Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape.

Structural variations (SVs) are a feature of plant genomes that has been largely unexplored despite their significant impact on plant phenotypic traits and local adaptation to abiotic and biotic stress. In this study, we employed woolly grape (Vitis retordii), a species native to the tropical and subtropical regions of East Asia with both coastal and inland habitats, as a valuable model for examining the impact of SVs on local adaptation. We assembled a haplotype-resolved chromosomal reference genome for woolly grape, and conducted population genetic analyses based on whole-genome sequencing (WGS) data from coastal and inland populations. The demographic analyses revealed recent bottlenecks in all populations and asymmetric gene flow from the inland to the coastal population. In total, 1,035 genes associated with plant adaptive regulation for salt stress, radiation, and environmental adaptation were detected underlying local selection by SVs and SNPs in the coastal population, of which 37.29% and 65.26% were detected by SVs and SNPs, respectively. Candidate genes such as FSD2, RGA1, and AAP8 associated with salt tolerance were found to be highly differentiated and selected during the process of local adaptation to coastal habitats in SV regions. Our study highlights the importance of SVs in local adaptation; candidate genes related to salt stress and climatic adaptation to tropical and subtropical environments are important genomic resources for future breeding programs of grapevine and its rootstocks.

Targeting P2Y14R protects against necroptosis of intestinal epithelial cells through PKA/CREB/RIPK1 axis in ulcerative colitis.

Purinergic signaling plays a causal role in the pathogenesis of inflammatory bowel disease. Among purinoceptors, only P2Y14R is positively correlated with inflammatory score in mucosal biopsies of ulcerative colitis patients, nevertheless, the role of P2Y14R in ulcerative colitis remains unclear. Here, based on the over-expressions of P2Y14R in the intestinal epithelium of mice with experimental colitis, we find that male mice lacking P2Y14R in intestinal epithelial cells exhibit less intestinal injury induced by dextran sulfate sodium. Mechanistically, P2Y14R deletion limits the transcriptional activity of cAMP-response element binding protein through cAMP/PKA axis, which binds to the promoter of Ripk1, inhibiting necroptosis of intestinal epithelial cells. Furthermore, we design a hierarchical strategy combining virtual screening and chemical optimization to develop a P2Y14R antagonist HDL-16, which exhibits remarkable anti-colitis effects. Summarily, our study elucidates a previously unknown mechanism whereby P2Y14R participates in ulcerative colitis, providing a promising therapeutic target for inflammatory bowel disease.

SnS/SnS2 Heterostructures Embedded in Hierarchical Porous Carbon as Polysulfides Immobilizer for High-Performance Lithium-Sulfur Batteries.

Driven by the strong adsorptive and catalytic ability of metal sulfides for soluble polysulfides, it is considered as a potential mediator to resolve the problems of shuttle effect and slow reaction kinetics of polysulfides in lithium-sulfur (Li-S) batteries. However, their further development is limited by poor electrical conductivity and bad long-term durability. Herein, one type of new catalyst composed of SnS/SnS2 heterostructures on hierarchical porous carbon (denoted as SnS/SnS2-HPC) by a simple hydrothermal method is reported and used as an interlayer coating on the conventional separator for blocking polysulfides. The SnS/SnS2-HPC integrates the advantages of a porous conductive network for promoting the transport of electrons and an enhanced electrocatalyst for accelerating polysulfides conversion. As a result, such a cell coupled with a SnS/SnS2-HPC interlayer exhibits a long-term lifespan of 1200 cycles. This work provides a new cell configuration by using heterostructures with a built-in electric field formed from a p-n heterojunction to improve the performance of Li-S batteries.

Unveiling Anoikis-related genes: A breakthrough in the prognosis of bladder cancer.

BACKGROUND: Bladder cancer (BLCA) is a prevalent malignancy worldwide. Anoikis remains a new form of cell death. It is necessary to explore Anoikis-related genes in the prognosis of BLCA. METHODS: We obtained RNA expression profiles from the The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus databases for dimensionality reduction analysis and isolated epithelial cells, T cells and fibroblasts for copy number variation analysis, pseudotime analysis and transcription factor analysis based on R package. We integrated machine-learning algorithms to develop the artificial intelligence-derived prognostic signature (AIDPS). RESULTS: The performance of AIDPS with clinical indicators was stable and robust in predicting BLCA and showed better performance in every validation dataset compared to other models. Mendelian randomization analysis was conducted. Single nucleotide polymorphism (SNP) sites of rs3100578 (HK2) and rs66467677 (HSP90B1) exhibited significant correlation of bladder problem (not cancer) and bladder cancer, whereasSNP sites of rs3100578 (HK2) and rs947939 (BAD) had correlation between bladder stone and bladder cancer. The immune infiltration analysis of the TCGA-BLCA cohort was calculated via the ESTIMATE (i.e. Estimation of STromal and Immune cells in MAlignantTumours using Expression data) algorithm which contains stromal, immune and estimate scores. We also found significant differences in the IC50 values of Bortezomib_1191, Docetaxel_1007, Staurosporine_1034 and Rapamycin_1084 among the high- and low-risk groups. CONCLUSIONS: In conclusion, these findings indicated Anoikis-related prognostic genes in BLCA and constructed an innovative machine-learning model of AIDPS with high prognostic value for BLCA.

Dysbiosis of gut microbiota and metabolites during AIDS: implications for CD4+ T cell reduction and immune activation.

OBJECTIVE: Identifying the gut microbiota associated with host immunity in the AIDS stage. DESIGN: We performed a cross-sectional study. METHODS: We recruited people living with HIV (PLWH) in the AIDS or non-AIDS stage and evaluated their gut microbiota and metabolites by using 16S ribosomal RNA (rRNA) sequencing and liquid chromatography-mass spectrometry (LC-MS). Machine learning (ML) models were used to analyze the correlations between key bacteria and CD4+ T cell count, CD4+ T cell activation, bacterial translocation, gut metabolites, and KEGG functional pathways. RESULTS: We recruited 114 PLWH in the AIDS stage and 203 PLWH in the non-AIDS stage. The α-diversity of gut microbiota was downregulated in the AIDS stage (P < 0.05). Several ML models could be used to identify key gut microbiota associated with AIDS, including the logistic regression model with area under the curve (AUC), sensitivity, specificity, and Brier scores of 0.854, 0.813, 0.813, and 0.160, respectively. The key bacteria ASV1 (Bacteroides sp.), ASV8 (Fusobacterium sp.), ASV30 (Roseburia sp.), ASV37 (Bacteroides sp.), and ASV41 (Lactobacillus sp.) decreased in the AIDS stage and were positively correlated with the CD4+ T cell count, the EndoCAb IgM level, 4-hydroxyphenylpyruvic acid abundance, and the predicted cell growth pathway were negatively correlated with the CD3+CD4+CD38+HLA-DR+ T cell count and the sCD14 level. CONCLUSIONS: ML has the potential to recognize key gut microbiota related to AIDS. The key five bacteria in the AIDS stage and their metabolites might be related to CD4+ T cell reduction and immune activation.

Human microbiota dysbiosis after SARS-CoV-2 infection have the potential to predict disease prognosis.

BACKGROUND: The studies on SARS-CoV-2 and human microbiota have yielded inconsistent results regarding microbiota α-diversity and key microbiota. To address these issues and explore the predictive ability of human microbiota for the prognosis of SARS-CoV-2 infection, we conducted a reanalysis of existing studies. METHODS: We reviewed the existing studies on SARS-CoV-2 and human microbiota in the Pubmed and Bioproject databases (from inception through October 29, 2021) and extracted the available raw 16S rRNA sequencing data of human microbiota. Firstly, we used meta-analysis and bioinformatics methods to reanalyze the raw data and evaluate the impact of SARS-CoV-2 on human microbial α-diversity. Secondly, machine learning (ML) was employed to assess the ability of microbiota to predict the prognosis of SARS-CoV-2 infection. Finally, we aimed to identify the key microbiota associated with SARS-CoV-2 infection. RESULTS: A total of 20 studies related to SARS-CoV-2 and human microbiota were included, involving gut (n = 9), respiratory (n = 11), oral (n = 3), and skin (n = 1) microbiota. Meta-analysis showed that in gut studies, when limiting factors were studies ruled out the effect of antibiotics, cross-sectional and case-control studies, Chinese studies, American studies, and Illumina MiSeq sequencing studies, SARS-CoV-2 infection was associated with down-regulation of microbiota α-diversity (P < 0.05). In respiratory studies, SARS-CoV-2 infection was associated with down-regulation of α-diversity when the limiting factor was V4 sequencing region (P < 0.05). Additionally, the α-diversity of skin microbiota was down-regulated at multiple time points following SARS-CoV-2 infection (P < 0.05). However, no significant difference in oral microbiota α-diversity was observed after SARS-CoV-2 infection. ML models based on baseline respiratory (oropharynx) microbiota profiles exhibited the ability to predict outcomes (survival and death, Random Forest, AUC = 0.847, Sensitivity = 0.833, Specificity = 0.750) after SARS-CoV-2 infection. The shared differential Prevotella and Streptococcus in the gut, respiratory tract, and oral cavity was associated with the severity and recovery of SARS-CoV-2 infection. CONCLUSIONS: SARS-CoV-2 infection was related to the down-regulation of α-diversity in the human gut and respiratory microbiota. The respiratory microbiota had the potential to predict the prognosis of individuals infected with SARS-CoV-2. Prevotella and Streptococcus might be key microbiota in SARS-CoV-2 infection.

Genome-Wide Association Study Unravels Quantitative Trait Loci and Genes Associated with Yield-Related Traits in Sugarcane.

Sugarcane, a major sugar and energy crop worldwide faces an increasing demand for higher yields. Identifying yield-related markers and candidate genes is valuable for breeding high-yield varieties using molecular techniques. In this work, seven yield-related traits were evaluated in a diversity panel of 159 genotypes, derived from Tripidium arundinaceum, Saccharum spontaneum, and modern sugarcane genotypes. All traits exhibited significant genetic variance with high heritability and high correlations. Genetic diversity analysis reveals a genomic decay of 23 kb and an average single nucleotide polymorphism (SNP) number of 25,429 per genotype. These 159 genotypes were divided into 4 subgroups. Genome-wide association analysis identified 47 SNPs associated with brix, spanning 36 quantitative trait loci (QTLs), and 138 SNPs for other traits across 104 QTLs, covering all 32 chromosomes. Interestingly, 12 stable QTLs associated with yield-related traits were identified, which contained 35 candidate genes. This work provides markers and candidate genes for marker-assisted breeding to improve sugarcane yields.

Alterations of the gut microbiota associated with the occurrence and progression of viral hepatitis.

Background: Gut microbiota is the largest population of microorganisms and is closely related to health. Many studies have explored changes in gut microbiota in viral hepatitis. However, the correlation between gut microbiota and the occurrence and progression of viral hepatitis has not been fully clarified. Methods: PubMed and BioProject databases were searched for studies about viral hepatitis disease and 16S rRNA gene sequencing of gut microbiota up to January 2023. With bioinformatics analyses, we explored changes in microbial diversity of viral hepatitis, screened out crucial bacteria and microbial functions related to viral hepatitis, and identified the potential microbial markers for predicting risks for the occurrence and progression of viral hepatitis based on ROC analysis. Results: Of the 1389 records identified, 13 studies met the inclusion criteria, with 950 individuals including 656 patient samples (HBV, n = 546; HCV, n = 86; HEV, n = 24) and 294 healthy controls. Gut microbial diversity is significantly decreased as the infection and progression of viral hepatitis. Alpha diversity and microbiota including Butyricimonas, Escherichia-Shigella, Lactobacillus, and Veillonella were identified as the potential microbial markers for predicting the risk of development of viral hepatitis (AUC>0.7). Microbial functions including tryptophan metabolism, fatty acid biosynthesis, lipopolysaccharide biosynthesis, and lipid metabolism related to the microbial community increased significantly as the development of viral hepatitis. Conclusions: This study demonstrated comprehensively the gut microbiota characteristics in viral hepatitis, screened out crucial microbial functions related to viral hepatitis, and identified the potential microbial markers for predicting the risk of viral hepatitis.

Genome-wide analysis of NBS-LRR genes revealed contribution of disease resistance from Saccharum spontaneum to modern sugarcane cultivar.

Introduction: During plant evolution, nucleotide-binding sites (NBS) and leucine-rich repeat (LRR) genes have made significant contributions to plant disease resistance. With many high-quality plant genomes sequenced, identification and comprehensive analyses of NBS-LRR genes at whole genome level are of great importance to understand and utilize them. Methods: In this study, we identified the NBS-LRR genes of 23 representative species at whole genome level, and researches on NBS-LRR genes of four monocotyledonous grass species, Saccharum spontaneum, Saccharum officinarum, Sorghum bicolor and Miscanthus sinensis, were focused. Results and discussion: We found that whole genome duplication, gene expansion, and allele loss could be factors affecting the number of NBS-LRR genes in the species, and whole genome duplication is likely to be the main cause of the number of NBS-LRR genes in sugarcane. Meanwhile, we also found a progressive trend of positive selection on NBS-LRR genes. These studies further elucidated the evolutionary pattern of NBS-LRR genes in plants. Transcriptome data from multiple sugarcane diseases revealed that more differentially expressed NBS-LRR genes were derived from S. spontaneum than from S. officinarum in modern sugarcane cultivars, and the proportion was significantly higher than the expected. This finding reveals that S. spontaneum has a greater contribution to disease resistance for modern sugarcane cultivars. In addition, we observed allelespecific expression of seven NBS-LRR genes under leaf scald, and 125 NBS-LRR genes responding to multiple diseases were identified. Finally, we built a plant NBS-LRR gene database to facilitate subsequent analysis and use of NBSLRR genes obtained here. In conclusion, this study complemented and completed the research of plant NBS-LRR genes, and discussed how NBS-LRR genes responding to sugarcane diseases, which provided a guide and genetic resources for further research and utilization of NBS-LRR genes.

Correlation of microbiomes in "plant-insect-soil" ecosystem.

Introduction: Traditional chemical control methods pose a damaging effect on farmland ecology, and their long-term use has led to the development of pest resistance. Methods: Here, we analyzed the correlations and differences in the microbiome present in the plant and soil of sugarcane cultivars exhibiting different insect resistance to investigate the role played by microbiome in crop insect resistance. We evaluated the microbiome of stems, topsoil, rhizosphere soil, and striped borers obtained from infested stems, as well as soil chemical parameters. Results and Discussion: Results showed that microbiome diversity was higher in stems of insect-resistant plants, and contrast, lower in the soil of resistant plants, with fungi being more pronounced than bacteria. The microbiome in plant stems was almost entirely derived from the soil. The microbiome of insect-susceptible plants and surrounding soil tended to change towards that of insect-resistant plants after insect damage. Insects' microbiome was mainly derived from plant stems and partly from the soil. Available potassium showed an extremely significant correlation with soil microbiome. This study validated the role played by the microbiome ecology of plant-soil-insect system in insect resistance and provided a pre-theoretical basis for crop resistance control.

Insights on Phytohormonal Crosstalk in Plant Response to Nitrogen Stress: A Focus on Plant Root Growth and Development.

Nitrogen (N) is a vital mineral component that can restrict the growth and development of plants if supplied inappropriately. In order to benefit their growth and development, plants have complex physiological and structural responses to changes in their nitrogen supply. As higher plants have multiple organs with varying functions and nutritional requirements, they coordinate their responses at the whole-plant level based on local and long-distance signaling pathways. It has been suggested that phytohormones are signaling substances in such pathways. The nitrogen signaling pathway is closely associated with phytohormones such as auxin (AUX), abscisic acid (ABA), cytokinins (CKs), ethylene (ETH), brassinosteroid (BR), strigolactones (SLs), jasmonic acid (JA), and salicylic acid (SA). Recent research has shed light on how nitrogen and phytohormones interact to modulate physiology and morphology. This review provides a summary of the research on how phytohormone signaling affects root system architecture (RSA) in response to nitrogen availability. Overall, this review contributes to identifying recent developments in the interaction between phytohormones and N, as well as serving as a foundation for further study.

The subgenome Saccharum spontaneum contributes to sugar accumulation in sugarcane as revealed by full-length transcriptomic analysis.

INTRODUCTION: Modern sugarcane cultivars (Saccharum spp. hybrids) derived from crosses between S. officinarum and S. spontaneum, with high-sugar traits and excellent stress tolerance inherited respectively. However, the contribution of the S. spontaneum subgenome to sucrose accumulation is still unclear. OBJECTIVE: To compensate for the absence of a high-quality reference genome, a transcriptome analysis method is needed to analyze the molecular basis of differential sucrose accumulation in sugarcane hybrids and to find clues to the contribution of the S. spontaneum subgenome to sucrose accumulation. METHODS: PacBio full-length sequencing was used to complement genome annotation, followed by the identification of differential genes between the high and low sugar groups using differential alternative splicing analysis and differential expression analysis. At the subgenomic level, the factors responsible for differential sucrose accumulation were investigated from the perspective of transcriptional and post-transcriptional regulation. RESULTS: A full-length transcriptome annotated at the subgenomic level was provided, complemented by 263,378 allele-defined transcript isoforms and 139,405 alternative splicing (AS) events. Differential alternative splicing (DA) analysis and differential expression (DE) analysis identified differential genes between high and low sugar groups and explained differential sucrose accumulation factors by the KEGG pathways. In some gene models, different or even opposite expression patterns of alleles from the same gene were observed, reflecting the potential evolution of these alleles toward novel functions in polyploid sugarcane. Among DA and DE genes in the sucrose source-sink complex pathway, we found some alleles encoding sucrose accumulation-related enzymes derived from the S. spontaneum subgenome were differentially expressed or had DA events between the two contrasting sugarcane hybrids. CONCLUSION: Full-length transcriptomes annotated at the subgenomic level could better characterize sugarcane hybrids, and the S. spontaneum subgenome was found to contribute to sucrose accumulation.

Haplotype variations of sucrose phosphate synthase B gene among sugarcane accessions with different sucrose content.

BACKGROUND: Sucrose phosphate synthase B (SPSB) gene encoding an important rate-limiting enzyme for sucrose synthesis in sugarcane is mainly expressed on leaves, where its alleles control sucrose synthesis. In this study, genetic variation of SPSB gene represented by different haplotypes in sugarcane was investigated in hybrid clones with high and low sugar content and various accessory species. RESULTS: A total of 39 haplotypes of SPSB gene with 2, 824 bp in size were identified from 18 sugarcane accessions. These haplotypes mainly distributed on Chr3B, Chr3C, and Chr3D according to the AP85-441 reference genome. Single nucleotide polymorphisms (SNPs) and insertion/deletion (InDels) were very dense (42 bp/sequence variation) including 44 transitional and 23 transversional SNPs among the 39 haplotypes. The sequence diversity related Hd, Eta, and Pi values were all lower in clones of high sucrose content (HS) than those in clones of low sucrose content (LS). The evolutionary network analysis showed that about half SPSB haplotypes (19 out of 39) were clustered into one group, including 6 (HAP4, HAP6, HAP7, HAP9, HAP17 and HAP20) haplotypes under positive selection in comparison to HAP26 identified in Badila (S. officinarum), an ancestry noble cane species and under purification selection (except HAP19 under neutral selection) in comparison to HAP18 identified from India1 (S. spontaneum), an ancestry species with low sugar content but high stress tolerance. The average number of haplotypes under positive selection in HS clones was twice as that in LS. Most of the SNPs and InDels sequence variation sites were positively correlated with sucrose and fiber content and negatively correlated with reducing sugar. CONCLUSIONS: A total of 39 haplotypes of SPSB gene were identified in this study. Haplotypes potentially associated with high sucrose synthesis efficiency were identified. The mutations of SPSB haplotypes in HS were favorable and tended to be selected and fixed. The results of this study are informative and beneficial to the molecular assisted breeding of sucrose synthesis in sugarcane in the future.

An urban crowd flow model integrating geographic characteristics.

Predicting urban crowd flow spatial distributions plays a critical role in optimizing urban public safety and traffic congestion management. The spatial dependency between regions and the temporal dynamics of the local crowd flow are two important features in urban crowd flow prediction. However, few studies considered geographic characteristic in terms of spatial features. To fill this gap, we propose an urban crowd flow prediction model integrating geographic characteristics (FPM-geo). First, three geographic characteristics, proximity, functional similarity, and road network connectivity, are fused by a residual multigraph convolution network to model the spatial dependency relationship. Then, a long short-term memory network is applied as a framework to integrate both the temporal dynamic patterns of local crowd flow and the spatial dependency between regions. A 4-day mobile phone dataset validates the effectiveness of the proposed method by comparing it with several widely used approaches. The result shows that the root mean square error decreases by 15.37% compared with those of the typical models with the prediction interval at the 15-min level. The prediction error increases with the crowd flow size in a local area. Moreover, the error reaches the top of the morning peak and the evening peak and slopes down to the bottom at night.

Comparative Analysis of Chloroplast Genome in Saccharum spp. and Related Members of 'Saccharum Complex'.

High ploids of the sugarcane nuclear genome limit its genomic studies, whereas its chloroplast genome is small and conserved, which is suitable for phylogenetic studies and molecular marker development. Here, we applied whole genome sequencing technology to sequence and assemble chloroplast genomes of eight species of the 'Saccharum Complex', and elucidated their sequence variations. In total, 19 accessions were sequenced, and 23 chloroplast genomes were assembled, including 6 species of Saccharum (among them, S. robustum, S. sinense, and S. barberi firstly reported in this study) and 2 sugarcane relative species, Tripidium arundinaceum and Narenga porphyrocoma. The plastid phylogenetic signal demonstrated that S. officinarum and S. robustum shared a common ancestor, and that the cytoplasmic origins of S. sinense and S. barberi were much more ancient than the S. offcinarum/S. robustum linage. Overall, 14 markers were developed, including 9 InDel markers for distinguishing Saccharum from its relative species, 4 dCAPS markers for distinguishing S. officinarum from S. robustum, and 1 dCAPS marker for distinguishing S. sinense and S. barberi from other species. The results obtained from our studies will contribute to the understanding of the classification and plastome evolution of Saccharinae, and the molecular markers developed have demonstrated their highly discriminatory power in Saccharum and relative species.

Differences in Alpha Diversity of Gut Microbiota in Neurological Diseases.

Background: Neurological diseases are difficult to diagnose in time, and there is currently a lack of effective predictive methods. Previous studies have indicated that a variety of neurological diseases cause changes in the gut microbiota. Alpha diversity is a major indicator to describe the diversity of the gut microbiota. At present, the relationship between neurological diseases and the alpha diversity of the gut microbiota remains unclear. Methods: We performed a systematic literature search of Pubmed and Bioproject databases up to January 2021. Six indices were used to measure alpha diversity, including community richness (observed species, Chao1 and ACE), community diversity (Shannon, Simpson), and phylogenetic diversity (PD). Random-effects meta-analyses on the standardized mean difference (SMD) were carried out on the alpha diversity indices. Subgroup analyses were performed to explore the sources of interstudy heterogeneity. Meta-analysis was performed on articles by matching the age, sex, and body mass index (BMI) of the disease group with the control group. Meanwhile, subgroup analysis was performed to control the variability of the sequencing region, platform, geographical region, instrument, and diseases. The area under the curve (AUC) value of the receiver operating characteristic (ROC) curve was calculated to assess the prediction effectiveness of the microbial alpha diversity indices. Results: We conducted a meta-analysis of 24 published studies on 16S rRNA gene amplified sequencing of the gut microbiota and neurological diseases from the Pubmed and Bioproject database (patients, n = 1,469; controls, n = 1,289). The pooled estimate demonstrated that there was no significant difference in the alpha diversity between patients and controls (P < 0.05). Alpha diversity decreased only in Parkinson's disease patients, while it increased in anorexia nervosa patients compared to controls. After adjusting for age, sex, BMI, and geographical region, none of the alpha diversity was associated with neurological diseases. In terms of Illumina HiSeq 2000 and the V3-V5 sequencing region, the results showed that alpha diversity increased significantly in comparison with the controls, while decreased in Illumina HiSeq 2500. ROC curves suggested that alpha diversity could be used as a biomarker to predict the AD (Simpson, AUC= 0.769, P = 0.0001), MS (observed species, AUC= 0.737, P = 0.001), schizophrenia (Chao1, AUC = 0.739, P = 0.002). Conclusions: Our review summarized the relationship between alpha diversity of the gut microbiota and neurological diseases. The alpha diversity of gut microbiota could be a promising predictor for AD, schizophrenia, and MS, but not for all neurological diseases.

Chromosomal Characterization of Tripidium arundinaceum Revealed by Oligo-FISH.

Sugarcane is of important economic value for producing sugar and bioethanol. Tripidium arundinaceum (old name: Erianthus arundinaceum) is an intergeneric wild species of sugarcane that has desirable resistance traits for improving sugarcane varieties. However, the scarcity of chromosome markers has hindered the cytogenetic study of T. arundinaceum. Here we applied maize chromosome painting probes (MCPs) to identify chromosomes in sorghum and T. arundinaceum using a repeated fluorescence in situ hybridization (FISH) system. Sequential FISH revealed that these MCPs can be used as reliable chromosome markers for T. arundinaceum, even though T. arundinaceum has diverged from maize over 18 MYs (million years). Using these MCPs, we identified T. arundinaceum chromosomes based on their sequence similarity compared to sorghum and labeled them 1 through 10. Then, the karyotype of T. arundinaceum was established by multiple oligo-FISH. Furthermore, FISH results revealed that 5S rDNA and 35S rDNA are localized on chromosomes 5 and 6, respectively, in T. arundinaceum. Altogether, these results represent an essential step for further cytogenetic research of T. arundinaceum in sugarcane breeding.

Advances in Genomics Approaches Shed Light on Crop Domestication.

Crop domestication occurred ~10,000-12,000 years ago when humans shifted from a hunter-gatherer to an agrarian society. Crops were domesticated by selecting the traits in wild plant species that were suitable for human use. Research is crucial to elucidate the mechanisms and processes involved in modern crop improvement and breeding. Recent advances in genomics have revolutionized our understanding of crop domestication. In this review, we summarized cutting-edge crop domestication research by presenting its (1) methodologies, (2) current status, (3) applications, and (4) perspectives. Advanced genomics approaches have clarified crop domestication processes and mechanisms, and supported crop improvement.

Genome-wide analysis of R2R3-MYB transcription factors family in the autopolyploid Saccharum spontaneum: an exploration of dominance expression and stress response.

BACKGROUND: Sugarcane (Saccharum) is the most critical sugar crop worldwide. As one of the most enriched transcription factor families in plants, MYB genes display a great potential to contribute to sugarcane improvement by trait modification. We have identified the sugarcane MYB gene family at a whole-genome level through systematic evolution analyses and expression profiling. R2R3-MYB is a large subfamily involved in many plant-specific processes. RESULTS: A total of 202 R2R3-MYB genes (356 alleles) were identified in the polyploid Saccharum spontaneum genomic sequence and classified into 15 subgroups by phylogenetic analysis. The sugarcane MYB family had more members by a comparative analysis in sorghum and significant advantages among most plants, especially grasses. Collinearity analysis revealed that 70% of the SsR2R3-MYB genes had experienced duplication events, logically suggesting the contributors to the MYB gene family expansion. Functional characterization was performed to identify 56 SsR2R3-MYB genes involved in various plant bioprocesses with expression profiling analysis on 60 RNA-seq databases. We identified 22 MYB genes specifically expressed in the stem, of which RT-qPCR validated MYB43, MYB53, MYB65, MYB78, and MYB99. Allelic expression dominance analysis implied the differential expression of alleles might be responsible for the high expression of MYB in the stem. MYB169, MYB181, MYB192 were identified as candidate C4 photosynthetic regulators by C4 expression pattern and robust circadian oscillations. Furthermore, stress expression analysis showed that MYB36, MYB48, MYB54, MYB61 actively responded to drought treatment; 19 and 10 MYB genes were involved in response to the sugarcane pokkah boeng and mosaic disease, respectively. CONCLUSIONS: This is the first report on genome-wide analysis of the MYB gene family in sugarcane. SsMYBs probably played an essential role in stem development and the adaptation of various stress conditions. The results will provide detailed insights and rich resources to understand the functional diversity of MYB transcription factors and facilitate the breeding of essential traits in sugarcane.

Correction: Genetic analysis of agronomic traits in elite sugarcane (Saccharum spp.) germplasm.

[This corrects the article DOI: 10.1371/journal.pone.0233752.].