A high-quality haplotype genome of Michelia alba DC reveals differences in methylation patterns and flower characteristics.

Michelia alba DC is a highly valuable ornamental plant of the Magnoliaceae family. This evergreen tropical tree commonly grows in Southeast Asia and is adored for its delightful fragrance. Our study assembled the M. alba haplotype genome MC and MM by utilizing Nanopore ultralong reads, Pacbio Hifi long reads and parental second-generation data. Moreover, the first methylation map of Magnoliaceae was constructed based on the methylation site data obtained using Nanopore data. Metabolomic datasets were generated from the flowers of three different species to assess variations in pigment and volatile compound accumulation. Finally, transcriptome data were generated to link genomic, methylation, and morphological patterns to reveal the reasons underlying the differences between M. alba and its parental lines in petal color, flower shape, and fragrance. We found that the AP1 and AP2 genes are crucial in M. alba petal formation, while the 4CL, PAL, and C4H genes control petal color. The data generated in this study serve as a foundation for future physiological and biochemical research on M. alba, facilitate the targeted improvement of M. alba varieties, and offer a theoretical basis for molecular research on Michelia L.

Methyltransferase TaSAMT1 mediates wheat freezing tolerance by integrating brassinosteroid and salicylic acid signaling.

Cold injury is a major environmental stress affecting the growth and yield of crops. Brassinosteroids (BRs) and salicylic acid (SA) play important roles in plant cold tolerance. However, whether or how BR signaling interacts with the SA signaling pathway in response to cold stress is still unknown. Here, we identified an SA methyltransferase, TaSAMT1, that converts SA to methyl SA (MeSA) and confers freezing tolerance in wheat (Triticum aestivum). TaSAMT1 overexpression greatly enhanced wheat freezing tolerance, with plants accumulating more MeSA and less SA, whereas Tasamt1 knockout lines were sensitive to freezing stress and accumulated less MeSA and more SA. Spraying plants with MeSA conferred freezing tolerance to Tasamt1 mutants, but SA did not. We revealed that BRASSINAZOLE-RESISTANT 1 (TaBZR1) directly binds to the TaSAMT1 promoter and induces its transcription. Moreover, TaBZR1 interacts with the histone acetyltransferase TaHAG1, which potentiates TaSAMT1 expression via increased histone acetylation and modulates the SA pathway during freezing stress. Additionally, overexpression of TaBZR1 or TaHAG1 altered TaSAMT1 expression and improved freezing tolerance. Our results demonstrate a key regulatory node that connects the BR and SA pathways in the plant cold stress response. The regulatory factors or genes identified could be effective targets for the genetic improvement of freezing tolerance in crops.

Advancing understanding of Ficus carica: a comprehensive genomic analysis reveals evolutionary patterns and metabolic pathway insights.

Ficus carica L. (dioecious), the most significant commercial species in the genus Ficus, which has been cultivated for more than 11,000 years and was one of the first species to be domesticated. Herein, we reported the most comprehensive F. carica genome currently. The contig N50 of the Orphan fig was 9.78 Mb, and genome size was 366.34 Mb with 13 chromosomes. Based on the high-quality genome, we discovered that F. carica diverged from Ficus microcarpa ~34 MYA, and a WGD event took place about 2─3 MYA. Throughout the evolutionary history of F. carica, chromosomes 2, 8, and 10 had experienced chromosome recombination, while chromosome 3 saw a fusion and fission. It is worth proposing that the chromosome 9 experienced both inversion and translocation, which facilitated the emergence of the F. carica as a new species. And the selections of F. carica for the genes of recombination chromosomal fragment are compatible with their goal of domestication. In addition, we found that the F. carica has the FhAG2 gene, but there are structural deletions and positional jumps. This gene is thought to replace the one needed for female common type F. carica to be pollinated. Subsequently, we conducted genomic, transcriptomic, and metabolomic analysis to demonstrate significant differences in the expression of CHS among different varieties of F. carica. The CHS playing an important role in the anthocyanin metabolism pathway of F. carica. Moreover, the CHS gene of F. carica has a different evolutionary trend compared to other Ficus species. These high-quality genome assembly, transcriptomic, and metabolomic resources further enrich F. carica genomics and provide insights for studying the chromosomes evolution, sexual system, and color characteristics of Ficus.

Insights into the genetic determination of tuber shape and eye depth in potato natural population based on autotetraploid potato genome.

Potato is one of the world's most important food crops, with a time-consuming breeding process. In this study, we performed a genome-wide association (GWAS) analysis of the two important traits of potato tuber shape and eye depth, using the tetraploid potato genome (2n=4x=48) as a reference. A total of 370 potatoes were divided into three subgroups based on the principal component analysis and evolutionary tree analysis. The genetic diversity within subgroups is low (5.18×10-5, 4.36×10-5 and 4.24×10-5). Genome-wide linkage disequilibrium (LD) analysis showed that their LD is about 60 Kb. GWAS analysis identified that 146 significant single nucleotide polymorphism (SNP) loci at Chr01A1:34.44-35.25 Mb and Chr02A1:28.35-28.54 Mb regions are significantly associated with potato tuber shape, and that three candidate genes that might be related to potato tuber traits, PLATZ transcription factor, UTP-glucose-1-phosphate uridylyltransferase and FAR1 DNA-binding domain, are in the association region of Chr02A1. GWAS analysis identified 53 significant SNP loci at Chr05A2: 49.644-50.146 Mb and Chr06A2: 25.866-26.384 Mb regions with robust associations with potato tuber eye depth. Hydrolase and methyltransferases are present in the association region of Chr05A2, and three CYPs are present in the association region of Chr06A2. Our findings suggested that these genes are closely associated with potato tuber shape and eye depth. Our study identified molecular markers and candidate genes for improving tetraploid potato tuber shape and eye depth and provided ideas and insights for tetraploid potato breeding.

Portable Diffuse Reflectance Spectroscopy of Potato Leaves for Pre-Symptomatic Detection of Late Blight Disease.

We report on the use of leaf diffuse reflectance spectroscopy for plant disease detection. A smartphone-operated, compact diffused reflectance spectrophotometer is used for field collection of leaf diffuse reflectance spectra to enable pre-symptomatic detection of the progression of potato late blight disease post inoculation with oomycete pathogen Phytophthora infestans. Neural-network-based analysis predicts infection with >96% accuracy, only 24 h after inoculation with the pathogen, and nine days before visual late blight symptoms appear. Our study demonstrates the potential of using portable optical spectroscopy in tandem with machine learning analysis for early diagnosis of plant diseases.

The autotetraploid potato genome provides insights into highly heterozygous species.

Potato (Solanum tuberosum L.) originated in the Andes and evolved its vegetative propagation strategy through short day-dependent tuber development. Herein, we present a high-quality, chromosome-scale reference genome sequence of a tetraploid potato cultivar. The total length of this genome assembly was 2.67 Gb, with scaffold N50 and contig N50 sizes of 46.24 and 2.19 Mb, respectively. In total, 1.69 Gb repetitive sequences were obtained through de novo annotation, and long terminal repeats were the main transposable elements. A total of 126 070 protein-coding genes were annotated, of which 125 077 (99.21%) were located on chromosomes. The 48 chromosomes were classified into four haplotypes. We annotated 31 506 homologous genes, including 5913 (18.77%) genes with four homologues, 11 103 (35.24%) with three homologues, 12 177 (38.65%) with two homologues and 2313 (7.34%) with one homologue. MLH3, MSH6/7 and RFC3, which are the genes involved in the mismatch repair pathway, were found to be significantly expanded in the tetraploid potato genome relative to the diploid potato genome. Genome-wide association analysis revealed that cytochrome P450, flavonoid synthesis, chalcone enzyme, glycosyl hydrolase and glycosyl transferase genes were significantly correlated with the flesh colours of potato tuber in 150 tetraploid potatoes. This study provides valuable insights into the highly heterozygous autotetraploid potato genome and may facilitate the development of tools for potato cultivar breeding and further studies on autotetraploid crops.

Feature Compression Applications of Genetic Algorithm.

With the rapid development of molecular breeding technology and many new varieties breeding, a method is urgently needed to identify different varieties accurately and quickly. Using this method can not only help farmers feel convenient and efficient in the normal cultivation and breeding process but also protect the interests of breeders, producers and users. In this study, single nucleotide polymorphism (SNP) data of 533 Oryza sativa, 284 Solanum tuberosum and 247 Sus scrofa and 544 Manihot esculenta Crantz were used. The original SNPs were filtered and screened to remove the SNPs with deletion number more than 1% or the homozygous genotype 0/0 and 1/1 number less than 2. The correlation between SNPs were calculated, and the two adjacent SNPs with correlation R2 > 0.95 were retained. The genetic algorithm program was developed to convert the genotype format and randomly combine SNPs to calculate a set of a small number of SNPs which could distinguish all varieties in different species as fingerprint data, using Matlab platform. The successful construction of three sets of fingerprints showed that the method developed in this study was effective in animals and plants. The population structure analysis showed that the genetic algorithm could effectively obtain the core SNPs for constructing fingerprints, and the fingerprint was practical and effective. At present, the two-dimensional code of Manihot esculenta Crantz fingerprint obtained by this method has been applied to field planting. This study provides a novel idea for the Oryza sativa, Solanum tuberosum, Sus scrofa and Manihot esculenta Crantz identification of various species, lays foundation for the cultivation and identification of new varieties, and provides theoretical significance for many other species fingerprints construction.

Citrate-based fluorometric sensor for multi-halide sensing.

Halides play important roles in human health and environmental monitoring. However, different halides interfere with each other in current measurement methods. Simultaneous sensing of multiple halides in a fast and low-cost manner remains a challenge. Here, we report a fluorometric multi-halide sensing method by using a single citrate-based fluorophore, CA-Cys, on a custom-made portable device. The fluorescence emitted by CA-Cys is quenched due to the dynamic quenching of halide ions; the sensitivities vary from halide types and pH, providing the capability to obtain multiple Stern-Volmer equations at various pH values. The concentration of each halide can then be obtained by solving the resultant set of equations. A mM scale detection limit is demonstrated, which is suitable for halide wastewater monitoring. A proof-of-concept smartphone-based portable device is also fabricated and tested. The results from the fluorometer and portable device indicated that our multi-halide system is promising for real-world multi-halide sensing applications. This work represents a new direction in developing portable, low-cost, and simultaneous multi-halide sensing technologies.

Polymeric biomaterials for biophotonic applications.

With the growing importance of optical techniques in medical diagnosis and treatment, there exists a pressing need to develop and optimize materials platform for biophotonic applications. Particularly, the design of biocompatible and biodegradable materials with desired optical, mechanical, chemical, and biological properties is required to enable clinically relevant biophotonic devices for translating in vitro optical techniques into in situ and in vivo use. This technological trend propels the development of natural and synthetic polymeric biomaterials to replace traditional brittle, nondegradable silica glass based optical materials. In this review, we present an overview of the advances in polymeric optical material development, optical device design and fabrication techniques, and the accompanying applications to imaging, sensing and phototherapy.

Controlling Disorder by Electric-Field-Directed Reconfiguration of Nanowires To Tune Random Lasing.

Top-down fabrication is commonly used to provide positioning control of optical structures; yet, it places stringent limitations on component materials, and oftentimes, dynamic reconfigurability is challenging to realize. Here, we present a reconfigurable nanoparticle platform that can integrate heterogeneous particle assembly of different shapes, sizes, and chemical compositions. We demonstrate dynamic control of disorder in this platform and use it to tune random laser emission characteristics for a suspension of titanium dioxide nanowires in a dye solution. Using an alternating current electric field, we control the nanowire orientation to dynamically engineer the collective scattering of the sample. Our theoretical model indicates that a change of up to 22% in scattering coefficient can be achieved for the experimentally determined nanowire length distribution upon alignment. Dependence of light confinement on anisotropic particle alignment provides a means to reversibly tune random laser characteristics; a nearly 20-fold increase in lasing intensity was observed with aligned particle orientation. We illustrate the generality of the approach by demonstrating enhanced lasing for aligned nanowires of other materials including gold, mixed gold/dielectric, and vanadium oxide.

Smartphone based optical spectrometer for diffusive reflectance spectroscopic measurement of hemoglobin.

We report a miniature, visible to near infrared G-Fresnel spectrometer that contains a complete spectrograph system, including the detection hardware and connects with a smartphone through a microUSB port for operational control. The smartphone spectrometer is able to achieve a resolution of ~5 nm in a wavelength range from 400 nm to 1000 nm. We further developed a diffuse reflectance spectroscopy system using the smartphone spectrometer and demonstrated the capability of hemoglobin measurement. Proof of concept studies of tissue phantoms yielded a mean error of 9.2% on hemoglobin concentration measurement, comparable to that obtained with a commercial benchtop spectrometer. The smartphone G-Fresnel spectrometer and the diffuse reflectance spectroscopy system can potentially enable new point-of-care opportunities, such as cancer screening.

Flexible biodegradable citrate-based polymeric step-index optical fiber.

Implanting fiber optical waveguides into tissue or organs for light delivery and collection is among the most effective ways to overcome the issue of tissue turbidity, a long-standing obstacle for biomedical optical technologies. Here, we report a citrate-based material platform with engineerable opto-mechano-biological properties and demonstrate a new type of biodegradable, biocompatible, and low-loss step-index optical fiber for organ-scale light delivery and collection. By leveraging the rich designability and processibility of citrate-based biodegradable polymers, two exemplary biodegradable elastomers with a fine refractive index difference and yet matched mechanical properties and biodegradation profiles were developed. Furthermore, we developed a two-step fabrication method to fabricate flexible and low-loss (0.4 db/cm) optical fibers, and performed systematic characterizations to study optical, spectroscopic, mechanical, and biodegradable properties. In addition, we demonstrated the proof of concept of image transmission through the citrate-based polymeric optical fibers and conducted in vivo deep tissue light delivery and fluorescence sensing in a Sprague-Dawley (SD) rat, laying the groundwork for realizing future implantable devices for long-term implantation where deep-tissue light delivery, sensing and imaging are desired, such as cell, tissue, and scaffold imaging in regenerative medicine and in vivo optogenetic stimulation.

A smartphone-based chloridometer for point-of-care diagnostics of cystic fibrosis.

Chloride in sweat is an important diagnostic marker for cystic fibrosis (CF), but the implementation of point-of-care systems for diagnosis is hindered by the prohibitive costs of existing chloride sensors. To enable low cost diagnostic solutions, we recently established a citrate-derived synthesis platform for the development of new fluorescence sensors with high selectivity for chloride. As a next step, we herein designed a smartphone operated chloridometer that optimizes the analytical performance of the citrate-derived sensor materials for the detection of chloride in sweat. The sensor material demonstrated a wide linear range of 0.8-200mM chloride and a diffusion-limited response time; sweat chloride levels corresponded to measurable changes in fluorescence emission that was captured by a smartphone. Clinical validation was performed with sweat from individuals with and without CF, demonstrating convenient sweat diagnostics with reliable detection of cystic fibrosis. To our knowledge, this is the first clinical study of a smartphone-based chloride sensor, paving the way for point-of-care diagnostic systems for CF.

Divided pulse soliton self-frequency shift: a multi-color, dual-polarization, power-scalable, broadly tunable optical source.

A versatile, broadly tunable, power scalable, multi-line, ultrafast source is presented, the operation of which is based on combining principles of pulse division with the phenomenon of the soliton self-frequency shift (SSFS). Interferometric pulse recombination is demonstrated showing that the source can decouple the generally limiting relationship between the output power and the center wavelength in SSFS-based optical sources. Broadly tunable two- and four-color soliton self-frequency shifted pulses are experimentally demonstrated. Simultaneous dual-polarization second-harmonic generation was performed with the source, demonstrating one novel imaging methodology that the source can enable. It is expected that this source architecture will be useful for advancing current nonlinear optical imaging methodologies.

G-Fresnel smartphone spectrometer.

We report a smartphone spectrometer with nanometer resolution working in the visible range. A G-Fresnel device with the dual functionality of focusing and dispersion is used to enable miniaturization. Proof of principle application to Bradford assay of protein concentration is also demonstrated.