Graph-based mitochondrial genomes of three foundation species in the Saccharum genus.

KEY MESSAGE: We reported the graph-based mitochondrial genomes of three foundation species (Saccharum spontaneum, S. robustum and S. officinarum) for the first time. The results revealed pan-structural variation and evolutionary processes in the mitochondrial genomes within Saccharum. Saccharum belongs to the Andropogoneae, and cultivars species in Saccharum contribute nearly 80% of sugar production in the world. To explore the genomic studies in Saccharum, we assembled 15 complete mitochondrial genomes (mitogenome) of three foundation species (Saccharum spontaneum, S. robustum and S. officinarum) using Illumina and Oxford Nanopore Technologies sequencing data. The mitogenomes of the three species were divided into a total of eight types based on contig numbers and linkages. All mitogenomes in the three species encoded 51 unique genes, including 32 protein-coding, 3 ribosomal RNA (rRNA) and 16 transfer RNA (tRNA) genes. The existence of long and short-repeat-mediated recombinations in the mitogenome of S. officinarum and S. robustum was revealed and confirmed through PCR validation. Furthermore, employing comparative genomics and phylogenetic analyses of the organelle genomes, we unveiled the evolutionary relationships and history of the major interspecific lineages in Saccharum genus. Phylogenetic analyses of homologous fragments between S. officinarum and S. robustum showed that S. officinarum and S. robustum are phylogenetically distinct and that they were likely parallel rather than domesticated. The variations between ancient (S. sinense and S. barberi) and modern cultivated species (S. hybrid) possibly resulted from hybridization involving different S. officinarum accessions. Lastly, this project reported the first graph-based mitogenomes of three Saccharum species, and a systematic comparison of the structural organization, evolutionary processes, and pan-structural variation of the Saccharum mitogenomes revealed the differential features of the Saccharum mitogenomes.

Agronomic performance and technological quality of sugarcane submitted to different poultry litter dosages.

Sugarcane is a central crop for sugar and ethanol production. Investing in sustainable practices can enhance productivity, technological quality, mitigate impacts, and contribute to a cleaner energy future. Among the factors that help increase the productivity of sugarcane, the physical, chemical and biological parameters of the soil are amongst the most important. The use of poultry litter has been an important alternative for soil improvement, as it acts as a soil conditioner. Therefore, this work aimed to verify the best doses of poultry litter for the vegetative, reproductive and technological components of sugarcane. The experiment was carried out at Usina Denusa Destilaria Nova União S/A in the municipality of Jandaia, GO. The experimental design used was a complete randomized block design with four replications: 5 × 4, totaling 20 experimental units. The evaluated factor consisted of four doses of poultry litter plus the control (0 (control), 2, 4, 6 and 8 t ha-1). In this study, were evaluated the number of tillers, lower stem diameter, average stem diameter, upper stem diameter, plant height, stem weight and productivity. The technological variables of total recoverable sugar, recoverable sugar, Brix, fiber, purity and percentage of oligosaccharides were also evaluated. It was observed, within the conditions of this experiment, that the insertion of poultry litter did not interfere significantly in most biometric, productive and technological variables of the sugarcane. But it can also be inferred that there was a statistical trend toward better results when the sugarcane was cultivated with 4 t ha-1 of poultry litter.

Effects of High Salinity and Water Stress on Wetland Grasses from the Spanish Mediterranean Coast.

The impacts of climate change are reaching unprecedented levels, heightening the risk of species loss and ecosystem service degradation. Wetlands, highly threatened ecosystems, serve vital ecological functions by capturing carbon, filtering water, and harbouring diverse wildlife. Coastal wetlands encounter many challenges, such as increased drought periods and escalating salinity levels, severely impacting plant biodiversity. Assessing how plants respond to various environmental stress factors is imperative for devising successful conservation strategies. In the present study, we examined three representative grass species found in various habitats within the Albufera Natural Park, close to the city of Valencia on the Spanish Mediterranean coast: Imperata cylindrica, Phragmites australis, and Saccharum ravennae. High salinity and water stress conditions were induced by subjecting the plants to irrigation with solutions containing 200, 400, 600, and 800 mM NaCl or withholding irrigation altogether to mimic coastal flooding and drought scenarios. The treatments were maintained until noticeable wilting of the plants occurred, at which point a range of stress biomarkers were determined, including photosynthetic pigments, ions, osmolytes, oxidative stress markers, and antioxidant metabolites, as well as antioxidant enzyme activities. Saccharum ravennae displayed the highest sensitivity to salt stress, whereas I. cylindrica appeared to be the most tolerant. The primary salinity tolerance mechanism observed in I. cylindrica and P. australis was a blockage of ion transport from the root zone to the aerial part, together with the salt-induced accumulation of proline and soluble sugars to high concentrations in the former. No significant effects of the water deficit treatment on the growth or biochemical parameters were observed for any of the analysed species. These findings offer valuable information for the effective management and conservation of coastal wetlands facing the challenges posed by climate change.

Unraveling the Potential of Saccharum officinarum and Chlorella vulgaris towards 5-Fluorouracil-Induced Nephrotoxicity in Rats.

5-Fluorouracil (5-FU) is often used as a chemotherapeutic agent in treating tumors and is said to have adverse effects, including nephrotoxicity. Therefore, the present study aimed to evaluate the protective effects of Chlorella vulgaris (VL) and Saccharum officinarum L. (SOL) against 5-FU-induced nephrotoxicity in rats through the measurement of renal histology, kidney damage indicators, and antioxidant measures. A total of forty-eight male rats were allotted into six groups: group 1 acted as a control negative group (control), group 2 received 5-FU and worked as a control positive group (FU), group 3 received SOL 15 mL/kg (SOL), group 4 received VL 400 mg/kg (VL), group 5 received 5-FU+SOL (5-FU+SOL), and group 6 received 5-FU+VL (5-FU+VL). After fifteen days, blood and renal tissue specimens were collected for hematological, biochemical, molecular, and histopathological examinations. Findings of the current investigation showed that 5-FU leads to hematological alterations and kidney injury evinced by elevated serum concentrations of uric acid, creatinine, and urea (p < 0.01), and a marked increase in kidney MDA and NO levels with a reduction in kidney CAT, SOD and GSH activities (p < 0.05). Alterations of the histopathological structure of kidney tissue in the FU group were noticed compared to the other groups. 5-FU administration elevated expression levels of TNF-α, lipocalin 2, and KIM1 (p < 0.01) compared to the control ones. 5-FU-induced nephrotoxicity was ameliorated after treatment with SOL and VL via their free radical scavenging, potent antioxidant, and anti-inflammatory effects. In conclusion, our findings demonstrate that the treatment with SOL and VL significantly improved nephrotoxicity induced by 5-FU in rats.

Mealybug Population Dynamics: A Comparative Analysis of Sampling Methods for Saccharicoccus sacchari and Heliococcus summervillei in Sugarcane (Saccharum sp. Hybrids).

This research is focused on a comparative field-based study of the population dynamics and sampling methods of two mealybug species, Saccharicoccus sacchari (Cockerell, 1895) (Hemiptera: Coccomorpha, Pseudococcidae) and Heliococcus summervillei (Brookes, 1978) (Hemiptera: Coccomorpha, Pseudococcidae), in sugarcane (Saccharum sp. hybrids) (f. Poaceae) over consecutive growing seasons. The research monitored and compared the above- and belowground populations and seasonal abundance of these two mealybug species in sugarcane fields in Far North Queensland, with non-destructive sampling techniques of yellow sticky traps, pan traps, and stem traps, and destructive sampling of the whole leaf and whole plant. The results indicated that S. sacchari (n = 29,137) was more abundant and detected throughout the growing season, with population peaks in the mid-season, while H. summervillei (n = 2706) showed peaks of the early-season activity. S. sacchari is primarily located on sugarcane stems and roots, compared to H. summervillei, which is located on leaves and roots. The whole-leaf collection and stem trap were the most effective sampling techniques for quantification of H. summervillei and S. sacchari, respectively. This study enhanced the understanding of S. sacchari and the first-ever record of H. summervillei on sugarcane in Australia and will contribute to the development of more effective pest management strategies.

Carbon savings from sugarcane straw-derived bioenergy: Insights from a life cycle perspective including soil carbon changes.

Sugarcane straw removal for bioenergy production will increase substantially in the next years, but this may deplete soil organic carbon (SOC) and exacerbate greenhouse gas (GHG) emissions. These aspects are not consistently approached in bioenergy life cycle assessment (LCA). Using SOC modeling and LCA approach, this study addressed the life cycle GHG balance from sugarcane agroindustry in different scenarios of straw removal, considering the potential SOC changes associated with straw management in sugarcane-cultivated soils in Brazil. Long-term simulations showed SOC losses of up to -0.5 Mg ha-1 yr-1 upon complete straw removal, whereas the moderate removal had little effects on SOC and the maintenance of all straw in the field increased SOC accumulation by up to 0.4 Mg ha-1 yr-1. Our analysis suggests that accounting for SOC changes in LCA calculations could lower the net GHG benefits of straw-derived bioenergy, whose emissions intensity varied according to soil type. Overall, SOC depletion induced by complete straw removal increased the life cycle GHG emissions of straw-derived bioenergy by 26 % (3.9 g CO2eq MJ-1) compared to a scenario without taking SOC changes into account. Straw removal for cellulosic ethanol could be effective for mitigating GHG emissions relative to gasoline, but it was not advantageous for bioelectricity generation depending on the energy sources that are displaced. Therefore, straw-induced change of SOC stocks is a critical factor to model life cycle GHG emissions of straw-derived bioenergy.

Determining Factors and Economic Injury Levels for Sphenophorus levis for Chemical and Biological Control in Irrigated and Non-irrigated Sugarcane Crops.

Globally, people use sugarcane (Saccharum officinarum) to produce sugar and ethanol. Rainfed or irrigated sugarcane agricultural systems are available. Among the pests affecting this crop, the weevil Sphenophorus levis, Vaurie 1978 (Coleoptera: Curculionidae), is increasingly becoming a significant threat in southern South America. Sphenophorus levis populations are controlled using chemical or biological measures. Control decisions hinge upon the economic injury level (EIL). The EIL delineates the pest density that results in financial losses for producers. This study aims to determine the EIL for S. levis, considering the factors favoring this insect pest and chemical and biological control methods in rainfed and irrigated systems. The intensity of S. levis attacks was monitored in commercial sugarcane plantations over four years in João Pinheiro, Minas Gerais, Brazil. Sampling occurred in a 50 × 50 × 30-cm-deep trench dug in the soil surrounding the sugarcane clump. The total number of stumps in the clump, including those attacked by S. levis, was tallied. The EILs for this pest were 5.93% and 4.85% of targeted stumps for chemical control in rainfed and irrigated crops, respectively. Biological control in sugarcane plots resulted in an EIL of 4.15% and 3.40% for stumps attacked in rainfed and irrigated crops, respectively. Pest attacks were more severe during rainy years and in older sugarcane crops. The EIL values determined in this study could inform integrated pest management programs for sugarcane crops.

Identification of male sterility-related genes in Saccharum officinarum and Saccharum spontaneum.

KEY MESSAGE: Candidate male sterility genes were identified in sugarcane, which interacts with kinase-related proteins, transcription factors, and plant hormone signaling pathways to regulate stamen and anther development. Saccharum officinarum is a cultivated sugarcane species that its predominant feature is high sucrose content in stems. Flowering is necessary for breeding new cultivars but will terminate plant growth and reduce sugar yield. The wild sugarcane species Saccharum spontaneum has robust and viable pollen, whereas most S. officinarum accessions are male sterile, which is a desirable trait of a maternal parent in sugarcane breeding. To study male sterility and related regulatory pathways in sugarcane, we carried out RNAseq using flowers in different developmental stages between male-sterile S. officinarum accession 'LA Purple' and fertile S. spontaneum accession 'SES208'. Gene expression profiles were used to detect how genes are differentially expressed between male sterile and fertile flowers and to identify candidate genes for male sterility. Weighted gene correlation networks analysis (WGCNA) was conducted to investigate the regulatory networks. Transcriptomic analyses showed that 988 genes and 2888 alleles were differentially expressed in S. officinarum compared to S. spontaneum. Ten differentially expressed genes and thirty alleles were identified as candidate genes and alleles for male sterility in sugarcane. The gene Sspon.03G0007630 and two alleles of the gene Sspon.08G0002270, Sspon.08G0002270-2B and Sspon.08G0014700-1A, were involved in the early stamen or carpel development stages, while the remaining genes were classified into the post-meiosis stage. Gibberellin, auxin, and jasmonic acid signaling pathways are involved in the stamen development in sugarcane. The results expanded our knowledge of male sterility-related genes in sugarcane and generated genomic resources to facilitate the selection of ideal maternal parents to improve breeding efficiency.

A study on waterlogging tolerance in sugarcane: a comprehensive review.

Sugarcane (Saccharum officinarum) is an important crop, native to tropical and subtropical regions and it is a major source of sugar and Bioenergy in the world. Abiotic stress is defined as environmental conditions that reduce growth and yield below the optimum level. To tolerate these abiotic stresses, plants initiate several molecular, cellular, and physiological changes. These responses to abiotic stresses are dynamic and complex; they may be reversible or irreversible. Waterlogging is an abiotic stress phenomenon that drastically reduces the growth and survival of sugarcane, which leads to a 15-45% reduction in cane's yield. The extent of damage due to waterlogging depends on genotypes, environmental conditions, stage of development and duration of stress. An improved understanding of the physiological, biochemical, and molecular responses of sugarcane to waterlogging stress could help to develop new breeding strategies to sustain high yields against this situation. The present review offers a summary of recent findings on the adaptation of sugarcane to waterlogging stress in terms of growth and development, yield and quality, as well as biochemical and adaptive-molecular processes that may contribute to flooding tolerance.

Sugarcane (Saccharum officinarum L.) induces psychostimulant, anxiolytic-like effects and improvement of motor performance in rats.

ETHNOPHARMACOLOGICAL RELEVANCE: Sugarcane (Saccharum officinarum L.) is reported by traditional medicine as tonic, stimulating and beneficial in increasing resistance to fatigue. Previous preclinical studies in rats using aqueous extract of sugarcane leaves (AE) revealed pharmacological effects on the central nervous and cardiovascular systems involving the participation of dopaminergic pathways. This neurotransmission system is also related to motor, emotional and cognitive activities, which could, in part, justify the ethnopharmacological information. AIM OF STUDY: The present study aimed to investigate the motor, emotional and cognitive activities of rats submitted to AE treatment using behavioral tests in order to correlate the pharmacological effects with the therapeutic benefits postulated by traditional medicine. Additionally, the chemical profile of AE was evaluated by HPLC-UV/Vis, and the presence of shikimic acid, vitexin, and ferulic acid, as possible chemical markers, was investigated through comparisons of chemical parameters with the authentic patterns, and a UV-Vis scan of known spectra. MATERIAL AND METHODS: Rats received water (1.5 mL/kg, p.o.) and AE (0.5, 10 and 500 mg/kg, p.o.) in the absence and presence of haloperidol (0.5 mg/kg, i.p.), 90 min before open field; rotarod; elevated plus maze and inhibitory avoidance tests for investigation of motor; emotional and cognitive responses. As a positive control was used apomorphine (0.25 mg/kg, s.c.). The chemical profile of AE was evaluated by HPLC-UV/Vis and the presence of shikimic acid, vitexin and ferulic acid, as possible chemical markers, was investigated through comparisons with the retention times, an increase of the integral of the peak area determined by co-injection of AE with the authentic patterns, and a UV-Vis scan of known spectra. RESULTS: In open field, it revealed that AE increased locomotion; reduced rearing but did not change freezing and grooming. Besides, AE increased motor performance in rotarod and reduced anxiety in elevated plus maze. A relation dose-response was observed in these tests where the lowest dose of AE was more effective in developing pharmacological responses. Previous administration of haloperidol inhibited the responses of AE. Inhibitory avoidance test revealed that AE did not modify fast-learning and associative memory. CONCLUSIONS: Sugarcane induced psychostimulant, anxiolytic-like effects, and improvement of motor performance in rats, with the involvement of dopaminergic pathways. The present study points to AE as a potential adaptogen but, in addition to behavioral assessments, metabolic and molecular aspects, that involve the participation of a variety of regulatory systems, will be investigated in futures studies. Phytochemical analyses showed that AE is a complex matrix and revealed shikimic acid, vitexin, and ferulic acid as potential chemical markers.

Uso de agrotóxicos em canaviais de Pernambuco e danos à saúde do trabalhador / Use of pesticides in Pernambuco sugarcane fields and damage to workers' health

RESUMO O presente estudo teve por objetivo analisar a exposição aos agrotóxicos e os danos à saúde dos trabalhadores das plantações de cana-de-açúcar em Pernambuco. Trata-se de pesquisa participante desenvolvida em territórios rurais de cinco municípios com forte expressão em área plantada de cana-de-açúcar. Os dados primários foram produzidos em oficinas com trabalhadores rurais para construção de diagnóstico rural participativo, analisados mediante condensação de significados e interpretados à luz do referencial teórico da epidemiologia crítico latino-americana. Os resultados estão apresentados em três seções: i) Fluxograma do trabalho nas plantações de cana-de-açúcar; ii) Exposição aos agrotóxicos utilizados nas lavouras; iii) Danos à saúde do trabalhador. Conclui-se que a exposição permanente aos agrotóxicos envolve o trabalho nas plantações de cana-de-açúcar e emerge de um construto histórico e socioambiental, em que se encontram subsumidos os modos de vida dos territórios sob o domínio do agronegócio canavieiro. Recomendam-se políticas públicas de fomento à agricultura familiar com diversificação, escoamento e distribuição da produção agroecológica, além do fortalecimento da Atenção Primária à Saúde e de ações integradas de vigilância epidemiológica, sanitária, ambiental e do trabalhador.

ABSTRACT This study aims to analyze exposure to pesticides and harm to the health of workers on sugarcane plantations in Pernambuco. This participatory research was conducted in rural territories of five municipalities with a strong presence in sugarcane-planted areas. The primary data were produced in workshops with rural workers to construct a participatory rural diagnosis, analyzed through condensation of meanings, and interpreted in light of the theoretical framework of Latin American critical epidemiology. The results are presented in three sections: i) Flowchart of work on sugarcane plantations; ii) Exposure to pesticides used on crops; iii) Harm to worker's health. We conclude that permanent exposure to pesticides involves working on sugarcane plantations and emerges from a historical and socio-environmental construct in which the ways of life of the territories under the control of sugarcane agribusiness are subsumed. Public policies are recommended to promote family farming with diversification, flow, distribution of agroecological production, and strengthening primary health care and integrated epidemiological, health, environmental, and worker surveillance actions.

Genome-Wide Identification and Characterization of Homeobox Transcription Factors in Phoma sorghina var. saccharum Causing Sugarcane Twisted Leaf Disease.

A homeobox transcription factor is a conserved transcription factor, ubiquitous in eukaryotes, that regulates the tissue formation of structure, cell differentiation, proliferation, and cancer. This study identified the homeobox transcription factor family and its distribution in Phoma sorghina var. saccharum at the whole genome level. It elucidated the gene structures and evolutionary characteristics of this family. Additionally, knockout experiments were carried out and the preliminary function of these transcription factors was studied. Through bioinformatics approaches, nine homeobox transcription factors (PsHOX1-PsHOX9) were identified in P. sorghina var. saccharum, and these contained HOX-conserved domains and helix-turn-helix secondary structures. Nine homeobox gene deletion mutants were obtained using the homologous recombinant gene knockout technique. Protoplast transformation was mediated by polyethylene glycol (PEG) and the transformants were identified using PCR. The knockouts of PsHOX1, PsHOX2, PsHOX3, PsHOX4, PsHOX6, PsHOX8, and PsHOX9 genes resulted in a smaller growth diameter in P. sorghina var. saccharum. In contrast, the knockouts of the PsHOX3, PsHOX6, and PsHOX9 genes inhibited the formation of conidia and led to a significant decrease in the pathogenicity. This study's results will provide insights for understanding the growth and development of P. sorghina var. saccharum. The pathogenic mechanism of the affected sugarcane will provide an essential theoretical basis for preventing and controlling sugarcane twisted leaf disease.

Untargeted metabolomics, optimization of microwave-assisted extraction using Box-Behnken design and evaluation of antioxidant, and antidiabetic activities of sugarcane bagasse.

INTRODUCTION: The fruit wastes, in particular agricultural wastes, are considered potential and inexpensive sources of bioactive compounds. OBJECTIVE: The current study was aimed at the preparation of an optimized extract of sugarcane bagasse using microwave-assisted extraction (MAE) technology and comparative evaluation of chemical composition, antioxidant, and antidiabetic activities with extract prepared through maceration technique. METHODOLOGY: Box-Behnken Design (BDD) with response surface methodology was applied to observe interactions of three independent variables (ethanol concentrations [%], microwave power [W], and extraction time [min]) on the dependent variables (total phenolic content [TPC] and antioxidant status via 2,2-diphenyl-1-picrylhydrazyl [DPPH] to establish optimal extraction conditions. The ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS) analysis was applied for untargeted metabolite profiling, and in vitro assays were used for evaluation of the antidiabetic and antioxidant potential of the extract. Moreover, an in silico study was used to predict the interaction of five dominant compounds from the UHPLC-Q-TOF-MS profile against the dipeptidyl peptidase-IV (DPP-IV) enzyme. RESULTS: The optimal conditions for the extraction were established at 60% (v/v) ethanol, 500 W microwave power, and 5 min time with TPC 12.83 ± 0.66 mg GAE/g d.w. and DPPH 45.09 ± 0.07%. The UHPLC-Q-TOF-MS analysis revealed the presence of a total of 106 compounds in the extract. Moreover, the extract prepared through MAE technology presented higher TPC and DPPH findings than the extract prepared through maceration. Similarly, the extract was also found with good antidiabetic activity by inhibiting the DPP-IV enzyme which was also rectified theoretically by a molecular docking study. CONCLUSION: The current study presents a sustainable and an optimized approach for the preparation of sugarcane bagasse extract with functional phytoconstituents and higher antidiabetic and antioxidant activities.

Assessment of energy cane bagasse-derived cellulosic microfiber hydrogels on the growth of potted chili peppers.

Energy cane (Saccharum spp.) bagasse, a type of biomass waste, is often underutilized, burned, or left to dispose of itself. This research aimed to evaluate the potential of converting this bagasse into high-value cellulosic microfiber hydrogels (CMH) for water conservation and potted chili (Capsicum annuum) plant growth. CMH offers a biodegradable alternative to synthetic polyacrylamide (PA) hydrogels and provides the dual benefit of improved water use efficiency and reduced environmental impact due to their ability to naturally break down in the soil. In this study, CMH and PA hydrogels were compared for water retention value (WRV), and reswelling kinetics (RK), as well as their effects on plant height, leaf count, root-to-shoot ratios (R:S ratio), and soil moisture retention. Two versions of CMH, CMH65 and CMH60, were prepared with varying cellulose-chitosan ratios: 65:35 and 60:40, respectively. The hydrogels were tested at four concentrations (0, 0.5, 1.0, and 2.0% w/w) by being mixed in Promix® soil. Observations were recorded over a 16-day period without additional water. Also, the WRV of hydrogels at 240 min and RK (10-180 min) were compared over three swelling-deswelling cycles. The PA hydrogel exhibited higher WRV (exceeding 450%) compared to CMH (45%). However, PA led to reduced plant height, leaf count, and R:S ratio when compared to higher concentrations of CMH65 and CMH60. In general, CMH60 (0.5% and 2%) exhibited superior plant growth. All hydrogels exhibited a significant decrease (p < 0.05) in WRV across successive cycles. Notably, during cycle 2, both CMH65 and CMH60 peaked in WRV at 10 and 20 min, respectively, compared to cycle 1. This study demonstrates the potential of bagasse-derived hydrogels as a value-added product for water conservation and crop growth.

Profiling genome-wide methylation in two maples: Fine-scale approaches to detection with nanopore technology.

DNA methylation is critical to the regulation of transposable elements and gene expression and can play an important role in the adaptation of stress response mechanisms in plants. Traditional methods of methylation quantification rely on bisulfite conversion that can compromise accuracy. Recent advances in long-read sequencing technologies allow for methylation detection in real time. The associated algorithms that interpret these modifications have evolved from strictly statistical approaches to Hidden Markov Models and, recently, deep learning approaches. Much of the existing software focuses on methylation in the CG context, but methylation in other contexts is important to quantify, as it is extensively leveraged in plants. Here, we present methylation profiles for two maple species across the full range of 5mC sequence contexts using Oxford Nanopore Technologies (ONT) long-reads. Hybrid and reference-guided assemblies were generated for two new Acer accessions: Acer negundo (box elder; 65x ONT and 111X Illumina) and Acer saccharum (sugar maple; 93x ONT and 148X Illumina). The ONT reads generated for these assemblies were re-basecalled, and methylation detection was conducted in a custom pipeline with the published Acer references (PacBio assemblies) and hybrid assemblies reported herein to generate four epigenomes. Examination of the transposable element landscape revealed the dominance of LTR Copia elements and patterns of methylation associated with different classes of TEs. Methylation distributions were examined at high resolution across gene and repeat density and described within the broader angiosperm context, and more narrowly in the context of gene family dynamics and candidate nutrient stress genes.

Identification and characterization of PAL genes involved in the regulation of stem development in Saccharum spontaneum L.

BACKGROUND: Saccharum spontaneum L. is a closely related species of sugarcane and has become an important genetic component of modern sugarcane cultivars. Stem development is one of the important factors for affecting the yield, while the molecular mechanism of stem development remains poorly understanding in S. spontaneum. Phenylalanine ammonia-lyase (PAL) is a vital component of both primary and secondary metabolism, contributing significantly to plant growth, development and stress defense. However, the current knowledge about PAL genes in S. spontaneum is still limited. Thus, identification and characterization of the PAL genes by transcriptome analysis will provide a theoretical basis for further investigation of the function of PAL gene in sugarcane. RESULTS: In this study, 42 of PAL genes were identified, including 26 SsPAL genes from S. spontaneum, 8 ShPAL genes from sugarcane cultivar R570, and 8 SbPAL genes from sorghum. Phylogenetic analysis showed that SsPAL genes were divided into three groups, potentially influenced by long-term natural selection. Notably, 20 SsPAL genes were existed on chromosomes 4 and 5, indicating that they are highly conserved in S. spontaneum. This conservation is likely a result of the prevalence of whole-genome replications within this gene family. The upstream sequence of PAL genes were found to contain conserved cis-acting elements such as G-box and SP1, GT1-motif and CAT-box, which collectively regulate the growth and development of S. spontaneum. Furthermore, quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis showed that SsPAL genes of stem had a significantly upregulated than that of leaves, suggesting that they may promote the stem growth and development, particularly in the + 6 stem (The sixth cane stalk from the top to down) during the growth stage. CONCLUSIONS: The results of this study revealed the molecular characteristics of SsPAL genes and indicated that they may play a vital role in stem growth and development of S. spontaneum. Altogether, our findings will promote the understanding of the molecular mechanism of S. spontaneum stem development, and also contribute to the sugarcane genetic improving.

Genome-wide identification of JAZ gene family in sugarcane and function analysis of ScJAZ1/2 in drought stress response and flowering regulation.

The JASMONATE ZIM DOMAIN (JAZ) proteins are a key inhibitors of the jasmonic acid (JA) signaling pathway that play an important role in the regulation of plant growth and development and environmental stress responses. However, there is no systematic identification and functional analysis of JAZ gene family members in sugarcane. In this study, a total of 49 SsJAZ genes were identified from the wild sugarcane species Saccharum spontaneum genome that were unevenly distributed on 13 chromosomes. Phylogenetic analysis showed that all SsJAZ members can be divided into six groups, and most of the SsJAZ genes contained photoreactive and ABA-responsive elements. RNA-seq analysis revealed that SsJAZ1-1/2/3/4 and SsJAZ7-1 were significantly upregulated under drought stress. The transcript level of ScJAZ1 which is the homologous gene of SsJAZ1 in modern sugarcane cultivars was upregulated by JA, PEG, and abscisic acid (ABA). Moreover, ScJAZ1 can interact with three other JAZ proteins to form heterodimers. The spatial and temporal expression analysis showed that SsJAZ2-1/2/3/4 were highly expressed in different tissues and growth stages and during the day-night rhythm between 10:00 and 18:00. Overexpression of ScJAZ2 in Arabidopsis accelerated flowering through activating the expression of AtSOC1, AtFT, and AtLFY. Moreover, the transcription level of ScJAZ2 was about 30-fold in the early-flowering sugarcane variety than that of the non-flowering variety, indicating ScJAZ2 positively regulated flowering. This first systematic analysis of the JAZ gene family and function analysis of ScJAZ1/2 in sugarcane provide key candidate genes and lay the foundation for sugarcane breeding.

Insights into Reactive Oxygen Species Production-Scavenging System Involved in Sugarcane Response to Xanthomonas albilineans Infection under Drought Stress.

Plants must adapt to the complex effects of several stressors brought on by global warming, which may result in interaction and superposition effects between diverse stressors. Few reports are available on how drought stress affects Xanthomonas albilineans (Xa) infection in sugarcane (Saccharum spp. hybrids). Drought and leaf scald resistance were identified on 16 sugarcane cultivars using Xa inoculation and soil drought treatments, respectively. Subsequently, four cultivars contrasting to drought and leaf scald resistance were used to explore the mechanisms of drought affecting Xa-sugarcane interaction. Drought stress significantly increased the occurrence of leaf scald and Xa populations in susceptible cultivars but had no obvious effect on resistant cultivars. The ROS bursting and scavenging system was significantly activated in sugarcane in the process of Xa infection, particularly in the resistant cultivars. Compared with Xa infection alone, defense response via the ROS generating and scavenging system was obviously weakened in sugarcane (especially in susceptible cultivars) under Xa infection plus drought stress. Collectively, ROS might play a crucial role involving sugarcane defense against combined effects of Xa infection and drought stress.

Effect of Irrigation on Sugarcane Morphophysiology in the Brazilian Cerrado.

Since sugarcane is semi-perennial, it has no escape from water stresses in the Brazilian Cerrado, and consequently, drought impacts plant growth and industrial quality. The objective of this study was to evaluate the morphophysiology and quality of the first ratoon of two sugarcane varieties submitted to irrigated and stressed treatments under field conditions. For the biometric characteristics, in general, significant decreases were observed under the stressed treatment for all periods, and only minor differences were detected between the studied cultivars. Physiological parameters decreased under stressed conditions, but to a different extent between the varieties. RB855536 was able to maintain a greater rate of transpiration. Productivity was reduced by 103 t ha-1 for variety RB855536 and 121 t ha-1 for RB867515, compared to plants with full irrigation during the dry period, but cane quality was similar in both genotypes. Measurements of physiological and morphological parameters may prove useful in the rapid identification of genotypes with greater tolerance to abiotic stress.

Penetrating Sugarcane Injury to Brain via Orbit: A Case Report.

Penetrating brain trauma is rare. We present a unique case involving a sugarcane injury that penetrated the brain via the orbit following a road traffic accident. A 32-year-old male arrived at our emergency department with a penetrating injury to his left eye. A non-contrast computerized tomography (NCCT) scan of the head showed a foreign body in the left orbit, extending to the frontal lobe. Left frontotemporal craniotomy, anterior cranial fossa exploration, retrieval of the foreign body (a sugarcane piece), and dural repair of the anterior cranial fossa were performed. The patient was discharged and showed positive progress on follow-up. Penetrating trauma to the eyes and brain can be fatal, leading to vision loss. Therefore, early surgical intervention and close coordination between ophthalmologists and neurosurgeons are imperative.