Pan-transcriptomic analysis reveals alternative splicing control of cold tolerance in rice.

Plants have evolved complex mechanisms to adapt to harsh environmental conditions. Rice (Oryza sativa) is a staple food crop that is sensitive to low temperatures. However, its cold stress responses remain poorly understood, thus limiting possibilities for crop engineering to achieve greater cold tolerance. In this study, we constructed a rice pan-transcriptome and characterized its transcriptional regulatory landscape in response to cold stress. We performed Iso-Seq and RNA-Seq of 11 rice cultivars subjected to a time-course cold treatment. Our analyses revealed that alternative splicing-regulated gene expression plays a significant role in the cold stress response. Moreover, we identified CATALASE C (OsCATC) and Os03g0701200 as candidate genes for engineering enhanced cold tolerance. Importantly, we uncovered central roles for the 2 serine-arginine-rich proteins OsRS33 and OsRS2Z38 in cold tolerance. Our analysis of cold tolerance and resequencing data from a diverse collection of 165 rice cultivars suggested that OsRS2Z38 may be a key selection gene in japonica domestication for cold adaptation, associated with the adaptive evolution of rice. This study systematically investigated the distribution, dynamic changes, and regulatory mechanisms of alternative splicing in rice under cold stress. Overall, our work generates a rich resource with broad implications for understanding the genetic basis of cold response mechanisms in plants.

Integrative multiomics profiling of passion fruit reveals the genetic basis for fruit color and aroma.

Passion fruit (Passiflora edulis) possesses a complex aroma and is widely grown in tropical and subtropical areas. Here, we conducted the de novo assembly, annotation, and comparison of PPF (P. edulis Sims) and YPF (P. edulis f. flavicarpa) reference genomes using PacBio, Illumina, and Hi-C technologies. Notably, we discovered evidence of recent whole-genome duplication events in P. edulis genomes. Comparative analysis revealed 7.6∼8.1 million single nucleotide polymorphisms, 1 million insertions/deletions, and over 142 Mb presence/absence variations among different P. edulis genomes. During the ripening of yellow passion fruit, metabolites related to flavor, aroma, and color were substantially accumulated or changed. Through joint analysis of genomic variations, differentially expressed genes, and accumulated metabolites, we explored candidate genes associated with flavor, aroma, and color distinctions. Flavonoid biosynthesis pathways, anthocyanin biosynthesis pathways, and related metabolites are pivotal factors affecting the coloration of passion fruit, and terpenoid metabolites accumulated more in PPF. Finally, by heterologous expression in yeast (Saccharomyces cerevisiae), we functionally characterized 12 terpene synthases. Our findings revealed that certain TPS homologs in both YPF and PPF varieties produce identical terpene products, while others yield distinct compounds or even lose their functionality. These discoveries revealed the genetic and metabolic basis of unique characteristics in aroma and flavor between the 2 passion fruit varieties. This study provides resources for better understanding the genome architecture and accelerating genetic improvement of passion fruits.

HUSCH: an integrated single-cell transcriptome atlas for human tissue gene expression visualization and analyses.

Understanding gene expression patterns across different human cell types is crucial for investigating mechanisms of cell type differentiation, disease occurrence and progression. The recent development of single-cell RNA-seq (scRNA-seq) technologies significantly boosted the characterization of cell type heterogeneities in different human tissues. However, the huge number of datasets in the public domain also posed challenges in data integration and reuse. We present Human Universal Single Cell Hub (HUSCH, http://husch.comp-genomics.org), an atlas-scale curated database that integrates single-cell transcriptomic profiles of nearly 3 million cells from 185 high-quality human scRNA-seq datasets from 45 different tissues. All the data in HUSCH were uniformly processed and annotated with a standard workflow. In the single dataset module, HUSCH provides interactive gene expression visualization, differentially expressed genes, functional analyses, transcription regulators and cell-cell interaction analyses for each cell type cluster. Besides, HUSCH integrated different datasets in the single tissue module and performs data integration, batch correction, and cell type harmonization. This allows a comprehensive visualization and analysis of gene expression within each tissue based on single-cell datasets from multiple sources and platforms. HUSCH is a flexible and comprehensive data portal that enables searching, visualizing, analyzing, and downloading single-cell gene expression for the human tissue atlas.

Oryza glumaepatula: A wild relative to improve drought tolerance in cultivated rice.

Developing drought-resistant rice (Oryza sativa, L.) is essential for improving field productivity, especially in rain-fed areas affected by climate change. Wild relatives of rice are potential sources for drought-resistant traits. Therefore, we compared root growth and drought response among 22 wild Oryza species, from which Oryza glumaepatula was selected as a promising source for further exploration. A geographically diverse panel of 69 O. glumaepatula accessions was then screened for drought stress-related traits, and 6 of these accessions showed lower shoot dry weight (SDW) reduction, greater percentage of deep roots, and lower stomatal density (STO) under drought than the drought tolerant O. sativa variety, Sahbhagi dhan. Based on whole-genome resequencing of all 69 O. glumaepatula accessions and variant calling to a high-quality O. glumaepatula reference genome, we detected multiple genomic loci colocating for SDW, root dry weight at 30 to 45 cm depth, and STO in consecutive drought trials. Geo-referencing indicated that the potential drought donors originated in flood-prone locations, corroborating previous hypotheses about the coexistence of flood and drought tolerance within individual Oryza genomes. These findings present potential donor accessions, traits, and genomic loci from an AA genome wild relative of rice that, together with the recently developed reference genome, may be useful for further introgression of drought tolerance into the O. sativa backgrounds.

Broadband continuous-wave differential absorption lidar for atmospheric remote sensing of water vapor.

What we believe to be a novel low-cost broadband continuous-wave water vapor differential absorption lidar (CW-DIAL) technique has been proposed and implemented by combing the Scheimpflug principle and the differential absorption method. The broadband CW-DIAL technique utilizes an 830-nm high-power multimode laser diode with 3-W output power as a tunable light source and a CMOS image sensor tilted at 45° as the detector. A retrieval algorithm dedicated for the broadband CW-DIAL technique has been developed to obtain range-resolved water vapor concentration from the DIAL signal. Atmospheric remote sensing of water vapor has been carried out on a near-horizontal water vapor path to validate the performance of the broadband CW-DIAL system. The retrieved water vapor concentration showed a good consistency with those measured by an air quality monitoring station, with a correlation coefficient of 0.9669. The fitting error of the water vapor concentration is found to be less than 10%. Numerical simulation studies have revealed that the aerosol-induced error on the water vapor concentration is below 5% with a background water vapor concentration of 5 g/m3 for most atmospheric conditions. The experimental results have successfully demonstrated the feasibility of the present broadband CW-DIAL technique for range-resolved water vapor remote sensing.

Graph-based pan-genomes: increased opportunities in plant genomics.

Due to the development of sequencing technology and the great reduction in sequencing costs, an increasing number of plant genomes have been assembled, and numerous genomes have revealed large amounts of variations. However, a single reference genome does not allow the exploration of species diversity, and therefore the concept of pan-genome was developed. A pan-genome is a collection of all sequences available for a species, including a large number of consensus sequences, large structural variations, and small variations including single nucleotide polymorphisms and insertions/deletions. A simple linear pan-genome does not allow these structural variations to be intuitively characterized, so graph-based pan-genomes have been developed. These pan-genomes store sequence and structural variation information in the form of nodes and paths to store and display species variation information in a more intuitive manner. The key role of graph-based pan-genomes is to expand the coordinate system of the linear reference genome to accommodate more regions of genetic diversity. Here, we review the origin and development of graph-based pan-genomes, explore their application in plant research, and further highlight the application of graph-based pan-genomes for future plant breeding.

Extracellular vesicle-derived LINC00511 promotes glycolysis and mitochondrial oxidative phosphorylation of pancreatic cancer through macrophage polarization by microRNA-193a-3p-dependent regulation of plasminogen activator urokinase.

OBJECTIVE: The involvement of tumor-derived extracellular vesicles (EVs) in macrophage polarization has been reported. In our present study, we tried to discuss the regulatory role of LINC00511 encapsulated in pancreatic cancer (PCa) cell-derived EVs in the development and progression of PCa. METHODS: EVs from PCa cell line BxPC-3 culture medium were collected and subsequently identified by electron microscopy and nanoparticle tracking analysis. The expression pattern of LINC00511 in PCa cell-derived EVs was determined. The interaction among LINC00511, microRNA-193a-3p, and plasminogen activator urokinase (PLAU) was explored. After co-culture of PCa cell-derived EVs with macrophages, the regulatory roles of LINC00511 in macrophage polarization, PCa cell functions, glucose consumption, lactate production, glycolysis, and mitochondrial oxidative phosphorylation were investigated. RESULTS: PCa cell line BxPC-3 had highly expressed LINC00511 and LINC00511 could be internalized by macrophages. LINC00511 affected macrophage polarization through miR-193a-3p-dependent regulation of PLAU expression. Besides, EV-derived LINC00511 accelerated glycolysis and promoted mitochondrial oxidative phosphorylation of PCa cells through macrophage polarization, thus inducing invasion and migration of PCa cells. CONCLUSION: LINC00511 encapsulated in PCa cell-derived EVs facilitates glycolysis of PCa cells through regulation of macrophage polarization in the tumor microenvironment.

Oil plant genomes: current state of the science.

Vegetable oils are an indispensable nutritional component of the human diet as well as important raw materials for a variety of industrial applications such as pharmaceuticals, cosmetics, oleochemicals, and biofuels. Oil plant genomes are highly diverse, and their genetic variation leads to a diversity in oil biosynthesis and accumulation along with agronomic traits. This review discusses plant oil biosynthetic pathways, current state of genome assembly, polyploidy and asymmetric evolution of genomes of oil plants and their wild relatives, and research progress of pan-genomics in oil plants. The availability of complete high-resolution genomes and pan-genomes has enabled the identification of structural variations in the genomes that are associated with the diversity of agronomic and environment fitness traits. These and future genomes also provide powerful tools to understand crop evolution and to harvest the rich natural variations to improve oil crops for enhanced productivity, oil quality, and adaptability to changing environments.

Structure and Physical Properties of the Layered Titanium-Based Pnictide Oxides (EuF)2Ti2Pn2O (Pn = Sb, Bi).

We report two novel titanium-based pnictide oxide compounds (EuF)2Ti2Pn2O (Pn = Sb, Bi), which are synthesized by replacing Sr2+ in (SrF)2Ti2Pn2O [Liu, R. H. Structure and Physical Properties of the Layered Pnictide-Oxides: (SrF)2Ti2Pn2O (Pn = As, Sb) and (SmO)2Ti2Sb2O. Chem. Mater. 2010, 22, 1503-1508] with Eu2+ using a solid-state reaction. (EuF)2Ti2Sb2O exhibits an obvious anomaly in resistivity and heat capacity at T ∼ 195 K, which may arise from the spin-density wave/charge-density wave instability. Similar features are also observed in BaTi2Pn2O, (SrF)2Ti2Pn2O, and Na2Ti2Pn2O (Pn = As and Sb) [Liu, R. H. Structure and Physical Properties of the Layered Pnictide-Oxides: (SrF)2Ti2Pn2O (Pn = As, Sb) and (SmO)2Ti2Sb2O. Chem. Mater. 2010, 22, 1503-1508, Ozawa, T. C. Chemistry of layered d-metal pnictide oxides and their potential as candidates for new superconductors. Sci. Technol. Adv. Mater. 2008, 9, 033003, Wang, X. F. Structure and physical properties for a new layered pnictide-oxide: BaTi2As2O. J. Phys.: Condens. Matter. 2010, 22, 075702, and Xu, H. C. Electronic structure of the BaTi2As2O parent compound of the titanium-based oxypnictide superconductor. Phys. Rev. B 2014, 89, 155108]. Magnetic susceptibility measurements indicate an antiferromagnetic transition at T ∼ 2.5 K for (EuF)2Ti2Sb2O. In particular, the electronic specific heat coefficients of both (EuF)2Ti2Sb2O and (EuF)2Ti2Bi2O are significantly enhanced compared to those of (SrF)2Ti2Pn2O, Na2Ti2Pn2O, and BaTi2Pn2O,1,5,6 which may be due to a strong electron correlation effect in this system. Thus, (EuF)2Ti2Pn2O (Pn = Sb, Bi) may provide new platforms for studying density wave, magnetic ordering, and electron correlation effects.

Patterns of genome-wide allele-specific expression in hybrid rice and the implications on the genetic basis of heterosis.

Utilization of heterosis has greatly increased the productivity of many crops worldwide. Although tremendous progress has been made in characterizing the genetic basis of heterosis using genomic technologies, molecular mechanisms underlying the genetic components are much less understood. Allele-specific expression (ASE), or imbalance between the expression levels of two parental alleles in the hybrid, has been suggested as a mechanism of heterosis. Here, we performed a genome-wide analysis of ASE by comparing the read ratios of the parental alleles in RNA-sequencing data of an elite rice hybrid and its parents using three tissues from plants grown under four conditions. The analysis identified a total of 3,270 genes showing ASE (ASEGs) in various ways, which can be classified into two patterns: consistent ASEGs such that the ASE was biased toward one parental allele in all tissues/conditions, and inconsistent ASEGs such that ASE was found in some but not all tissues/conditions, including direction-shifting ASEGs in which the ASE was biased toward one parental allele in some tissues/conditions while toward the other parental allele in other tissues/conditions. The results suggested that these patterns may have distinct implications in the genetic basis of heterosis: The consistent ASEGs may cause partial to full dominance effects on the traits that they regulate, and direction-shifting ASEGs may cause overdominance. We also showed that ASEGs were significantly enriched in genomic regions that were differentially selected during rice breeding. These ASEGs provide an index of the genes for future pursuit of the genetic and molecular mechanism of heterosis.

Zn and Ag Doping on Hydroxyapatite: Influence on the Adhesion Strength of High-Molecular Polymer Polycaprolactone.

In this study, density functional theory was employed to calculate the adsorption of polycaprolactone (PCL) by pure hydroxyapatite (HA), Zn-doped HA, and Ag-doped HA, and the interaction of PCL on the surface of HA (001) was simulated. The results show that there was significant electron transfer between the carbonyl O in PCL and the Zn, Ag, and Ca in HA, forming coordinate bonds. The binding energies of Ag-doped HA/PCL and Zn-doped HA/PCL were much higher than those of HA/PCL. HA doped with Ag had the highest binding energy to PCL. Therefore, we believe that when HA is doped with Ag atoms, its adsorption capacity for PCL can be increased. The results obtained in this study can be used as a guide for the development of HA/PCL bone graft composite material doped with appropriate metal ions to improve its adsorption capacity.

Long-read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant.

Genome structural variation (SV) contributes strongly to trait variation in eukaryotic species and may have an even higher functional significance than single-nucleotide polymorphism (SNP). In recent years, there have been a number of studies associating large chromosomal scale SV ranging from hundreds of kilobases all the way up to a few megabases to key agronomic traits in plant genomes. However, there have been little or no efforts towards cataloguing small- (30-10 000 bp) to mid-scale (10 000-30 000 bp) SV and their impact on evolution and adaptation-related traits in plants. This might be attributed to complex and highly duplicated nature of plant genomes, which makes them difficult to assess using high-throughput genome screening methods. Here, we describe how long-read sequencing technologies can overcome this problem, revealing a surprisingly high level of widespread, small- to mid-scale SV in a major allopolyploid crop species, Brassica napus. We found that up to 10% of all genes were affected by small- to mid-scale SV events. Nearly half of these SV events ranged between 100 bp and 1000 bp, which makes them challenging to detect using short-read Illumina sequencing. Examples demonstrating the contribution of such SV towards eco-geographical adaptation and disease resistance in oilseed rape suggest that revisiting complex plant genomes using medium-coverage long-read sequencing might reveal unexpected levels of functional gene variation, with major implications for trait regulation and crop improvement.

Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63.

Asian cultivated rice consists of two subspecies: Oryza sativa subsp. indica and O. sativa subsp. japonica Despite the fact that indica rice accounts for over 70% of total rice production worldwide and is genetically much more diverse, a high-quality reference genome for indica rice has yet to be published. We conducted map-based sequencing of two indica rice lines, Zhenshan 97 (ZS97) and Minghui 63 (MH63), which represent the two major varietal groups of the indica subspecies and are the parents of an elite Chinese hybrid. The genome sequences were assembled into 237 (ZS97) and 181 (MH63) contigs, with an accuracy >99.99%, and covered 90.6% and 93.2% of their estimated genome sizes. Comparative analyses of these two indica genomes uncovered surprising structural differences, especially with respect to inversions, translocations, presence/absence variations, and segmental duplications. Approximately 42% of nontransposable element related genes were identical between the two genomes. Transcriptome analysis of three tissues showed that 1,059-2,217 more genes were expressed in the hybrid than in the parents and that the expressed genes in the hybrid were much more diverse due to their divergence between the parental genomes. The public availability of two high-quality reference genomes for the indica subspecies of rice will have large-ranging implications for plant biology and crop genetic improvement.

Direct atomic fabrication and dopant positioning in Si using electron beams with active real-time image-based feedback.

Semiconductor fabrication is a mainstay of modern civilization, enabling the myriad applications and technologies that underpin everyday life. However, while sub-10 nanometer devices are already entering the mainstream, the end of the Moore's law roadmap still lacks tools capable of bulk semiconductor fabrication on sub-nanometer and atomic levels, with probe-based manipulation being explored as the only known pathway. Here we demonstrate that the atomic-sized focused beam of a scanning transmission electron microscope can be used to manipulate semiconductors such as Si on the atomic level, inducing growth of crystalline Si from the amorphous phase, reentrant amorphization, milling, and dopant front motion. These phenomena are visualized in real-time with atomic resolution. We further implement active feedback control based on real-time image analytics to automatically control the e-beam motion, enabling shape control and providing a pathway for atom-by-atom correction of fabricated structures in the near future. These observations open a new epoch for atom-by-atom manufacturing in bulk, the long-held dream of nanotechnology.

Enhanced Photocatalytic Degradation of Rhodamine B Dye by Iron-Doped Europium Oxide Nanoparticles.

As a wide-bandgap rare-earth oxide, Eu2O3 was often utilized as an auxiliary material of other photocatalysts because its photocatalytic performance was limited by the luminescence characteristics of Eu3+ and low light utilization. In this study, we improved the photocatalytic degradation performance of the Eu2O3 nanoparticles by doping with Fe cations. The Eu2O3 nanoparticles with different Fe-doping concentrations (1, 3, and 5%, noted as EF1.0, EF3.0, and EF5.0, respectively) were synthesized via chemical precipitation and calcination methods. It was found that doping could reduce Eu2O3's bandgap, which probably originated from the introduction of oxygen vacancies with lower energy levels than the conduction band of Eu2O3. Compared with the undoped Eu2O3 nanoparticles with a removal efficiency of 22% for degrading rhodamine B dye within 60 min, the photocatalytic degradation efficiencies of EF1.0, EF3.0, and EF5.0 were demonstrated to be improved to 42, 48, and 33%, respectively, and EF3.0's performance was the best. The enhanced photocatalytic performance of the doped samples was related to the oxygen vacancies acting as capture centers for electrons, such that the photogenerated electron-hole pairs were efficiently separated and the redox reactions on the surface of the nanoparticles were enhanced accordingly. Additionally, the enhanced light absorption and broadened spectral band further improved EF3.0's degradation efficiency.

Visible-Light Self-Powered Photodetector with High Sensitivity Based on the Type-II Heterostructure of CdPSe3/MoS2.

Transition metal thiophosphates (MTPs) are a group of emerging van der Waals materials with widely tunable band gaps. In the MTP family, CdPSe3 is demonstrated to possess a wide energy band gap and high carrier mobility, making it a potential candidate in optoelectronic applications. Here, we reported photoelectric response behaviors of both CdPSe3- and CdPSe3/MoS2-based photodetectors (noted as CPS and CM, respectively); these showed prominent photoelectric performances, and the latter proved to be significantly superior to the former. These devices exhibited ultralow dark current at a magnitude order of 10-12 A and fine cycle and air stabilities. Compared with CPS, CM demonstrated the highest responsivity (91.12 mA/W) and detectivity (1.74 × 1011 Jones) at 5 V under 425 nm light illumination. Besides, CM showed self-powered photoelectric responses at zero bias, which was attributed to the improved separation efficiency of photogenerated carriers by the built-in electric field at the interface of the p-n junction. This work proves a prospect for the CM device in portable, self-powered optoelectronic device applications.

High-integrity Pueraria montana var. lobata genome and population analysis revealed the genetic diversity of Pueraria genus.

Pueraria montana var. lobata (P. lobata) is a traditional medicinal plant belonging to the Pueraria genus of Fabaceae family. Pueraria montana var. thomsonii (P. thomsonii) and Pueraria montana var. montana (P. montana) are its related species. However, evolutionary history of the Pueraria genus is still largely unknown. Here, a high-integrity, chromosome-level genome of P. lobata and an improved genome of P. thomsonii were reported. It found evidence for an ancient whole-genome triplication and a recent whole-genome duplication shared with Fabaceae in three Pueraria species. Population genomics of 121 Pueraria accessions demonstrated that P. lobata populations had substantially higher genetic diversity, and P. thomsonii was probably derived from P. lobata by domestication as a subspecies. Selection sweep analysis identified candidate genes in P. thomsonii populations associated with the synthesis of auxin and gibberellin, which potentially play a role in the expansion and starch accumulation of tubers in P. thomsonii. Overall, the findings provide new insights into the evolutionary and domestication history of the Pueraria genome and offer a valuable genomic resource for the genetic improvement of these species.

High-quality genome assemblies for two Australimusa bananas (Musa spp.) and insights into regulatory mechanisms of superior fiber properties.

Bananas (Musa spp.) are monocotyledonous plants with high genetic diversity in the Musaceae family that are cultivated mainly in tropical and subtropical countries. The fruits are a popular food, and the plants themselves have diverse uses. Four genetic groups (genomes) are thought to have contributed to current banana cultivars: Musa acuminata (A genome), Musa balbisiana (B genome), Musa schizocarpa (S genome), and species of the Australimusa section (T genome). However, the T genome has not been effectively explored. Here, we present the high-quality TT genomes of two representative accessions, Abaca (Musa textilis), with high-quality natural fiber, and Utafun (Musa troglodytarum, Fe'i group), with abundant ß-carotene. Both the Abaca and Utafun assemblies comprise 10 pseudochromosomes, and their total genome sizes are 613 Mb and 619 Mb, respectively. Comparative genome analysis revealed that the larger size of the T genome is likely attributable to rapid expansion and slow removal of transposons. Compared with those of Musa AA or BB accessions or sisal (Agava sisalana), Abaca fibers exhibit superior mechanical properties, mainly because of their thicker cell walls with a higher content of cellulose, lignin, and hemicellulose. Expression of MusaCesA cellulose synthesis genes peaks earlier in Abaca than in AA or BB accessions during plant development, potentially leading to earlier cellulose accumulation during secondary cell wall formation. The Abaca-specific expressed gene MusaMYB26, which is directly regulated by MusaMYB61, may be an important regulator that promotes precocious expression of secondary cell wall MusaCesAs. Furthermore, MusaWRKY2 and MusaNAC68, which appear to be involved in regulating expression of MusaLAC and MusaCAD, may at least partially explain the high accumulation of lignin in Abaca. This work contributes to a better understanding of banana domestication and the diverse genetic resources in the Musaceae family, thus providing resources for Musa genetic improvement.