Annu Rev Phytopathol , IF:12.623 , 2019 Aug , V57 : P63-90 doi: 10.1146/annurev-phyto-082718-100034
Revisiting the Concept of Host Range of Plant Pathogens.
Pathologie Vegetale, INRA, 84140, Montfavet, France; email: cindy.morris@inra.fr.
Strategies to manage plant disease-from use of resistant varieties to crop rotation, elimination of reservoirs, landscape planning, surveillance, quarantine, risk modeling, and anticipation of disease emergences-all rely on knowledge of pathogen host range. However, awareness of the multitude of factors that influence the outcome of plant-microorganism interactions, the spatial and temporal dynamics of these factors, and the diversity of any given pathogen makes it increasingly challenging to define simple, all-purpose rules to circumscribe the host range of a pathogen. For bacteria, fungi, oomycetes, and viruses, we illustrate that host range is often an overlapping continuum-more so than the separation of discrete pathotypes-and that host jumps are common. By setting the mechanisms of plant-pathogen interactions into the scales of contemporary land use and Earth history, we propose a framework to assess the frontiers of host range for practical applications and research on pathogen evolution.
PMID: 31082307
Microbiome , IF:11.607 , 2019 Aug , V7 (1) : P125 doi: 10.1186/s40168-019-0736-0
Differential dynamics of microbial community networks help identify microorganisms interacting with residue-borne pathogens: the case of Zymoseptoria tritici in wheat.
UMR BIOGER, INRA, AgroParisTech, Universite Paris-Saclay, 78850, Thiverval-Grignon, France. lydiekerdraon@gmail.com.; UMR IRHS, INRA, Agrocampus Ouest, Universite d'Angers, 49071, Beaucouze, France.; UMR BIOGER, INRA, AgroParisTech, Universite Paris-Saclay, 78850, Thiverval-Grignon, France.; UMR BIOGER, INRA, AgroParisTech, Universite Paris-Saclay, 78850, Thiverval-Grignon, France. frederic.suffert@inra.fr.
BACKGROUND: Wheat residues are a crucial determinant of the epidemiology of Septoria tritici blotch, as they support the sexual reproduction of the causal agent Zymoseptoria tritici. We aimed to characterize the effect of infection with this fungal pathogen on the microbial communities present on wheat residues and to identify microorganisms interacting with it. We used metabarcoding to characterize the microbiome associated with wheat residues placed outdoors, with and without preliminary Z. tritici inoculation, comparing the first set of residues in contact with the soil and a second set without contact with the soil, on four sampling dates in two consecutive years. RESULTS: The diversity of the tested conditions, leading to the establishment of different microbial communities according to the origins of the constitutive taxa (plant only, or plant and soil), highlighted the effect of Z. tritici on the wheat residue microbiome. Several microorganisms were affected by Z. tritici infection, even after the disappearance of the pathogen. Linear discriminant analyses and ecological network analyses were combined to describe the communities affected by the infection. The number of fungi and bacteria promoted or inhibited by inoculation with Z. tritici decreased over time and was smaller for residues in contact with the soil. The interactions between the pathogen and other microorganisms appeared to be mostly indirect, despite the strong position of the pathogen as a keystone taxon in networks. Direct interactions with other members of the communities mostly involved fungi, including other wheat pathogens. Our results provide essential information about the alterations to the microbial community in wheat residues induced by the mere presence of a fungal pathogen, and vice versa. Species already described as beneficial or biocontrol agents were found to be affected by pathogen inoculation. CONCLUSIONS: The strategy developed here can be viewed as a proof-of-concept focusing on crop residues as a particularly rich ecological compartment, with a high diversity of fungal and bacterial taxa originating from both the plant and soil compartments, and for Z. tritici-wheat as a model pathosystem. By revealing putative antagonistic interactions, this study paves the way for improving the biological control of residue-borne diseases.
PMID: 31470910
Bioresour Technol , IF:7.539 , 2019 Aug , V286 : P121375 doi: 10.1016/j.biortech.2019.121375
Effects of seaweed fertilizer on enzyme activities, metabolic characteristics, and bacterial communities during maize straw composting.
Poyang Lake Eco-economy Research Center, Jiujiang University, Jiujiang 332005, China; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.; Poyang Lake Eco-economy Research Center, Jiujiang University, Jiujiang 332005, China; Office of Mountain-River-Lake Development Committee of Jiangxi Province, Nanchang 330046, China. Electronic address: qiuxiuwen5@163.com.; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.; Poyang Lake Eco-economy Research Center, Jiujiang University, Jiujiang 332005, China.
The objective of this study was to investigate microbial responses when seaweed fertilizer was added to maize straw compost. The metabolic characteristics and bacterial communities were assessed using 16S rRNA sequencing and Biolog analysis. Results showed that the urease, dehydrogenase, and metabolic activities improved on day 21 after the addition of seaweed fertilizer. Firmicutes, Proteobacteria, and Actinobacteria were the dominant phyla in the compost. The relative abundances of Proteobacteria and Actinobacteria were increased by addition of seaweed fertilizer during the early composting stage. Temperature, NH4(+)-N, NO3(-)-N concentrations, and carbon source metabolism had close relationships with bacterial community variation during composting. A network analysis revealed that NO3(-)-N content had a positive association with Aeromicrobium, and seaweed fertilizer application improved the growth of keystone species related to N cycling. These results suggested that seaweed fertilizer influenced bacterial community succession through its effects on N concentrations during the composting process.
PMID: 31030066
Food Chem , IF:6.306 , 2019 Aug , V290 : P64-71 doi: 10.1016/j.foodchem.2019.03.016
Impact of altered starch functionality on wheat dough microstructure and its elongation behaviour.
Technical University of Munich, Brewing and Beverage Technology, Research Group Cereal Technology and Process Engineering, Weihenstephaner Steig 20, 85354 Freising, Germany.; Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Str. 34, D-85354 Freising, Germany.; Technical University of Munich, Brewing and Beverage Technology, Research Group Cereal Technology and Process Engineering, Weihenstephaner Steig 20, 85354 Freising, Germany. Electronic address: mjekle@tum.de.
The effect of kneading on dough microstructure development, dough elongation and bread volume was investigated using wheat flour with a high mechanical starch modification (MSM) level. The resistance to extension (Rmax) of dough produced from wheat flour with a high MSM level increased by 52.5% because of higher protein network connectivity with prolonged kneading time. The improved network structure was caused by an increased protein branching rate (+14.8%), a decreased protein end-point rate (-24.3%) and a decreased mean lacunarity (-64%). Rmax was highly correlated with specific bread volume (r=0.97, P<0.05) only if the dough was not over-kneaded. Kneading time adaptation of the dough produced from high MSM flour significantly increased specific bread volume by 24.4%. Differences compared with the standard can be attributed to weakened network connectivity because of weakened protein interfacial interactions and larger cavities within the gluten network, both caused by starch swelling.
PMID: 31000057
J Exp Bot , IF:5.908 , 2019 Aug , V70 (16) : P4155-4170 doi: 10.1093/jxb/erz260
Sulphur systems biology-making sense of omics data.
Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.; Nara Institute of Science and Technology, Ikoma, Japan.
Systems biology approaches have been applied over the last two decades to study plant sulphur metabolism. These 'sulphur-omics' approaches have been developed in parallel with the advancing field of systems biology, which is characterized by permanent improvements of high-throughput methods to obtain system-wide data. The aim is to obtain a holistic view of sulphur metabolism and to generate models that allow predictions of metabolic and physiological responses. Besides known sulphur-responsive genes derived from previous studies, numerous genes have been identified in transcriptomics studies. This has not only increased our knowledge of sulphur metabolism but has also revealed links between metabolic processes, thus indicating a previously unexpected complex interconnectivity. The identification of response and control networks has been supported through metabolomics and proteomics studies. Due to the complex interlacing nature of biological processes, experimental validation using targeted or systems approaches is ongoing. There is still room for improvement in integrating the findings from studies of metabolomes, proteomes, and metabolic fluxes into a single unifying concept and to generate consistent models. We therefore suggest a joint effort of the sulphur research community to standardize data acquisition. Furthermore, focusing on a few different model plant systems would help overcome the problem of fragmented data, and would allow us to provide a standard data set against which future experiments can be designed and compared.
PMID: 31404467
J Exp Bot , IF:5.908 , 2019 Aug , V70 (15) : P3709-3717 doi: 10.1093/jxb/erz148
Perception, transduction, and integration of nitrogen and phosphorus nutritional signals in the transcriptional regulatory network in plants.
Biotechnology Research Center, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo.
Nitrate and phosphate ions are major sources of nitrogen and phosphorus for plants. In addition to their vital roles as indispensable macronutrients, these ions function as signalling molecules and induce a variety of responses. Plants adapt to different levels of nutrients by altering their gene expression profile and subsequent physiological and morphological responses. Advances made in recent years have provided novel insights into plant nutrient sensing and modulation of gene expression. Key breakthroughs include elucidation of the mechanisms underlying post-translational regulation of NIN-LIKE PROTEIN (NLP) and PHOSPHATE STARVATION RESPONSE (PHR) family transcription factors, which function as master regulators of responses to nitrate and phosphate starvation, respectively. Determination of the mechanisms whereby these nutrient signals are integrated through NIGT1/HHO family proteins has likewise represented important progress. Further studies have revealed novel roles in nutrient signalling of transcription factors that have previously been shown to be associated with other signals, such as light and phytohormones. Nitrate and phosphate signals are thus transmitted through an intricate gene regulatory network with the help of various positive and negative transcriptional regulators. These complex regulatory patterns enable plants to integrate input signals from various environmental factors and trigger appropriate responses, as exemplified by the regulatory module involving NIGT1/HHO family proteins. These mechanisms collectively support nutrient homeostasis in plants.
PMID: 30949701
J Cell Physiol , IF:5.546 , 2019 Aug , V234 (10) : P17433-17443 doi: 10.1002/jcp.28365
Potential candidate biomarkers associated with osteoarthritis: Evidence from a comprehensive network and pathway analysis.
School of Public Health, Xi'an Jiaotong University Health Science Center, Key Laboratory of Trace Elements and Endemic Diseases of National Health Commission of the People's Republic of China, Xi'an, China.; Shaanxi University of Chinese Medicine, Xianyang, China.
Osteoarthritis (OA) is one of the most common forms of arthritis world widely. Some key genes and diagnostic markers have been reported due to the development of modern molecular biology technologies. However, the etiology and pathogenesis of OA remains unknown. In this study, an integrated network and pathway analysis towards the biological function of OA-associated genes was conducted to provide valuable information to further explore the etiology and pathogenesis of OA. A total of 2,548 genes which reported a statistically significant association with OA were screened. An integrated network and pathway analysis was performed to identify the pathways and genes most associated to OA. Moreover, OA-specific protein-protein interaction (PPI) network was constructed by cytocluster based on the Molecular Complex Detection Algorithm (MCODE) to screen its candidate biomarkers. Quantitative real-time polymerase chain reaction was used to confirm the expression levels and to validate the results of MCODE cluster analysis by six genes. The pathway networks suggested that extracellular matrix (ECM) organization, collagen degradation and collagen formation showed important associations with OA. In top two PPI clusters, 61 of the OA-associated genes were included in the OA-specific PPI network, which also included 23 candidate genes that are likely to be highly associated with OA based on MCODE clusters. Analysis of mRNA showed that the expression levels of COL9A1, COL9A2, ITGA3, COL9A3, ITGA2, and LAMA1 in the peripheral blood mononuclear cells of OA patients were significantly lower than those of the normal controls (p<0.005). To our knowledge, this is the first comprehensive and systematic report based on OA-related genes demonstrating that the functional destruction of collagen in cartilage may be a very important contributing factor to OA. Quantitative detection of collagen synthesis may be of great help in early identification and prediction of OA. Maintaining the quality and quantity of collagen can be a potential target for clinical treatment of OA in the future practice.
PMID: 30820958
BMC Genomics , IF:3.594 , 2019 Aug , V20 (1) : P658 doi: 10.1186/s12864-019-6027-0
Investigation into the underlying regulatory mechanisms shaping inflorescence architecture in Chenopodium quinoa.
Key Laboratory of Coarse Cereal Processing Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengluo road 2025, Shiling town, Longquanyi District, Chengdu, 610106, Sichuan province, People's Republic of China. jerviswuqi@126.com.; National Research and Development Center for Coarse Cereal Processing, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, People's Republic of China. jerviswuqi@126.com.; Key Laboratory of Coarse Cereal Processing Ministry of Agriculture and Rural Affairs, College of Pharmacy and Biological Engineering, Chengdu University, Chengluo road 2025, Shiling town, Longquanyi District, Chengdu, 610106, Sichuan province, People's Republic of China.; National Research and Development Center for Coarse Cereal Processing, College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, People's Republic of China.
BACKGROUND: Inflorescence architecture is denoted by the spatial arrangement of various lateral branches and florets formed on them, which is shaped by a complex of regulators. Unveiling of the regulatory mechanisms underlying inflorescence architecture is pivotal for improving crop yield potential. Quinoa (Chenopodium quinoa Willd), a pseudo cereal originated from Andean region of South America, has been widely recognized as a functional super food due to its excellent nutritional elements. Increasing worldwide consumption of this crop urgently calls for its yield improvement. However, dissection of the regulatory networks underlying quinoa inflorescence patterning is lacking. RESULTS: In this study, we performed RNA-seq analysis on quinoa inflorescence samples collected from six developmental stages, yielding a total of 138.8 GB data. We screened 21,610 differentially expressed genes (DEGs) among all the stages through comparative analysis. Weighted Gene Co-Expression Network Analysis (WGCNA) was performed to categorize the DEGs into ten different modules. Subsequently, we placed emphasis on investigating the modules associated with none branched and branched inflorescence samples. We manually refined the coexpression networks with stringent edge weight cutoffs, and generated core networks using transcription factors and key inflorescence architecture related genes as seed nodes. The core networks were visualized and analyzed by Cytoscape to obtain hub genes in each network. Our finding indicates that the specific occurrence of B3, TALE, WOX, LSH, LFY, GRAS, bHLH, EIL, DOF, G2-like and YABBY family members in early reproductive stage modules, and of TFL, ERF, bZIP, HD-ZIP, C2H2, LBD, NAC, C3H, Nin-like and FAR1 family members in late reproductive stage modules, as well as the several different MADS subfamily members identified in both stages may account for shaping quinoa inflorescence architecture. CONCLUSION: In this study we carried out comparative transcriptome analysis of six different stages quinoa inflorescences, and using WGCNA we obtained the most highly potential central hubs for shaping inflorescence. The data obtained from this study will enhance our understanding of the gene network regulating quinoa inflorescence architecture, as well will supply with valuable genetic resources for high-yield elite breeding in the future.
PMID: 31419932
BMC Plant Biol , IF:3.497 , 2019 Aug , V19 (1) : P379 doi: 10.1186/s12870-019-1888-6
The cotton GhWIN2 gene activates the cuticle biosynthesis pathway and influences the salicylic and jasmonic acid biosynthesis pathways.
College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China.; State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China.; State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China. aylifug@126.com.; College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China. yuxiacau@163.com.
BACKGROUND: Metabolic pathways are interconnected and yet relatively independent. Genes involved in metabolic modules are required for the modules to run. Study of the relationships between genes and metabolic modules improves the understanding of metabolic pathways in plants. The WIN transcription factor activates the cuticle biosynthesis pathway and promotes cuticle biosynthesis. The relationship between the WIN transcription factor and other metabolic pathways is unknown. Our aim was to determine the relationships between the main genes involved in cuticle biosynthesis and those involved in other metabolic pathways. We did this by cloning a cotton WIN gene, GhWIN2, and studying its influence on other pathways. RESULTS: As with other WIN genes, GhWIN2 regulated expression of cuticle biosynthesis-related genes, and promoted cuticle formation. Silencing of GhWIN2 resulted in enhanced resistance to Verticillium dahliae, caused by increased content of salicylic acid (SA). Moreover, silencing of GhWIN2 suppressed expression of jasmonic acid (JA) biosynthesis-related genes and content. GhWIN2 positively regulated the fatty acid biosynthesis pathway upstream of the JA biosynthesis pathway. Silencing of GhWIN2 reduced the content of stearic acid, a JA biosynthesis precursor. CONCLUSIONS: GhWIN2 not only regulated the cuticle biosynthesis pathway, but also positively influenced JA biosynthesis and negatively influenced SA biosynthesis.
PMID: 31455203
BMC Plant Biol , IF:3.497 , 2019 Aug , V19 (1) : P373 doi: 10.1186/s12870-019-1976-7
Gene co-expression network analysis reveals pathways associated with graft healing by asymmetric profiling in tomato.
Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. shanglab211@126.com.
BACKGROUND: The ability of severed rootstocks and shoots to re-establish vascular connections is used to generate grafted plants that combine desirable traits from both scions and rootstocks. Clarifying the mechanisms of graft healing is essential for its further application. We performed RNA sequencing of internodes near the cut position, making a distinction between separated or grafted tissues above and below the cut, in order to obtain a genetic description of graft union formation. RESULTS: Using weighted gene co-expression analysis, variable transcripts were clustered into 10 distinct co-expression networks (modules) based on expression profiles, and genes with the most "hubness" ("hub" genes show the most connections in a network) within each module were predicted. A large proportion of modules were related to Position, and represent asymmetric expression networks from different pathways. Expression of genes involved in auxin and sugar transport and signaling, and brassinosteroid biosynthesis was increased above the cut, while stress response genes were up-regulated below the cut. Some modules were related to graft union formation, among which oxidative detoxification genes were co-expressed along with both wounding response and cell wall organization genes. CONCLUSIONS: The present work provides a comprehensive understanding of graft healing-related gene networks in tomato. Also, the candidate pathways and hub genes identified here will be valuable for future studies of grafting in tomato.
PMID: 31445524
Molecules , IF:3.267 , 2019 Aug , V24 (16) doi: 10.3390/molecules24162959
Exploration in the Mechanism of Action of Licorice by Network Pharmacology.
College of Traditional Chinese Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China. chenmeimei1984@163.com.; College of Traditional Chinese Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China.; College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.; College of Traditional Chinese Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China. 1998009@fjtcm.edu.cn.; College of Chemistry and Materials Science, Fujian Normal University, Fuzhou 350007, China. yangfafu@fjnu.edu.cn.
Licorice is a popular sweetener and a thirst quencher in many food products particularly in Europe and the Middle East and also one of the oldest and most frequently used herbs in traditional Chinese medicine. As a wide application of food additive, it is necessary to clarify bioactive chemical ingredients and the mechanism of action of licorice. In this study, a network pharmacology approach that integrated drug-likeness evaluation, structural similarity analysis, target identification, network analysis, and KEGG pathway analysis was established to elucidate the potential molecular mechanism of licorice. First, we collected and evaluated structural information of 282 compounds in licorice and found 181 compounds that met oral drug rules. Then, structural similarity analysis with known ligands of targets in the ChEMBL database (similarity threshold = 0.8) was applied to the initial target identification, which found 63 compounds in licorice had 86 multi-targets. Further, molecular docking was performed to study their binding modes and interactions, which screened out 49 targets. Finally, 17 enriched KEGG pathways (p < 0.01) of licorice were obtained, exhibiting a variety of biological activities. Overall, this study provided a feasible and accurate approach to explore the safe and effective application of licorice as a food additive and herb medicine.
PMID: 31443210
Ecol Evol , IF:2.392 , 2019 Aug , V9 (16) : P9076-9086 doi: 10.1002/ece3.5453
Sea surface temperature dictates movement and habitat connectivity of Atlantic cod in a coastal fjord system.
Department of Ecology, Environment and Plant Sciences Stockholm University Stockholm Sweden.; AquaBiota Water Research Stockholm Sweden.; Institute of Zoology Zoological Society of London, Regent's Park London UK.; Department of Aquatic Resources Swedish University of Agricultural Sciences Lysekil Sweden.; The County Administrative Board of Vastra Gotaland Gothenburg Sweden.; Department of Biological and Environmental Sciences University of Gothenburg Fiskebackskil Sweden.
While movements of organisms have been studied across a myriad of environments, information is often lacking regarding spatio-seasonal patterning in complex temperate coastal systems. Highly mobile fish form an integral part of marine food webs providing linkages within and among habitats, between patches of habitats, and at different life stages. We investigated how movement, activity, and connectivity patterns of Atlantic cod (Gadus morhua) are influenced by dynamic environmental conditions. Movement patterns of 39 juvenile and subadult Atlantic cod were assessed in two coastal sites in the Swedish Skagerrak for 5 months. We used passive acoustic telemetry and network analysis to assess seasonal and spatial movement patterns of cod and their relationships to different environmental factors, using statistical correlations, analysis of recurrent spatial motifs, and generalized linear mixed models. Temperature, in combination with physical barriers, precludes significant connectivity (complex motifs) within the system. Sea surface temperature had a strong influence on connectivity (node strength, degree, and motif frequency), where changes from warmer summer waters to colder winter waters significantly reduced movement activity of fish. As the seasons changed, movement of fish gradually decreased from large-scale (km) linkages in the summer to more localized movement patterns in the winter (limited to 100s m). Certain localized areas, however, were identified as important for connectivity throughout the whole study period, likely due to these multiple-habitat areas fulfilling functions required for foraging and shelter. This study provides new knowledge regarding inshore movement dynamics of juvenile and subadult Atlantic cod that use complex, coastal fjord systems. The findings show that connectivity, seasonal patterns in particular, should be carefully considered when selecting conservation areas to promote marine stewardship.
PMID: 31463005
Insects , IF:2.22 , 2019 Aug , V10 (8) doi: 10.3390/insects10080245
Genome-Wide Identification of Long Non-Coding RNAs and Their Regulatory Networks Involved in Apis mellifera ligustica Response to Nosema ceranae Infection.
College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.; College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China. ruiguo@fafu.edu.cn.
Long non-coding RNAs (lncRNAs) are a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins, and lncRNAs have been proven to play pivotal roles in a wide range of biological processes in animals and plants. However, knowledge of expression patterns and potential roles of honeybee lncRNA response to Nosema ceranae infection is completely unknown. Here, we performed whole transcriptome strand-specific RNA sequencing of normal midguts of Apis mellifera ligustica workers (Am7CK, Am10CK) and N. ceranae-inoculated midguts (Am7T, Am10T), followed by comprehensive analyses using bioinformatic and molecular approaches. A total of 6353 A. m. ligustica lncRNAs were identified, including 4749 conserved lncRNAs and 1604 novel lncRNAs. These lncRNAs had minimal sequence similarities with other known lncRNAs in other species; however, their structural features were similar to counterparts in mammals and plants, including shorter exon and intron length, lower exon number, and lower expression level, compared with protein-coding transcripts. Further, 111 and 146 N. ceranae-responsive lncRNAs were identified from midguts at 7-days post-inoculation (dpi) and 10 dpi compared with control midguts. Twelve differentially expressed lncRNAs (DElncRNAs) were shared by Am7CK vs. Am7T and Am10CK vs. Am10T comparison groups, while the numbers of unique DElncRNAs were 99 and 134, respectively. Functional annotation and pathway analysis showed that the DElncRNAs may regulate the expression of neighboring genes by acting in cis and trans fashion. Moreover, we discovered 27 lncRNAs harboring eight known miRNA precursors and 513 lncRNAs harboring 2257 novel miRNA precursors. Additionally, hundreds of DElncRNAs and their target miRNAs were found to form complex competitive endogenous RNA (ceRNA) networks, suggesting that these DElncRNAs may act as miRNA sponges. Furthermore, DElncRNA-miRNA-mRNA networks were constructed and investigated, the results demonstrated that a portion of the DElncRNAs were likely to participate in regulating the host material and energy metabolism as well as cellular and humoral immune host responses to N. ceranae invasion. Our findings revealed here offer not only a rich genetic resource for further investigation of the functional roles of lncRNAs involved in the A. m. ligustica response to N. ceranae infection, but also a novel insight into understanding the host-pathogen interaction during honeybee microsporidiosis.
PMID: 31405016
Prog Biophys Mol Biol , IF:2.175 , 2019 Aug , V145 : P19-39 doi: 10.1016/j.pbiomolbio.2018.12.002
Decoding systems biology of plant stress for sustainable agriculture development and optimized food production.
National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, 560065, India.; National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, 560065, India; Department of Biotechnology and Crop Improvement, K.R.C. College of Horticulture, Arabhavi, 591218, University of Horticulture Sciences, Bagalkot, Karnataka, India.; National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, 560065, India; The University of Trans-Disciplinary Health Sciences & Technology (TDU), Bangalore, 560064, Karnataka, India.; National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, 560065, India. Electronic address: mini@ncbs.res.in.
Plants are essential facilitators of human life on planet earth. Plants play a critical functional role in mediating the quality of air, availability of food and the sustainability of agricultural resources. However, plants are in constant interaction with its environment and often hampered by various types of stresses like biotic and abiotic ones. Biotic stress is a significant reason for crop-loss and causes yield loss in the range of 31-42%, post-harvest loss due to biotic stress is in the range of 6-20%, and abiotic stress causes 6-20% of the crop damage. Recognizing the molecular factors driving plant stress-related events, and developing molecular strategies to aid plants to tolerate, resist or adapt to biotic and abiotic stress are critical for sustainable agriculture practice. In this review, we discuss how recent advances in bioinformatics, plant genomics, and data science could help to improve our understanding of plant stress biology and improve the scale of global food production. We present various areas of scientific and technological advances, such as increased availability of genomics data through whole genome sequencing that require attention. We also discuss emerging techniques including CRISPR-Cas9 based genome engineering systems to develop plant varieties that can handle combinatorial stress signals. Growing trend of converging multiple omics technologies and availability of accurate, multi-scale models of plant stress through the study of orthologs and synteny studies, would improve our knowledge of how plants perceive, respond, and manage stress to thrive as resilient crop species and thus help to reduce global food crisis.
PMID: 30562539
J Environ Sci (China) , 2019 Aug , V82 : P24-38 doi: 10.1016/j.jes.2019.02.023
Abundance of antibiotic resistance genes and their association with bacterial communities in activated sludge of wastewater treatment plants: Geographical distribution and network analysis.
Key Laboratory of Northwest Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China. Electronic address: zhanghaihan@xauat.edu.cn.; Key Laboratory of Northwest Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.; Xi'an Environmental Monitoring Center, Xi'an 710119, China.; Research Institute of Applied Biology, Shanxi University, Taiyuan 030006, China.
Wastewater treatment plants (WWTPs) are deemed reservoirs of antibiotic resistance genes (ARGs). Bacterial phylogeny can shape the resistome in activated sludge. However, the co-occurrence and interaction of ARGs abundance and bacterial communities in different WWTPs located at continental scales are still not comprehensively understood. Here, we applied quantitative PCR and Miseq sequence approaches to unveil the changing profiles of ARGs (sul1, sul2, tetW, tetQ, tetX), intI1 gene, and bacterial communities in 18 geographically distributed WWTPs. The results showed that the average relative abundance of sul1and sul2 genes were 2.08x10(-1) and 1.32x10(-)(1)copies/16S rRNA copies, respectively. The abundance of tetW gene was positively correlated with the Shannon diversity index (H'), while both studied sul genes had significant positive relationship with the intI1gene. The highest average relative abundances of sul1, sul2, tetX, and intI1 genes were found in south region and oxidation ditch system. Network analysis found that 16 bacterial genera co-occurred with tetW gene. Co-occurrence patterns were revealed distinct community interactions between aerobic/anoxic/aerobic and oxidation ditch systems. The redundancy analysis model plot of the bacterial community composition clearly demonstrated that the sludge samples were significant differences among those from the different geographical areas, and the shifts in bacterial community composition were correlated with ARGs. Together, these findings from the present study will highlight the potential risks of ARGs and bacterial populations carrying these ARGs, and enable the development of suitable technique to control the dissemination of ARGs from WWTPs into aquatic environments.
PMID: 31133267