumeria graminis f. sp. tritici, is an important foliar disease of wheat worldwide. Wild emmer (Triticum turgidum var. dicoccoides) is a valuable genetic resource for improving disease resistance in common wheat. A powdery mildew resistance gene conferring resistance to B. graminis f. sp. tritici isolate E09 at the seedling and adult stages was identified in wild emmer accession IW170 introduced from Israel. An incomplete dominant gene, temporarily designated MlIW170, was responsible for the resistance. Through molecular marker and bulked segregant analyses of an F(2) population and F(3) families derived from a cross between susceptible durum wheat line 81086A and IW170, MlIW170 was located in the distal chromosome bin 2BS3-0.84-1.00 and flanked by SSR markers Xcfd238 and Xwmc243. MlIW170 co-segregated with Xcau516, an STS marker developed from RFLP marker Xwg516 that co-segregated with powdery mildew resistance gene Pm26 on 2BS. Four EST-STS markers, BE498358, BF201235, BQ160080, and BF146221, were integrated into the genetic linkage map of MlIW170. Three AFLP markers, XPaacMcac, XPagcMcta, XPaacMcag, and seven AFLP-derived SCAR markers, XcauG2, XcauG3, XcauG6, XcauG8, XcauG10, XcauG20, and XcauG25, were linked to MlIW170. XcauG3, a resistance gene analog (RGA)-like sequence, co-segregated with MlIW170. The non-glaucousness locus Iw1 was 18.77 cM distal to MlIW170. By comparative genomics of wheat-Brachypodium-rice genomic co-linearity, four EST-STS markers, CJ658408, CJ945509, BQ169830, CJ945085, and one STS marker XP2430, were developed and MlIW170 was mapped in an 2.69 cM interval that is co-linear with a 131 kb genomic region in Brachypodium and a 105 kb genomic region in rice. Four RGA-like sequences annotated in the orthologous Brachypodium genomic region could serve as chromosome landing target regions for map-based cloning of MlIW170.

Identification and genetic mapping of pm42, a new recessive wheat powdery mildew resistance gene derived from wild emmer (Triticum turgidum var. dicoccoides).

Powdery mildew, caused by Blumeria graminis f. sp. tritici, is one of the most important wheat diseases worldwide in areas with cool or maritime climates. Wild emmer (Triticum turgidum var. dicoccoides) is an important potential donor of disease resistances and other traits for common wheat improvement. A powdery mildew resistance gene was transferred from wild emmer accession G-303-1M to susceptible common wheat by crossing and backcrossing, resulting in inbred line P63 (Yanda1817/G-303-1 M//3*Jing411, BC(2)F(6)). Genetic analysis of an F(2) population and the F(2:3) families developed from a cross of P63 and a susceptible common wheat line Xuezao showed that the powdery mildew resistance in P63 was controlled by a single recessive gene. Molecular markers and bulked segregant analysis were used to characterize and map the powdery mildew resistance gene. Nine genomic SSR markers (Xbarc7, Xbarc55, Xgwm148, Xgwm257, Xwmc35, Xwmc154, Xwmc257, Xwmc382, Xwmc477), five AFLP-derived SCAR markers (XcauG3, XcauG6, XcauG10, XcauG20, XcauG22), three EST-STS markers (BQ160080, BQ160588, BF146221) and one RFLP-derived STS marker (Xcau516) were linked to the resistance gene, designated pm42, in P63. pm42 was physically mapped on chromosome 2BS bin 0.75-0.84 using Chinese Spring nullisomic-tetrasomic, ditelosomic and deletion lines, and was estimated to be more than 30 cM proximal to Xcau516, a RFLP-derived STS marker that co-segregated with the wild emmer-derived Pm26 which should be physically located in 2BS distal bin 0.84-1.00. pm42 was highly effective against 18 of 21 differential Chinese isolates of B. graminis f. sp. tritici. The closely linked molecular markers will enable the rapid transfer of pm42 to wheat breeding populations thus adding to their genetic diversity.