Abstract:
BACKGROUND:Tomato plant growth is frequently hampered by a high susceptibility to pests and diseases. Traditional chemical control causes a serious impact on both the environment and human health. Therefore, seeking environment-friendly and cost-effective green methods in agricultural production becomes crucial nowadays. Plant Growth Promoting Rhizobacteria (PGPR) can promote plant growth through biological activity. Their use is considered to be a promising sustainable approach for crop growth. Moreover, a vast number of biosynthetic gene clusters (BGCs) for secondary metabolite production are being revealed in PGPR, which helps to find potential anti-microbial activities for tomato disease control. RESULTS:We isolated 181 Bacillus-like strains from healthy tomato, rhizosphere soil, and tomato tissues. In vitro antagonistic assays revealed that 34 Bacillus strains have antimicrobial activity against Erwinia carotovora, Pseudomonas syringae; Rhizoctonia solani; Botrytis cinerea; Verticillium dahliae and Phytophthora infestans. The genomes of 10 Bacillus and Paenibacillus strains with good antagonistic activity were sequenced. Via genome mining approaches, we identified 120 BGCs encoding NRPs, PKs-NRPs, PKs, terpenes and bacteriocins, including known compounds such as fengycin, surfactin, bacillibactin, subtilin, etc. In addition, several novel BGCs were identified. We discovered that the NRPs and PKs-NRPs BGCs in Bacillus species are encoding highly conserved known compounds as well as various novel variants. CONCLUSIONS:This study highlights the great number of varieties of BGCs in Bacillus strains. These findings pave the road for future usage of Bacillus strains as biocontrol agents for tomato disease control and are a resource arsenal for novel antimicrobial discovery.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Zhou L,Song C,Li Z,Kuipers OPdoi
10.1186/s12864-020-07346-8subject
Has Abstractpub_date
2021-01-07 00:00:00pages
29issue
1issn
1471-2164pii
10.1186/s12864-020-07346-8journal_volume
22pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:The floral transition plays a vital role in the life of ornamental plants. Despite progress in model plants, the molecular mechanisms of flowering regulation remain unknown in perennial plants. Rosa chinensis 'Old Blush' is a unique plant that can flower continuously year-round. In this study, gene expressio...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3584-y
更新日期:2017-02-23 00:00:00
abstract:BACKGROUND:Maternal undernutrition leads to an increased risk of metabolic disorders in offspring including obesity and insulin resistance, thought to be due to a programmed thrifty phenotype which is inappropriate for a subsequent richer nutritional environment. In a rat model, both male and female offspring of undern...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-49
更新日期:2014-01-21 00:00:00
abstract:BACKGROUND:Pancreatic cancer is a deadly disease with a five-year survival of less than 5%. A better understanding of the underlying biology may suggest novel therapeutic targets. Recent surveys of the pancreatic cancer genome have uncovered numerous new alterations; yet systematic functional characterization of candid...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-624
更新日期:2013-09-16 00:00:00
abstract:BACKGROUND:Alternative splicing (AS) is a central mechanism in the generation of genomic complexity and is a major contributor to transcriptome and proteome diversity. Alterations of the splicing process can lead to deregulation of crucial cellular processes and have been associated with a large spectrum of human disea...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-S5-S4
更新日期:2010-12-22 00:00:00
abstract:BACKGROUND:Rapid acquisition of accurate genotyping information is essential for all genetic marker-based studies. For species with relatively small genomes, complete genome resequencing is a feasible approach for genotyping; however, for species with large and highly repetitive genomes, the acquisition of whole genome...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-448
更新日期:2013-07-05 00:00:00
abstract:BACKGROUND:Genomic characterization of rotavirus (RoV) has not been adopted at large-scale due to the complexity of obtaining sequences for all 11 segments, particularly when feces are used as starting material. METHODS:To overcome these limitations, we developed a novel RoV capture and genome sequencing method combin...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3714-6
更新日期:2017-04-24 00:00:00
abstract:BACKGROUND:Current technologies in next-generation sequencing are offering high throughput reads at low costs, but still suffer from various sequencing errors. Although pyro- and ion semiconductor sequencing both have the advantage of delivering long and high quality reads, problems might occur when sequencing homopoly...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4544-x
更新日期:2018-02-21 00:00:00
abstract:BACKGROUND:Actinobacillus pleuropneumoniae causes pleuropneumonia in pigs, a disease which is associated with high morbidity and mortality, as well as impaired animal welfare. To obtain in-depth understanding of this infection, the interplay between virulence factors of the pathogen and defense mechanisms of the porcin...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1557-6
更新日期:2015-05-28 00:00:00
abstract:BACKGROUND:Ammonia is one of the most common toxicological environment factors affecting shrimp health. Although ammonia tolerance in shrimp is closely related to successful industrial production, few genetic studies of this trait are available. RESULTS:In this study, we constructed a high-density genetic map of the P...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07254-x
更新日期:2020-12-02 00:00:00
abstract:BACKGROUND:As consumers continue to request food products that have health advantages, it will be important for the livestock industry to supply a product that meet these demands. One such nutrient is fatty acids, which have been implicated as playing a role in cardiovascular disease. Therefore, the objective of this s...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-730
更新日期:2013-10-25 00:00:00
abstract:BACKGROUND:Genomic approaches provide unique opportunities to study interactions of insects with their pathogens. We developed a cDNA microarray to analyze the gene transcription profile of the lepidopteran pest Spodoptera frugiperda in response to injection of the polydnavirus HdIV associated with the ichneumonid wasp...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-160
更新日期:2006-06-21 00:00:00
abstract:BACKGROUND:The tropical green-lipped mussel Perna viridis is a common biomonitor throughout the Indo-Pacific region that is used for environmental monitoring and ecotoxicological investigations. However, there is limited molecular data available regarding this species. We sought to establish a global transcriptome data...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-804
更新日期:2014-09-19 00:00:00
abstract:BACKGROUND:The ultimate phenome of any organism is modulated by regulated transcription of many genes. Characterization of genetic makeup is thus crucial for understanding the molecular basis of phenotypic diversity, evolution and response to intra- and extra-cellular stimuli. Chickpea is the world's third most importa...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-415
更新日期:2009-09-05 00:00:00
abstract:BACKGROUND:Babesia bovis is an apicomplexan parasite that causes babesiosis in infected cattle. Genomes of pathogens contain promising information that can facilitate the development of methods for controlling infections. Although the genome of B. bovis is publically available, annotated gene models are not highly reli...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-678
更新日期:2014-08-13 00:00:00
abstract:BACKGROUND:Tumor necrosis factor alpha (TNF) is able to induce a variety of biological responses in the nervous system including inflammation and neuroprotection. Human astrocytoma cells U373 have been widely used as a model for inflammatory cytokine actions in the nervous system. Here we used cDNA microarrays to analy...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-4-46
更新日期:2003-11-25 00:00:00
abstract:BACKGROUND:Precise identification of three-dimensional genome organization, especially enhancer-promoter interactions (EPIs), is important to deciphering gene regulation, cell differentiation and disease mechanisms. Currently, it is a challenging task to distinguish true interactions from other nearby non-interacting o...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4459-6
更新日期:2018-05-09 00:00:00
abstract:BACKGROUND:Large difference in cerebrum size exist between avian species and populations of the same species and is believed to reflect differences in processing power, i.e. in the speed and efficiency of processing information in this brain region. During domestication chickens developed a larger cerebrum compared to ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06908-0
更新日期:2020-07-29 00:00:00
abstract::In 2009 the International Society for Computational Biology (ISCB) started to roll out regional bioinformatics conferences in Africa, Latin America and Asia. The open and competitive bid for the first meeting in Asia (ISCB-Asia) was awarded to Asia-Pacific Bioinformatics Network (APBioNet) which has been running the I...
journal_title:BMC genomics
pub_type:
doi:10.1186/1471-2164-12-S3-S1
更新日期:2011-11-30 00:00:00
abstract:BACKGROUND:Most microbial eukaryotes are uncultivated and thus poorly suited to standard genomic techniques. This is the case for Polykrikos lebouriae, a dinoflagellate with ultrastructurally aberrant plastids. It has been suggested that these plastids stem from a novel symbiosis with either a diatom or haptophyte, but...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1636-8
更新日期:2015-07-17 00:00:00
abstract:BACKGROUND:Chemosensory receptors including olfactory receptors (ORs), gustatory receptors (GRs) and ionotropic receptors (IRs) play a central role in sensing chemical signals and guiding insect behaviours, and are potential target genes in insect pest control. The cotton bollworm Helicoverpa armigera is one of the mos...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-597
更新日期:2014-07-15 00:00:00
abstract:BACKGROUND:Dermal papilla cells (DPCs), the "signaling center" of hair follicle (HF), delicately master continual growth of hair in mammals including cashmere, the fine fiber annually produced by secondary HF embedded in cashmere goat skins. Such unparalleled capacity bases on their exquisite character in instructing t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5861-4
更新日期:2019-06-20 00:00:00
abstract:BACKGROUND:Mice of the genus Apodemus are one the most common mammals in the Palaearctic region. Despite their broad range and long history of ecological observations, there are no whole-genome data available for Apodemus, hindering our ability to further exploit the genus in evolutionary and ecological genomics contex...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6603-3
更新日期:2020-03-18 00:00:00
abstract:BACKGROUND:Compromised intestinal barrier (CIB) has been associated with many enteropathies, including colorectal cancer (CRC) and inflammatory bowel disease (IBD). We hypothesized that CIB could lead to increased host-derived contents including epithelial cells into the gut, change its physio-metabolic properties, and...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6749-z
更新日期:2020-05-11 00:00:00
abstract:BACKGROUND:Single cell transcriptome sequencing has become an increasingly valuable technology for dissecting complex biology at a resolution impossible with bulk sequencing. However, the gap between the technical expertise required to effectively work with the resultant high dimensional data and the biological experti...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6053-y
更新日期:2019-08-27 00:00:00
abstract:BACKGROUND:Non-coding small RNAs play critical roles in various cellular processes in a wide spectrum of eukaryotic organisms. Their responses to abiotic stress have become a popular topic of economic and scientific importance in biological research. Several studies in recent years have reported a small number of non-c...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-289
更新日期:2011-06-03 00:00:00
abstract:BACKGROUND:Understanding the diversity of repair outcomes after introducing a genomic cut is essential for realizing the therapeutic potential of genomic editing technologies. Targeted PCR amplification combined with Next Generation Sequencing (NGS) or enzymatic digestion, while broadly used in the genome editing field...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4561-9
更新日期:2018-03-21 00:00:00
abstract:BACKGROUND:The regenerative response of Schwann cells after peripheral nerve injury is a critical process directly related to the pathophysiology of a number of neurodegenerative diseases. This SC injury response is dependent on an intricate gene regulatory program coordinated by a number of transcription factors and m...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-84
更新日期:2013-02-06 00:00:00
abstract:BACKGROUND:Hibernation is a physiological state exploited by many animals exposed to prolonged adverse environmental conditions associated with winter. Large changes in metabolism and cellular function occur, with many stress response pathways modulated to tolerate physiological challenges that might otherwise be letha...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5750-x
更新日期:2019-06-06 00:00:00
abstract:BACKGROUND:Archived formalin fixed paraffin embedded (FFPE) samples are valuable clinical resources to examine clinically relevant morphology features and also to study genetic changes. However, DNA quality and quantity of FFPE samples are often sub-optimal, and resulting NGS-based genetics variant detections are prone...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6056-8
更新日期:2019-09-02 00:00:00
abstract:BACKGROUND:Identifying the set of intrinsically conserved genes, or the genomic core, among related genomes is crucial for understanding prokaryotic genomes where horizontal gene transfers are common. Although core genome identification appears to be obvious among very closely related genomes, it becomes more difficult...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-515
更新日期:2008-10-31 00:00:00