Abstract:
BACKGROUND:The WRKY gene family is one of the most important families in higher plants. As transcription factors, they actively respond to biotic and abiotic stress and are also involved in plant development. Chinese jujube (Ziziphus jujuba Mill.) is the largest type of dried fruit tree in China in terms of production, but its production is largely limited by phytoplasma infection, and the information about the role of WRKY genes under phytoplasma stress was still limited. RESULTS:We identified 54 ZjWRKYs in the jujube genome and classified them into three subgroups according to conserved WRKY domains and zinc-finger structure. 41 ZjWRKYs were distributed on 11 of 12 pseudo chromosomes in Chinese jujube. The majority of ZjWRKYs were highly expressed in the seven examined tissues, indicating that they play multiple roles in these vegetative and reproductive organs. Transcriptome data showed that most of the characterised ZjWRKYs were highly expressed at later stages of fruit development. RT-qPCR demonstrated that the expression of 23 ZjWRKYs changed following phytoplasma infection, suggesting that they are involved in signalling pathways that respond to phytoplasma stress. Then, STRING analysis and yeast two-hybrid screening proved that some ZjWRKY proteins were interacting with ZjMAPKK proteins, which were also involved in phytoplasma invasion. Moreover, their differential expressions were further confirmed in resistant and susceptible jujube varieties under phytoplasma stress. These results suggest that ZjWRKYs play significant roles in phytoplasma tolerance and should be crucial candidate genes for jujube-phytoplasma interaction. CONCLUSIONS:54 ZjWRKYs in Chinese jujube were identified and classified into three subgroups. 41 ZjWRKYs were unevenly distributed along the chromosomes. The majority of ZjWRKYs were highly expressed in various tissues. Most of the ZjWRKYs were positive responses to phytoplasma invasion, and that provided candidate genes for the future studies of jujube-phytoplasma interaction.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Xue C,Li H,Liu Z,Wang L,Zhao Y,Wei X,Fang H,Liu M,Zhao Jdoi
10.1186/s12864-019-5789-8subject
Has Abstractpub_date
2019-06-07 00:00:00pages
464issue
1issn
1471-2164pii
10.1186/s12864-019-5789-8journal_volume
20pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Genome-scale metabolic models (GSMM) integrating transcriptomics have been widely used to study cancer metabolism. This integration is achieved through logical rules that describe the association between genes, proteins, and reactions (GPRs). However, current gene-to-reaction formulation lacks the stoichiome...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5979-4
更新日期:2019-08-15 00:00:00
abstract:BACKGROUND:The reconstruction of gene regulatory networks from high-throughput "omics" data has become a major goal in the modelling of living systems. Numerous approaches have been proposed, most of which attempt only "one-shot" reconstruction of the whole network with no intervention from the user, or offer only simp...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-S3-S17
更新日期:2009-12-03 00:00:00
abstract:BACKGROUND:The genetic mechanisms underlying hemangioblastoma development are still largely unknown. We used high-resolution single nucleotide polymorphism microarrays and droplet digital PCR analysis to detect copy number variations (CNVs) in total of 45 hemangioblastoma tumors. RESULTS:We identified 94 CNVs with a m...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2370-6
更新日期:2016-01-14 00:00:00
abstract:BACKGROUND:Research on the aryl hydrocarbon receptor (AHR) has largely focused on variations in toxic outcomes resulting from its activation by halogenated aromatic hydrocarbons. But the AHR also plays key roles in regulating pathways critical for development, and after decades of research the mechanisms underlying phy...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1053
更新日期:2014-12-03 00:00:00
abstract:BACKGROUND:Selenium (Se) is a trace element that occurs in proteins in the form of selenocysteine (Sec) and in tRNAs in the form of selenouridine (SeU). Selenophosphate synthetase (SelD) is required for both utilization traits. However, previous research also revealed SelDs in two organisms lacking Sec and SeU, suggest...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-251
更新日期:2008-05-29 00:00:00
abstract:BACKGROUND:Infectious disease outbreaks form major setbacks to aquaculture production and to further development of this important sector. Cyprinid herpes virus-3 (CyHV-3) is a dsDNA virus widely hampering production of common carp (Cyprinus carpio), one of the most farmed fish species worldwide. Genetically disease re...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6391-9
更新日期:2019-12-26 00:00:00
abstract:BACKGROUND:Whilst adaptive facultative sex allocation has been widely studied at the phenotypic level across a broad range of organisms, we still know remarkably little about its genetic architecture. Here, we explore the genome-wide basis of sex ratio variation in the parasitoid wasp Nasonia vitripennis, perhaps the b...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06904-4
更新日期:2020-07-20 00:00:00
abstract:BACKGROUND:Endogenous α-synuclein (α-Syn) is involved in many pathophysiological processes in the secondary injury stage after acute spinal cord injury (SCI), and the mechanism governing these functions has not been thoroughly elucidated to date. This research aims to characterize the effect of α-Syn knockdown on trans...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6244-6
更新日期:2019-11-14 00:00:00
abstract:BACKGROUND:The question of whether synonymous codon choice is affected by cellular tRNA abundance has been positively answered in many organisms. In some recent works, concerning the human genome, this relation has been studied, but no conclusive answers have been found. In the human genome, the variation in base compo...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-67
更新日期:2006-04-03 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::ᅟ: Upon publication of the original article [1], the authors had flagged that there was an error in Fig. 1c, as the key in this figure was displaying incorrectly. The colours had not displayed in the key in the final published article, and instead appear as plain white. ...
journal_title:BMC genomics
pub_type: 杂志文章,已发布勘误
doi:10.1186/s12864-018-4614-0
更新日期:2018-04-11 00:00:00
abstract:BACKGROUND:In plants carotenoids play an important role in the photosynthetic process and photo-oxidative protection, and are the substrate for the synthesis of abscisic acid and strigolactones. In addition to their protective role as antioxidants and precursors of vitamin A, in wheat carotenoids are important as they ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3395-6
更新日期:2017-01-31 00:00:00
abstract:BACKGROUND:Limited nutrient availability during development is associated with metabolic diseases in adulthood. The molecular cause for these defects is unclear. Here, we investigate if transcriptional changes caused by developmental malnutrition reveal an early response that can be linked to metabolism and metabolic d...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1654-6
更新日期:2015-06-04 00:00:00
abstract:BACKGROUND:Arrhythmogenic cardiomyopathy (ACM) is a genetic autosomal disease characterized by abnormal cell-cell adhesion, cardiomyocyte death, progressive fibro-adipose replacement of the myocardium, arrhythmias and sudden death. Several different cell types contribute to the pathogenesis of ACM, including, as recent...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4876-6
更新日期:2018-06-25 00:00:00
abstract:BACKGROUND:Phenomics provides new technologies and platforms as a systematic phenome-genome approach. However, few studies have reported on the systematic mining of shared genetics among clinical biochemical indices based on phenomics methods, especially in China. This study aimed to apply phenomics to systematically e...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6363-0
更新日期:2019-12-16 00:00:00
abstract:BACKGROUND:Two strains of the silver fox (Vulpes vulpes), with markedly different behavioral phenotypes, have been developed by long-term selection for behavior. Foxes from the tame strain exhibit friendly behavior towards humans, paralleling the sociability of canine puppies, whereas foxes from the aggressive strain a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-482
更新日期:2011-10-03 00:00:00
abstract:BACKGROUND:Identification of acute or recent hepatitis C virus (HCV) infections is important for detecting outbreaks and devising timely public health interventions for interruption of transmission. Epidemiological investigations and chemistry-based laboratory tests are 2 main approaches that are available for identifi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4269-2
更新日期:2017-12-06 00:00:00
abstract:BACKGROUND:Distinguishing orthologous and paralogous relationships between genes across multiple species is essential for comparative genomic analyses. Various computational approaches have been developed to resolve these evolutionary relationships, but strong trade-offs between precision and recall of orthologue predi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4079-6
更新日期:2017-08-31 00:00:00
abstract:BACKGROUND:Nicotiana benthamiana is a widely used model plant species for research on plant-pathogen interactions as well as other areas of plant science. It can be easily transformed or agroinfiltrated, therefore it is commonly used in studies requiring protein localization, interaction, or plant-based systems for pro...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2209-6
更新日期:2015-12-01 00:00:00
abstract:BACKGROUND:The Multinational Brassica rapa Genome Sequencing Project (BrGSP) has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for Brassica rapa. An integrated linkage map between the amphidiploid B. napus and diploid B. rapa will fac...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-594
更新日期:2010-10-22 00:00:00
abstract:BACKGROUND:Sheath blight (SB), caused by Rhizoctonia solani, is a common rice disease worldwide. Currently, rice cultivars with robust resistance to R. solani are still lacking. To provide theoretic basis for molecular breeding of R. solani-resistant rice cultivars, the changes of transcriptome profiles in response to ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6645-6
更新日期:2020-03-19 00:00:00
abstract:BACKGROUND:A major goal in the post-genomic era is to identify and characterise disease susceptibility genes and to apply this knowledge to disease prevention and treatment. Rodents and humans have remarkably similar genomes and share closely related biochemical, physiological and pathological pathways. In this work we...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-5-28
更新日期:2004-04-29 00:00:00
abstract:BACKGROUND:Effective bioinformatics solutions are needed to tackle challenges posed by industrial-scale genome annotation. We present Bcheck, a wrapper tool which predicts RNase P RNA genes by combining the speed of pattern matching and sensitivity of covariance models. The core of Bcheck is a library of subfamily spec...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-432
更新日期:2010-07-13 00:00:00
abstract:BACKGROUND:White spot syndrome (WSS) is a viral disease that affects most of the commercially important shrimps and causes serious economic losses to the shrimp farming industry worldwide. However, little information is available in terms of the molecular mechanisms of the host-virus interaction. In this study, we used...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-120
更新日期:2007-05-16 00:00:00
abstract:BACKGROUND:Genetic diversity within a species reflects population evolution, ecology, and ability to adapt. Genome-wide population surveys of both natural and introduced populations provide insights into genetic diversity, the evolutionary processes and the genetic basis underlying local adaptation. Grass carp is the m...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5872-1
更新日期:2019-06-07 00:00:00
abstract:BACKGROUND:New gene emergence is so far assumed to be mostly driven by duplication and divergence of existing genes. The possibility that entirely new genes could emerge out of the non-coding genomic background was long thought to be almost negligible. With the increasing availability of fully sequenced genomes across ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-117
更新日期:2013-02-21 00:00:00
abstract:BACKGROUND:Synthetic systems that use positive feedback have been developed to control human disease vectors and crop pests. The tTAV system, which has been deployed in several insect species, relies on a positive feedback circuit that can be inhibited via dietary tetracycline. Although insects carrying tTAV fail to su...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4385-z
更新日期:2017-12-28 00:00:00
abstract:BACKGROUND:The hard clam or northern quahog, Mercenaria mercenaria, is one of the most valuable seafood products in the United States representing the first marine resource in some Northeastern states. Severe episodes of hard clam mortality have been consistently associated with infections caused by a thraustochytrid p...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-245
更新日期:2014-03-28 00:00:00
abstract:BACKGROUND:Protein phosphorylation is responsible for a large portion of the regulatory functions of eukaryotic cells. Although the list of sequenced genomes of filamentous fungi has grown rapidly, the kinomes of recently sequenced species have not yet been studied in detail. The objective of this study is to apply a c...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-133
更新日期:2010-02-24 00:00:00
abstract:BACKGROUND:Circular chromosome conformation capture (4C) has provided important insights into three dimensional (3D) genome organization and its critical impact on the regulation of gene expression. We developed a new quantitative framework based on polymer physics for the analysis of paired-end sequencing 4C (PE-4Cseq...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2137-5
更新日期:2015-11-21 00:00:00