Ectopic expression of OsWOX9A alters leaf anatomy and plant architecture in rice.

MAIN CONCLUSION: Ectopic expression of OsWOX9A induces narrow adaxially rolled rice leaves with larger bulliform cells and fewer large veins, probably through regulating the expression of auxin-related and expansin genes. The WUSCHEL-related homeobox (WOX) family plays a pivotal role in plant development by regulating genes involved in various aspects of growth and differentiation. OsWOX9A (DWT1) has been linked to tiller growth, uniform plant growth, and flower meristem activity. However, its impact on leaf growth and development in rice has not been studied. In this study, we investigated the biological role of OsWOX9A in rice growth and development using transgenic plants. Overexpression of OsWOX9A conferred narrow adaxially rolled rice leaves and altered plant architecture. These plants exhibited larger bulliform cells and fewer larger veins compared to wild-type plants. OsWOX9A overexpression also reduced plant height, tiller number, and seed-setting rate. Comparative transcriptome analysis revealed several differentially expressed auxin-related and expansin genes in OsWOX9A overexpressing plants, consistent with their roles in leaf and plant development. These results indicate that the ectopic expression of OsWOX9A may have multiple effects on the development and growth of rice, providing a more comprehensive picture of how the WOX9 subfamily contributes to leaf development and plant architecture.

Spatiotemporal transcriptomic landscape of rice embryonic cells during seed germination.

Characterizing cellular features during seed germination is crucial for understanding the complex biological functions of different embryonic cells in regulating seed vigor and seedling establishment. We performed spatially enhanced resolution omics sequencing (Stereo-seq) and single-cell RNA sequencing (scRNA-seq) to capture spatially resolved single-cell transcriptomes of germinating rice embryos. An automated cell-segmentation model, employing deep learning, was developed to accommodate the analysis requirements. The spatial transcriptomes of 6, 24, 36, and 48 h after imbibition unveiled both known and previously unreported embryo cell types, including two unreported scutellum cell types, corroborated by in situ hybridization and functional exploration of marker genes. Temporal transcriptomic profiling delineated gene expression dynamics in distinct embryonic cell types during seed germination, highlighting key genes involved in nutrient metabolism, biosynthesis, and signaling of phytohormones, reprogrammed in a cell-type-specific manner. Our study provides a detailed spatiotemporal transcriptome of rice embryo and presents a previously undescribed methodology for exploring the roles of different embryonic cells in seed germination.

Current status of community resources and priorities for weed genomics research.

Weeds are attractive models for basic and applied research due to their impacts on agricultural systems and capacity to swiftly adapt in response to anthropogenic selection pressures. Currently, a lack of genomic information precludes research to elucidate the genetic basis of rapid adaptation for important traits like herbicide resistance and stress tolerance and the effect of evolutionary mechanisms on wild populations. The International Weed Genomics Consortium is a collaborative group of scientists focused on developing genomic resources to impact research into sustainable, effective weed control methods and to provide insights about stress tolerance and adaptation to assist crop breeding.

High-throughput single-microbe RNA sequencing reveals adaptive state heterogeneity and host-phage activity associations in human gut microbiome.

Microbial communities such as those residing in the human gut are highly diverse and complex, and many with important implications in health and diseases. The effects and functions of these microbial communities are determined not only by their species compositions and diversities but also by the dynamic intra- and inter-cellular states at the transcriptional level. Powerful and scalable technologies capable of acquiring single-microbe-resolution RNA sequencing information in order to achieve comprehensive understanding of complex microbial communities together with their hosts is therefore utterly needed. Here we report the development and utilization of a droplet-based smRNA-seq (single-microbe RNA sequencing) method capable of identifying large species varieties in human samples, which we name smRandom-seq2. Together with a triple-module computational pipeline designed for the bacteria and bacteriophage sequencing data by smRandom-seq2 in four human gut samples, we established a single-cell level bacterial transcriptional landscape of human gut microbiome, which included 29,742 single microbes and 329 unique species. Distinct adaptive responses states among species in Prevotella and Roseburia genus and intrinsic adaptive strategy heterogeneity in Phascolarctobacterium succinatutens were uncovered. Additionally, we identified hundreds of novel host-phage transcriptional activity associations in the human gut microbiome. Our results indicated the smRandom-seq2 is a high-throughput and high-resolution smRNA-seq technique that is highly adaptable to complex microbial communities in real-word situations and promises new perspectives in the understanding of human microbiomes.

Technology-enabled great leap in deciphering plant genomes.

Plant genomes provide essential and vital basic resources for studying many aspects of plant biology and applications (for example, breeding). From 2000 to 2020, 1,144 genomes of 782 plant species were sequenced. In the past three years (2021-2023), 2,373 genomes of 1,031 plant species, including 793 newly sequenced species, have been assembled, representing a great leap. The 2,373 newly assembled genomes, of which 63 are telomere-to-telomere assemblies and 921 have been generated in pan-genome projects, cover the major phylogenetic clades. Substantial advances in read length, throughput, accuracy and cost-effectiveness have notably simplified the achievement of high-quality assemblies. Moreover, the development of multiple software tools using different algorithms offers the opportunity to generate more complete and complex assemblies. A database named N3: plants, genomes, technologies has been developed to accommodate the metadata associated with the 3,517 genomes that have been sequenced from 1,575 plant species since 2000. We also provide an outlook for emerging opportunities in plant genome sequencing.

A reference genome of Commelinales provides insights into the commelinids evolution and global spread of water hyacinth (Pontederia crassipes).

Commelinales belongs to the commelinids clade, which also comprises Poales that includes the most important monocot species, such as rice, wheat, and maize. No reference genome of Commelinales is currently available. Water hyacinth (Pontederia crassipes or Eichhornia crassipes), a member of Commelinales, is one of the devastating aquatic weeds, although it is also grown as an ornamental and medical plant. Here, we present a chromosome-scale reference genome of the tetraploid water hyacinth with a total length of 1.22 Gb (over 95% of the estimated size) across 8 pseudochromosome pairs. With the representative genomes, we reconstructed a phylogeny of the commelinids, which supported Zingiberales and Commelinales being sister lineages of Arecales and shed lights on the controversial relationship of the orders. We also reconstructed ancestral karyotypes of the commelinids clade and confirmed the ancient commelinids genome having 8 chromosomes but not 5 as previously reported. Gene family analysis revealed contraction of disease-resistance genes during polyploidization of water hyacinth, likely a result of fitness requirement for its role as a weed. Genetic diversity analysis using 9 water hyacinth lines from 3 continents (South America, Asia, and Europe) revealed very closely related nuclear genomes and almost identical chloroplast genomes of the materials, as well as provided clues about the global dispersal of water hyacinth. The genomic resources of P. crassipes reported here contribute a crucial missing link of the commelinids species and offer novel insights into their phylogeny.

Multidimensional assessment of the biological effects of electronic cigarettes on lung bronchial epithelial cells.

Cigarette smoke (CS) exposure is known to cause injury to respiratory tract epithelial cells and is a contributing factor in the development of chronic obstructive pulmonary disease and lung cancer. Electronic cigarettes (e-cigarettes) are gaining popularity as a potential substitute for conventional cigarettes due to their potential for aiding smoking cessation. However, the safety of e-cigarettes remains uncertain, and scientific evidence on this topic is still limited. In this study, we aimed to investigate the effects of CS and e-cigarette smoke (ECS) of different flavors on human lung bronchial epithelial cells. Real-time smoke exposure was carried out using an air-liquid interface system, and cell viability was assessed. RNA-Seq transcriptome analysis was performed to compare the differences between CS and ECS. The transcriptome analysis revealed a significantly higher number of differentially expressed genes in CS than in ECS. Moreover, the impact of mint-flavored e-cigarettes on cells was found to be greater than that of tobacco-flavored e-cigarettes, as evidenced by the greater number of differentially expressed genes. These findings provide a reference for future safety research on traditional cigarettes and e-cigarettes, particularly those of different flavors. The use of omics-scale methodologies has improved our ability to understand the biological effects of CS and ECS on human respiratory tract epithelial cells, which can aid in the development of novel approaches for smoking cessation and lung disease prevention.

Population genomic analysis unravels the evolutionary roadmap of pericarp color in rice.

Pigmented rice stands out for its nutritional value and is gaining more and more attention. Wild rice, domesticated red rice, and weedy rice all have a red pericarp and a comprehensive genetic background in terms of the red-pericarp phenotype. We performed population genetic analyses using 5104 worldwide rice accessions, including 2794 accessions with red or black pericarps, 85 of which were newly sequenced in this study. The results suggested an evolutionary trajectory of red landraces originating from wild rice, and the split times of cultivated red and white rice populations were estimated to be within the past 3500 years. Cultivated red rice was found to feralize to weedy rice, and weedy rice could be further re-domesticated to cultivated red rice. A genome-wide association study based on the 2794 accessions with pigmented pericarps revealed several new candidate genes associated with the red-pericarp trait for further functional characterization. Our results provide genomic evidence for the origin of pigmented rice and a valuable genomic resource for genetic investigation and breeding of pigmented rice.

MicroRNAs constitute an additional layer in plant response to simultaneous bio- and abiotic stresses as exemplified by UV-B radiation and flg22-treatment on Arabidopsis thaliana.

Plants are confronted with various environmental stresses and develop sophisticated adaptive mechanisms. Our previous work demonstrated that the crosstalk of flg22 and ultraviolet (UV)-B-induced signalling cascades reprograms the expression of flavonol pathway genes (FPGs), benefiting plant defence responses. Although several transcription factors have been identified to be involved in this crosstalk, the underlying mechanism is largely unclear. Here, we analyzed microRNAs (miRNAs) and identified 126, 129 and 113 miRNAs with altered abundances compared to untreated control in flg22-, UV-B- and flg22/UV-B-treated seedlings, respectively. Two distinct modules were identified: The first consists of 10 miRNAs repressed by UV-B but up-regulated by flg22, and the second with five miRNAs repressed by flg22 but up-regulated by UV-B. In Arabidopsis, the knockdown of miR858a, a representative of module I, increased the abundance of CHS (a marker gene for FPGs), whereas its overexpression reduced CHS. Conversely, knockout of miR164b from module II decreased CHS and its overexpression increased CHS transcript levels. These data suggest a decisive role of miRNAs in the crosstalk. In the next, we described the interaction between miR858a and its target MYB111 (a positive regulator of FPGs) from module I in detail. We showed that MYB111 was profoundly post-transcriptionally regulated by miR858a during the crosstalk, whose expression was specifically but antagonistically controlled by UVR8- and FLS2-mediated signallings. Moreover, transcriptional monitoring using the GUS reporter gene demonstrates that miRNA-mediated posttranscriptional regulation is the main driving force in reprogramming the expression of FPGs and regulates plant adaptation to multiple concurrent environmental stresses.

Poaceae Chloroplast Genome Sequencing: Great Leap Forward in Recent Ten Years.

The first complete chloroplast genome of rice (Oryza sativa) was published in 1989, ushering in a new era of studies of chloroplast genomics in Poaceae. Progresses in Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS) technologiesand in the development of genome assembly software, have significantly advanced chloroplast genomics research. Poaceae is one of the most targeted families in chloroplast genome research because of its agricultural, ecological, and economic importance. Over the last 30 years, 2,050 complete chloroplast genome sequences from 40 tribes and 282 genera have been generated, most (97%) of them in the recent ten years. The wealth of data provides the groundwork for studies on species evolution, phylogeny, genetic transformation, and other aspects of Poaceae chloroplast genomes. As a result, we have gained a deeper understanding of the properties of Poaceae chloroplast genomes. Here, we summarize the achievements of the studies of the Poaceae chloroplast genomes and envision the challenges for moving the area ahead.

A syntelog-based pan-genome provides insights into rice domestication and de-domestication.

BACKGROUND: Asian rice is one of the world's most widely cultivated crops. Large-scale resequencing analyses have been undertaken to explore the domestication and de-domestication genomic history of Asian rice, but the evolution of rice is still under debate. RESULTS: Here, we construct a syntelog-based rice pan-genome by integrating and merging 74 high-accuracy genomes based on long-read sequencing, encompassing all ecotypes and taxa of Oryza sativa and Oryza rufipogon. Analyses of syntelog groups illustrate subspecies divergence in gene presence-and-absence and haplotype composition and identify massive genomic regions putatively introgressed from ancient Geng/japonica to ancient Xian/indica or its wild ancestor, including almost all well-known domestication genes and a 4.5-Mbp centromere-spanning block, supporting a single domestication event in main rice subspecies. Genomic comparisons between weedy and cultivated rice highlight the contribution from wild introgression to the emergence of de-domestication syndromes in weedy rice. CONCLUSIONS: This work highlights the significance of inter-taxa introgression in shaping diversification and divergence in rice evolution and provides an exploratory attempt by utilizing the advantages of pan-genomes in evolutionary studies.

Dynamic associations between the respiratory tract and gut antibiotic resistome of patients with COVID-19 and its prediction power for disease severity.

The antibiotic resistome is the collection of all antibiotic resistance genes (ARGs) present in an individual. Whether an individual's susceptibility to infection and the eventual severity of coronavirus disease 2019 (COVID-19) is influenced by their respiratory tract antibiotic resistome is unknown. Additionally, whether a relationship exists between the respiratory tract and gut ARGs composition has not been fully explored. We recruited 66 patients with COVID-19 at three disease stages (admission, progression, and recovery) and conducted a metagenome sequencing analysis of 143 sputum and 97 fecal samples obtained from them. Respiratory tract, gut metagenomes, and peripheral blood mononuclear cell (PBMC) transcriptomes are analyzed to compare the gut and respiratory tract ARGs of intensive care unit (ICU) and non-ICU (nICU) patients and determine relationships between ARGs and immune response. Among the respiratory tract ARGs, we found that Aminoglycoside, Multidrug, and Vancomycin are increased in ICU patients compared with nICU patients. In the gut, we found that Multidrug, Vancomycin, and Fosmidomycin were increased in ICU patients. We discovered that the relative abundances of Multidrug were significantly correlated with clinical indices, and there was a significantly positive correlation between ARGs and microbiota in the respiratory tract and gut. We found that immune-related pathways in PBMC were enhanced, and they were correlated with Multidrug, Vancomycin, and Tetracycline ARGs. Based on the ARG types, we built a respiratory tract-gut ARG combined random-forest classifier to distinguish ICU COVID-19 patients from nICU patients with an AUC of 0.969. Cumulatively, our findings provide some of the first insights into the dynamic alterations of respiratory tract and gut antibiotic resistome in the progression of COVID-19 and disease severity. They also provide a better understanding of how this disease affects different cohorts of patients. As such, these findings should contribute to better diagnosis and treatment scenarios.

Asymmetric variation in DNA methylation during domestication and de-domestication of rice.

Hundreds of plant species have been domesticated to feed human civilization, while some crops have undergone de-domestication into agricultural weeds, threatening global food security. To understand the genetic and epigenetic basis of crop domestication and de-domestication, we generated DNA methylomes from 95 accessions of wild rice (Oryza rufipogon L.), cultivated rice (Oryza sativa L.) and weedy rice (O. sativa f. spontanea). We detected a significant decrease in DNA methylation over the course of rice domestication but observed an unexpected increase in DNA methylation through de-domestication. Notably, DNA methylation changes occurred in distinct genomic regions for these 2 opposite stages. Variation in DNA methylation altered the expression of nearby and distal genes through affecting chromatin accessibility, histone modifications, transcription factor binding, and the formation of chromatin loops, which may contribute to morphological changes during domestication and de-domestication of rice. These insights into population epigenomics underlying rice domestication and de-domestication provide resources and tools for epigenetic breeding and sustainable agriculture.

Weed genomics: yielding insights into the genetics of weedy traits for crop improvement.

Weeds cause tremendous economic and ecological damage worldwide. The number of genomes established for weed species has sharply increased during the recent decade, with some 26 weed species having been sequenced and de novo genomes assembled. These genomes range from 270 Mb (Barbarea vulgaris) to almost 4.4 Gb (Aegilops tauschii). Importantly, chromosome-level assemblies are now available for 17 of these 26 species, and genomic investigations on weed populations have been conducted in at least 12 species. The resulting genomic data have greatly facilitated studies of weed management and biology, especially origin and evolution. Available weed genomes have indeed revealed valuable weed-derived genetic materials for crop improvement. In this review, we summarize the recent progress made in weed genomics and provide a perspective for further exploitation in this emerging field.

High-throughput single nucleus total RNA sequencing of formalin-fixed paraffin-embedded tissues by snRandom-seq.

Formalin-fixed paraffin-embedded (FFPE) tissues constitute a vast and valuable patient material bank for clinical history and follow-up data. It is still challenging to achieve single cell/nucleus RNA (sc/snRNA) profile in FFPE tissues. Here, we develop a droplet-based snRNA sequencing technology (snRandom-seq) for FFPE tissues by capturing full-length total RNAs with random primers. snRandom-seq shows a minor doublet rate (0.3%), a much higher RNA coverage, and detects more non-coding RNAs and nascent RNAs, compared with state-of-art high-throughput scRNA-seq technologies. snRandom-seq detects a median of >3000 genes per nucleus and identifies 25 typical cell types. Moreover, we apply snRandom-seq on a clinical FFPE human liver cancer specimen and reveal an interesting subpopulation of nuclei with high proliferative activity. Our method provides a powerful snRNA-seq platform for clinical FFPE specimens and promises enormous applications in biomedical research.

Transcriptomic profiling reveals candidate allelopathic genes in rice responsible for interactions with barnyardgrass.

Echinochloa crus-galli (barnyardgrass) is one of the most damaging weeds in rice fields worldwide. Allelopathy has been considered a possible application for weed management. Thus understanding its molecular mechanisms is important for rice production. This study generated transcriptomes from rice under mono- and co-culture with barnyardgrass at two-time points to identify the candidate genes controlling allelopathic interactions between rice and barnyardgrass. A total of 5,684 differentially expressed genes (DEGs) were detected, amongst which 388 genes were transcription factors. These DEGs include genes associated with momilactone and phenolic acid biosynthesis, which play critical roles in allelopathy. Additionally, we found significantly more DEGs at 3 hours than at 3 days, suggesting a quick allelopathic response in rice. Up-regulated DEGs involve diverse biological processes, such as response to stimulus and pathways related to phenylpropanoid and secondary metabolites biosynthesis. Down-regulated DEGs were involved in developmental processes, indicating a balance between growth and stress response to allelopathy from barnyardgrass. Comparison of DEGs between rice and barnyardgrass shows few common genes, suggesting different mechanisms underlying allelopathic interaction in these two species. Our results offer an important basis for identifying of candidate genes responsible for rice and barnyardgrass interactions and contribute valuable resources for revealing its molecular mechanisms.

Proteomic and single-cell landscape reveals novel pathogenic mechanisms of HBV-infected intrahepatic cholangiocarcinoma.

Despite the epidemiological association between intrahepatic cholangiocarcinoma (ICC) and hepatitis B virus (HBV) infection, little is known about the relevant oncogenic effects. A cohort of 32 HBV-infected ICC and 89 non-HBV-ICC patients were characterized using whole-exome sequencing, proteomic analysis, and single-cell RNA sequencing. Proteomic analysis revealed decreased cell-cell junction levels in HBV-ICC patients. The cell-cell junction level had an inverse relationship with the epithelial-mesenchymal transition (EMT) program in ICC patients. Analysis of the immune landscape found that more CD8 T cells and Th2 cells were present in HBV-ICC patients. Single-cell analysis indicated that transforming growth factor beta signaling-related EMT program changes increased in tumor cells of HBV-ICC patients. Moreover, ICAM1+ tumor-associated macrophages are correlated with a poor prognosis and contributed to the EMT in HBV-ICC patients. Our findings provide new insights into the behavior of HBV-infected ICC driven by various pathogenic mechanisms involving decreased cell junction levels and increased progression of the EMT program.

Single-cell transcriptome of Nepeta tenuifolia leaves reveal differentiation trajectories in glandular trichomes.

The peltate glandular trichomes (PGTs) on Nepeta tenuifolia leaves can secrete and store bioactive essential oils. ScRNA-seq is a powerful tool for uncovering heterogeneous cells and exploring the development and differentiation of specific cells. Due to leaves rich in PGTs, the young leaves were used to isolated protoplasts and successfully captured 33,254 protoplasts for sequencing purposes. After cell type annotation, all the cells were partitioned into six broad populations with 19 clusters. Cells from PGTs were identified based on the expression patterns of trichome-specific genes, monoterpene biosynthetic genes, and metabolic analysis of PGT secretions. The developmental trajectories of PGTs were delineated by pseudotime analysis. Integrative analysis of scRNA-seq data from N. tenuifolia leaves and Arabidopsis thaliana shoot revealed that PGTs were specific to N. tenuifolia. Thus, our results provide a promising basis for exploring cell development and differentiation in plants, especially glandular trichome initiation and development.