Haplotype-resolved genomes of octoploid species in Phyllanthaceae family reveal a critical role for polyploidization and hybridization in speciation.

The Phyllanthaceae family comprises a diverse range of plants with medicinal, edible, and ornamental value, extensively cultivated worldwide. Polyploid species commonly occur in Phyllanthaceae. Due to the rather complex genomes and evolutionary histories, their speciation process has been still lacking in research. In this study, we generated chromosome-scale haplotype-resolved genomes of two octoploid species (Phyllanthus emblica and Sauropus spatulifolius) in Phyllanthaceae family. Combined with our previously reported one tetraploid (Sauropus androgynus) and one diploid species (Phyllanthus cochinchinensis) from the same family, we explored their speciation history. The three polyploid species were all identified as allopolyploids with subgenome A/B. Each of their two distinct subgenome groups from various species was uncovered to independently share a common diploid ancestor (Ancestor-AA and Ancestor-BB). Via different evolutionary routes, comprising various scenarios of bifurcating divergence, allopolyploidization (hybrid polyploidization), and autopolyploidization, they finally evolved to the current tetraploid S. androgynus, and octoploid S. spatulifolius and P. emblica, respectively. We further discuss the variations in copy number of alleles and the potential impacts within the two octoploids. In addition, we also investigated the fluctuation of metabolites with medical values and identified the key factor in its biosynthesis process in octoploids species. Our study reconstructed the evolutionary history of these Phyllanthaceae species, highlighting the critical roles of polyploidization and hybridization in their speciation processes. The high-quality genomes of the two octoploid species provide valuable genomic resources for further research of evolution and functional genomics.

Smart windows based on ultraviolet-B persistent luminescence phosphors for bacterial inhibition and food preservation.

Herein, ultraviolet B (UVB) persistent luminescence phosphors containing SrAl12O19: Ce3+, Sc3+ nanoparticles were reported. Thermoluminescence (TL) spectrum analysis reveals that the shallow trap induced by Sc3+ co-doping plays an important role in photoluminescence persistent luminescence (PersL) development, while the deep trap dominates the generation of optical stimulated luminescence (OSL). Owing the appearance of deep trap, the OSL is observed under light (700 nm - 900 nm) excitation. UVB luminescence exerts good bactericidal effects on pathogenic bacteria involved in the process of food spoilage. Thus, the smart window with SrAl12O19: Ce3+, Sc3+/PDMS produces UVB PersL to efficiently inactivate Escherichia coli and Staphylococcus aureus. In addition, the presence of the smart window delays the critical point of pork decay, and greatly reduces the time of pork spoilage. It maximizes the convenience of eradicating bacteria and preserving food, thus offering a fresh perspective on the use of UV light for food sterilization and preservation.

Soil nitrogen availability and microbial carbon use efficiency are dependent more on chemical fertilization than winter drought in a maize-soybean rotation system.

Soil nitrogen (N) availability is one of the limiting factors of crop productivity, and it is strongly influenced by global change and agricultural management practices. However, very few studies have assessed how the winter drought affected soil N availability during the subsequent growing season under chemical fertilization. We conducted a field investigation involving snow removal to simulate winter drought conditions in a Mollisol cropland in Northeast China as part of a 6-year fertilization experiment, and we examined soil physicochemical properties, microbial characteristics, and N availability. Our results demonstrated that chemical fertilization significantly increased soil ammonium and total N availability by 42.9 and 90.3%, respectively; a combined winter drought and fertilization treatment exhibited the highest soil N availability at the end of the growing season. As the growing season continued, the variation in soil N availability was explained more by fertilization than by winter drought. The Mantel test further indicated that soil Olsen-P content and microbial carbon use efficiency (CUE) were significantly related to soil ammonium availability. A microbial community structure explained the largest fraction of the variation in soil nitrate availability. Microbial CUE showed the strongest correlation with soil N availability, followed by soil available C:P and bacteria:fungi ratios under winter drought and chemical fertilization conditions. Overall, we clarified that, despite the weak effect of the winter drought on soil N availability, it cannot be ignored. Our study also identified the important role of soil microorganisms in soil N transformations, even in seasonally snow-covered northern croplands.

Complete mitochondrial genome of Basilepta melanopus Lefèvre, 1893 (coleoptera: chrysomelidae: eumolpinae), a tea pest from Southern China.

The tea pest, Basilepta melanopus Lefèvre 1893 (Chrysomelidae), belongs to the subfamily Eumolpinae. In this study, the complete mitochondrial genome sequence of B. melanopus from southern China was sequenced using the next-generation sequencing technique, assembled, and annotated using bioinformatics tools. The complete mitochondrial genome was 15,905 bp in length. The overall GC content was 22.51%, in which the percentages for the bases A, T, C, and G were 41.23%, 36.26%, 8.92%, and 13.59%, respectively. Thirty-seven genes were predicted, including 13 protein-coding, 22 transfer RNA, and two ribosomal RNA genes. Phylogenetic analysis based on the complete mitochondrial genome sequences of 18 Chrysomelidae taxa revealed that B. melanopus was closely related to Basilepta fulvipes.

Genome and GWAS analysis identified genes significantly related to phenotypic state of Rhododendron bark.

As an important horticultural plant, Rhododendron is often used in urban greening and landscape design. However, factors such as the high rate of genetic recombination, frequent outcrossing in the wild, weak linkage disequilibrium, and the susceptibility of gene expression to environmental factors limit further exploration of functional genes related to important horticultural traits, and make the breeding of new varieties require a longer time. Therefore, we choose bark as the target trait which is not easily affected by environmental factors, but also has ornamental properties. Genome-wide association study (GWAS) of Rhododendron delavayi (30 samples), R. irroratum (30 samples) and their F1 generation R. agastum (200 samples) was conducted on the roughness of bark phenotypes. Finally, we obtained 2416.31 Gbp of clean data and identified 5 328 800 high-quality SNPs. According to the P-value and the degree of linkage disequilibrium of SNPs, we further identified 4 out of 11 candidate genes that affect bark roughness. The results of gene differential expression analysis further indicated that the expression levels of Rhdel02G0243600 and Rhdel08G0220700 in different bark phenotypes were significantly different. Our study identified functional genes that influence important horticultural traits of Rhododendron, and illustrated the powerful utility and great potential of GWAS in understanding and exploiting wild germplasm genetic resources of Rhododendron.

[Genome-wide identification and expression analysis of TCP gene family of Andrographis paniculata under abiotic stress].

Andrographis paniculata is an important medicinal plant in the Lingnan region of China, which has the functions of clearing heat, removing toxins, and resisting bacteria and inflammation. The TCP gene family is a class of transcription factors that regulate plant growth, development, and stress response. In order to analysis the role of the TCP gene family under abiotic stress in A. paniculata, this study identified the TCP gene family of A. paniculata at the genome-wide level and analyzed its expression pattern in response to abiotic stress. The results showed that the A. paniculata TCP gene family had 23 members, with length of amino acid ranging from 136 to 508, the relative molecular mass between 14 854.71 and 55 944.90 kDa, and the isoelectric point between 5.67 and 10.39. All members were located in the nucleus and unevenly distributed on 13 chromosomes. Phylogenetic analysis classified them into three subfamilies: PCF, CIN and CYC/TB1. Gene structure and conserved motif analysis showed that most members of the TCP gene family contained motif 1, motif 2, motif 3 in the same order and 1-3 CDS. The analysis of promoter cis-acting elements showed that the transcriptional expression of the TCP gene family in A. paniculata might be induced by light, hormones, and adversity stress. In light of the expression pattern analysis and qRT-PCR verification, the expression of ApTCP4, ApTCP5, ApTCP6, and ApTCP11 involved in response by various abiotic stresses such as drought, high temperature, and MeJA. This study lays the foundation for in-depth exploration of the functions of A. paniculata TCP genes in response to abiotic stress.

Fungal community dynamics associated with the outbreaks of sugarcane root rot disease.

Sugarcane is a critical sugar and bioenergy crop in China. However, numerous factors, including root rot disease, hamper its yield. Root rot disease is a severe agricultural issue, reducing yield and threatening sustainable crop production. The current study aimed to explore the fungal community structure, identify and characterize the primary pathogen for sugarcane root rot in Guangzhou, China. Eighty-nine samples of sugarcane root, stalk, rhizosphere soil, and irrigation water were collected from five sites in Guangzhou, China. Subsequently, 276 fungal strains were isolated to identify the primary pathogens. The five most common genera identified were Penicillium, Fusarium, Gongronella, Trichoderma, and Cladosporium. Fusarium was more prevalent in the infected soil samples than in healthy ones. Pathogenic assays of the strains revealed that the strain GX4-46 caused 80% of the disease. The strain was confirmed as Fusarium commune through phylogenetic and genome sequence analysis. Rhizosphere soil samples from different regional crops were collected to better understand the fungal community structure and the primary pathogen. We observed a significant presence of Fusarium in irrigation water, indicating that the root rot disease could originate from the irrigation water and then spread as a soil-borne disease. This research is pioneering and one of the most comprehensive investigations on the occurrence and prevalence of sugarcane root rot disease. This study will serve as a reference for expanding the sugarcane industry and a foundation for further exploration and control of root rot.IMPORTANCESugarcane, a significant economic crop, faces challenges due to root rot pathogens that accumulate each year in plants and soil through ratoon planting. This disrupts soil microbial balance and greatly impedes sugarcane industry growth. Symptoms range from wilting and yellowing leaves to stunted growth and reduced seedling tillers. The rhizosphere microbiota plays an important role in plant development and soil health. Little is known about root rot fungal community structure, especially in sugarcane. Here, we focused on exploring the main causative pathogen of root rot in the area alongside a detailed survey of the rhizosphere soil of different severity sugarcane cultivars and rotation crops of the region. To validate the findings, we also investigated the irrigation water of the area. Our study revealed Fusarium commune as the causative pathogen of root rot in the area, primarily originating from water and later as soil-borne. Using Trichoderma can control the disease effectively.

DNA methylation remodeled amino acids biosynthesis regulates flower senescence in carnation (Dianthus caryophyllus).

Dynamic DNA methylation regulatory networks are involved in many biological processes. However, how DNA methylation patterns change during flower senescence and their relevance with gene expression and related molecular mechanism remain largely unknown. Here, we used whole genome bisulfite sequencing to reveal a significant increase of DNA methylation in the promoter region of genes during natural and ethylene-induced flower senescence in carnation (Dianthus caryophyllus L.), which was correlated with decreased expression of DNA demethylase gene DcROS1. Silencing of DcROS1 accelerated while overexpression of DcROS1 delayed carnation flower senescence. Moreover, among the hypermethylated differentially expressed genes during flower senescence, we identified two amino acid biosynthesis genes, DcCARA and DcDHAD, with increased DNA methylation and reduced expression in DcROS1 silenced petals, and decreased DNA methylation and increased expression in DcROS1 overexpression petals, accompanied by decreased or increased amino acids content. Silencing of DcCARA and DcDHAD accelerates carnation flower senescence. We further showed that adding corresponding amino acids could largely rescue the senescence phenotype of DcROS1, DcCARA and DcDHAD silenced plants. Our study not only demonstrates an essential role of DcROS1-mediated remodeling of DNA methylation in flower senescence but also unravels a novel epigenetic regulatory mechanism underlying DNA methylation and amino acid biosynthesis during flower senescence.

Understanding the role of pathways in a deep neural network.

Deep neural networks have demonstrated superior performance in artificial intelligence applications, but the opaqueness of their inner working mechanism is one major drawback in their application. The prevailing unit-based interpretation is a statistical observation of stimulus-response data, which fails to show a detailed internal process of inherent mechanisms of neural networks. In this work, we analyze a convolutional neural network (CNN) trained in the classification task and present an algorithm to extract the diffusion pathways of individual pixels to identify the locations of pixels in an input image associated with object classes. The pathways allow us to test the causal components which are important for classification and the pathway-based representations are clearly distinguishable between categories. We find that the few largest pathways of an individual pixel from an image tend to cross the feature maps in each layer that is important for classification. And the large pathways of images of the same category are more consistent in their trends than those of different categories. We also apply the pathways to understanding adversarial attacks, object completion, and movement perception. Further, the total number of pathways on feature maps in all layers can clearly discriminate the original, deformed, and target samples.

EVLncRNAs 3.0: an updated comprehensive database for manually curated functional long non-coding RNAs validated by low-throughput experiments.

Long noncoding RNAs (lncRNAs) have emerged as crucial regulators across diverse biological processes and diseases. While high-throughput sequencing has enabled lncRNA discovery, functional characterization remains limited. The EVLncRNAs database is the first and exclusive repository for all experimentally validated functional lncRNAs from various species. After previous releases in 2018 and 2021, this update marks a major expansion through exhaustive manual curation of nearly 25 000 publications from 15 May 2020, to 15 May 2023. It incorporates substantial growth across all categories: a 154% increase in functional lncRNAs, 160% in associated diseases, 186% in lncRNA-disease associations, 235% in interactions, 138% in structures, 234% in circular RNAs, 235% in resistant lncRNAs and 4724% in exosomal lncRNAs. More importantly, it incorporated additional information include functional classifications, detailed interaction pathways, homologous lncRNAs, lncRNA locations, COVID-19, phase-separation and organoid-related lncRNAs. The web interface was substantially improved for browsing, visualization, and searching. ChatGPT was tested for information extraction and functional overview with its limitation noted. EVLncRNAs 3.0 represents the most extensive curated resource of experimentally validated functional lncRNAs and will serve as an indispensable platform for unravelling emerging lncRNA functions. The updated database is freely available at https://www.sdklab-biophysics-dzu.net/EVLncRNAs3/.

Effects of a mixture of glycerol monolaurate and cinnamaldehyde supplementation on laying performance, egg quality, and antioxidant status in laying hens.

BACKGROUND: This study aimed to determine the effects of a mixture of glycerol monolaurate and cinnamaldehyde (GCM) supplementation on the laying performance, egg quality, antioxidant capacity, and serum parameters of laying hens. A total of 1120 14-week-old Jingfen-1 strain laying hens with similar performance were randomly allocated to four dietary treatments: control, and GCM groups supplemented with 250, 500, or 1000 mg kg-1 for 12 weeks. RESULTS: Compared with the control group, GCM-supplemented groups significantly reduced (P < 0.05) the rate of unqualified eggs of laying hens aged 17-24 weeks. Supplementation of GCM significantly increased (P < 0.05) yolk color and serum glutathione peroxidase (GSH-Px) activity but decreased (P < 0.05) the hydrogen peroxide (H2 O2 ) content in the serum of laying hens at the age of 20 weeks. Furthermore, groups supplemented with GCM showed a significant increase (P < 0.05) in Haugh unit, yolk color, activities of total superoxide dismutase and GSH-Px, and the glucose content in serum, and a decrease (P < 0.05) in the content of urea nitrogen and H2 O2 and malondialdehyde in serum of laying hens at the age of 24 weeks. 500 mg kg-1 GCM supplementation significantly increased (P < 0.05) the number of large white follicles and 1000 mg kg-1 GCM supplementation decreased the number of large yellow follicles in 28-week-old laying hens. CONCLUSION: These results indicated that GCM supplementation has positive effects on reducing egg loss and improving egg quality in the early laying period of laying hens. © 2023 Society of Chemical Industry.

Origin and evolution of the triploid cultivated banana genome.

Most fresh bananas belong to the Cavendish and Gros Michel subgroups. Here, we report chromosome-scale genome assemblies of Cavendish (1.48 Gb) and Gros Michel (1.33 Gb), defining three subgenomes, Ban, Dh and Ze, with Musa acuminata ssp. banksii, malaccensis and zebrina as their major ancestral contributors, respectively. The insertion of repeat sequences in the Fusarium oxysporum f. sp. cubense (Foc) tropical race 4 RGA2 (resistance gene analog 2) promoter was identified in most diploid and triploid bananas. We found that the receptor-like protein (RLP) locus, including Foc race 1-resistant genes, is absent in the Gros Michel Ze subgenome. We identified two NAP (NAC-like, activated by apetala3/pistillata) transcription factor homologs specifically and highly expressed in fruit that directly bind to the promoters of many fruit ripening genes and may be key regulators of fruit ripening. Our genome data should facilitate the breeding and super-domestication of bananas.

Disruption of the Contents of Endogenous Hormones Cause Pollen Development Obstruction and Abortion in Male-Sterile Hybrid Lily Populations.

Lilies are well-known flowers with large anthers and a high quantity of pollen that easily contaminates clothing and tepals. The anthers need to be artificially removed, leading to production problems. Cultivating male-sterile or pollen-free lilies could solve these problems. The key period of male sterility in a specific male-sterile hybrid lily population was determined through cytological observation. The contents of hormones, soluble sugar, soluble protein, and proline were determined by high-performance liquid chromatography, tandem mass spectrometry and colorimetry. Transcriptome sequencing was used to identify the genes with altered expression. The key period of male sterility was determined to be the microspore mother and tetrad stages. The hormone contents were abnormal in the sterile line compared with the fertile line. The indole-3-acetic acid (IAA) content was higher in the sterile line than in the fertile line at all stages, while the gibberellic acid 4 (GA4) content showed the opposite result. Abscisic acid (ABA) accumulated in the sterile line in both the microspore mother and tetrad stages, and the zeatin riboside (ZR) content in the sterile line increased at the microspore mother stage but decreased at the tetrad stage. The contents of soluble sugar, soluble protein and proline were higher in the fertile line than in the sterile line. Genes involved in auxin and ABA synthesis and signalling pathways were highly expressed in the male-sterile line. Our data suggested that abnormal contents of hormones in the microspore mother and tetrad stages resulted in pollen abortion in a male-sterile hybrid lily population, which indicated that the hormone balance in specific stages plays critical functions in pollen development in lilies.

Heterologous Expression of Platycodon grandiflorus PgF3'5'H Modifies Flower Color Pigmentation in Tobacco.

Flavonoid-3',5'-hydroxylase (F3'5'H) is the key enzyme for the biosynthesis of delphinidin-based anthocyanins, which are generally required for purple or blue flowers. Previously, we isolated a full-length cDNA of PgF3'5'H from Platycodon grandiflorus, which shared the highest homology with Campanula medium F3'5'H. In this study, PgF3'5'H was subcloned into a plant over-expression vector and transformed into tobacco via Agrobacterium tumefaciens to investigate its catalytic function. Positive transgenic tobacco T0 plants were obtained by hygromycin resistance screening and PCR detection. PgF3'5'H showed a higher expression level in all PgF3'5'H transgenic tobacco plants than in control plants. Under the drive of the cauliflower mosaic virus (CaMV) 35S promoter, the over-expressed PgF3'5'H produced dihydromyricetin (DHM) and some new anthocyanin pigments (including delphinidin, petunidin, peonidin, and malvidin derivatives), and increased dihydrokaempferol (DHK), taxifolin, tridactyl, cyanidin derivatives, and pelargonidin derivatives in PgF3'5'H transgenic tobacco plants by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) analysis, resulting in a dramatic color alteration from light pink to magenta. These results indicate that PgF3'5'H products have F3'5'H enzyme activity. In addition, PgF3'5'H transfer alters flavonoid pigment synthesis and accumulation in tobacco. Thus, PgF3'5'H may be considered a candidate gene for gene engineering to enhance anthocyanin accumulation and the molecular breeding project for blue flowers.

Ganoderic acid C2 exerts the pharmacological effects against cyclophosphamide-induced immunosuppression: a study involving molecular docking and experimental validation.

Triterpenoids, as the main active ingredient of Ganoderma lucidum fermented extract, exert multiple pharmacological activities, including immunomodulatory properties. Our study aimed to reveal the pharmacological effects and potential mechanisms of Ganoderic acid C2 (GAC) against cyclophosphamide (CY)-associated immunosuppression. Target genes were collected from several public databases, including the DisGeNET, Comparative Toxicogenomics Database, GeneCards, and PharmMapper. STRING database was used to construct the protein-protein interaction of network. Subsequently, molecular docking was carried out to visualize the protein-GAC interactions. Experimental validations, including ELISA and qRT-PCR were performed to confirm the pharmacological activities of GAC on CY-induced immunosuppression model. A total of 56 GAC-related targets were identified to be closely associated with CY-induced immunosuppression. Enrichment analyses results revealed that these targets were mainly involved in immune and inflammatory response-related pathways. STAT3 and TNF were identified as the core targets of GAC. Molecular docking indicated that GAC combined well with STAT3 and TNF protein. In addition, animal experiments indicated that GAC improved immunity as well as STAT3 and TNF genes expression in CY-induced immunosuppression, which further verified the prediction through bioinformatics analysis and molecular docking. We successfully revealed the potential therapeutics mechanisms underlying the effect of GAC against CY-induced immunosuppression based on the combination of bioinformatics analysis, molecular docking, and animal experiments. Our findings lay a theoretical foundation for the in-depth development and utilization of Ganoderma lucidum fermentation product in the future, and also provide theoretical guidance for the development of innovative drugs that assist in improving immunity.

Genomic-wide identification and expression analysis of R2R3-MYB transcription factors related to flavonol biosynthesis in Morinda officinalis.

BACKGROUND: The R2R3-MYB transcription factors are a crucial and extensive gene family in plants, which participate in diverse processes, including development, metabolism, defense, differentiation, and stress response. In the Lingnan region of China, Morinda officinalis is extensively grown and is renowned for its use as both a medicinal herb and food source. However, there are relatively few reports on the R2R3-MYB transcription factor family in M.officinalis. RESULTS: In this study, we identified 97 R2R3-MYB genes in the genome of Morinda officinalis and classified them into 32 subgroups based on phylogenetic comparison with Arabidopsis thaliana. The lack of recent whole-genome duplication events in M.officinalis may be the reason for the relatively few members of the R2R3-MYB family. We also further analyzed the physical and chemical characteristics, conserved motifs, gene structure, and chromosomal location. Gene duplication events found 21 fragment duplication pairs and five tandem duplication event R2R3-MYB genes in M.officinalis may also affect gene family expansion. Based on phylogenetic analysis, cis-element analysis, co-expression analysis and RT-qPCR, we concluded that MoMYB33 might modulate flavonol levels by regulating the expression of 4-coumarate-CoA ligase Mo4CL2, chalcone isomerase MoCHI3, and flavonol synthase MoFLS4/11/12. MoMYB33 and AtMYB111 showed the highest similarity of 79% and may be involved in flavonol synthase networks by the STRING database. Moreover, we also identified MoMYB genes that respond to methyl Jasmonate (MeJA) and abscisic acid (ABA) stress by RT-qPCR. CONCLUSIONS: This study offers a thorough comprehension of R2R3-MYB in M.officinalis, which lays the foundation for the regulation of flavonol synthesis and the response of MoMYB genes to phytohormones in M.officinalis.

Genome-Wide Identification and Functional Characterization of FAR1-RELATED SEQUENCE (FRS) Family Members in Potato (Solanum tuberosum).

FAR1-RELATED SEQUENCE (FRS) transcription factors are generated by transposases and play vital roles in plant growth and development, light signaling transduction, phytohormone response, and stress resistance. FRSs have been described in various plant species. However, FRS family members and their functions remain poorly understood in vegetative crops such as potato (Solanum tuberosum, St). In the present study, 20 putative StFRS proteins were identified in potato via genome-wide analysis. They were non-randomly localized to eight chromosomes and phylogenetic analysis classified them into six subgroups along with FRS proteins from Arabidopsis and tomato. Conserved protein motif, protein domain, and gene structure analyses supported the evolutionary relationships among the FRS proteins. Analysis of the cis-acting elements in the promoters and the expression profiles of StFRSs in various plant tissues and under different stress treatments revealed the spatiotemporal expression patterns and the potential roles of StFRSs in phytohormonal and stress responses. StFRSs were differentially expressed in the cultivar "Xisen 6", which is exposed to a variety of stresses. Hence, these genes may be critical in regulating abiotic stress. Elucidating the StFRS functions will lay theoretical and empirical foundations for the molecular breeding of potato varieties with high light use efficiency and stress resistance.

Overcoming Debye length limitations: Three-dimensional wrinkled graphene field-effect transistor for ultra-sensitive adenosine triphosphate detection.

Adenosine triphosphate (ATP) is closely related to the pathogenesis of certain diseases, so the detection of trace ATP is of great significance to disease diagnosis and drug development. Graphene field-effect transistors (GFETs) have been proven to be a promising platform for the rapid and accurate detection of small molecules, while the Debye shielding limits the sensitive detection in real samples. Here, a three-dimensional wrinkled graphene field-effect transistor (3D WG-FET) biosensor for ultra-sensitive detection of ATP is demonstrated. The lowest detection limit of 3D WG-FET for analyzing ATP is down to 3.01 aM, which is much lower than the reported results. In addition, the 3D WG-FET biosensor shows a good linear electrical response to ATP concentrations in a broad range of detection from 10 aM to 10 pM. Meanwhile, we achieved ultra-sensitive (LOD: 10 aM) and quantitative (range from 10 aM to 100 fM) measurements of ATP in human serum. The 3D WG-FET also exhibits high specificity. This work may provide a novel approach to improve the sensitivity for the detection of ATP in complex biological matrix, showing a broad application value for early clinical diagnosis and food health monitoring. Electronic supplementary materials: The online version contains supplementary material available at 10.1007/s11467-023-1281-7 and https://journal.hep.com.cn/fop/EN/10.1007/s11467-023-1281-7.

Evolutionary history of two evergreen Rhododendron species as revealed by chromosome-level genome assembly.

Background: The genus Rhododendron (Ericaceae), a species-rich and widely distributed genus of woody plants, is distinguished for the beautiful and diverse flowers. Rhododendron delavayi Franch. and Rhododendron irroratum Franch., are highly attractive species widely distributed in south-west China and abundant new varieties have been selected from their genetic resources. Methods: We constructed chromosome-scale genome assemblies for Rhododendron delavayi and Rhododendron irroratum. Phylogenetic and whole-genome duplication analyses were performed to elucidate the evolutionary history of Rhododendron. Further, different types of gene duplications were identified and their contributions to gene family expansion were investigated. Finally, comprehensive characterization and evolutionary analysis of R2R3-MYB and NBS-encoding genes were conducted to explore their evolutionary patterns. Results: The phylogenetic analysis classified Rhododendron species into two sister clades, 'rhododendrons' and 'azaleas'. Whole-genome duplication (WGD) analysis unveiled only one WGD event that occurred in Rhododendron after the ancestral γ triplication. Gene duplication and gene family expansion analyses suggested that the younger tandem and proximal duplications contributed greatly to the expansion of gene families involved in secondary metabolite biosynthesis and stress response. The candidate R2R3-MYB genes likely regulating anthocyanin biosynthesis and stress tolerance in Rhododendron will facilitate the breeding for ornamental use. NBS-encoding genes had undergone significant expansion and experienced species-specific gain and loss events in Rhododendron plants. Conclusions: The reference genomes presented here will provide important genetic resources for molecular breeding and genetic improvement of plants in this economically important Rhododendron genus.