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 protein expression and purification. To discover and characterize the miRNAs and their cleaved target mRNAs in N. benthamiana, we sequenced small RNA transcriptomes and degradomes of two N. benthamiana accessions and validated them by Northern blots. RESULTS:We used a comprehensive molecular approach to detect and to experimentally validate N. benthamiana miRNAs and their target mRNAs from various tissues. We identified 40 conserved miRNA families and 18 novel microRNA candidates and validated their target mRNAs with a genomic scale approach. The accumulation of thirteen novel miRNAs was confirmed by Northern blot analysis. The conserved and novel miRNA targets were found to be involved in various biological processes including transcription, RNA binding, DNA modification, signal transduction, stress response and metabolic process. Among the novel miRNA targets we found the mRNA of REPRESSOR OF SILENCING (ROS1). Regulation of ROS1 by a miRNA provides a new regulatory layer to reinforce transcriptional gene silencing by a post-transcriptional repression of ROS1 activity. CONCLUSIONS:The identified conserved and novel miRNAs along with their target mRNAs also provides a tissue specific atlas of known and new miRNA expression and their cleaved target mRNAs of N. benthamiana. Thus this study will serve as a valuable resource to the plant research community that will be beneficial well into the future.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Baksa I,Nagy T,Barta E,Havelda Z,Várallyay É,Silhavy D,Burgyán J,Szittya Gdoi
10.1186/s12864-015-2209-6subject
Has Abstractpub_date
2015-12-01 00:00:00pages
1025issn
1471-2164pii
10.1186/s12864-015-2209-6journal_volume
16pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:In research laboratories using DNA-microarrays, usually a number of researchers perform experiments, each generating possible sources of error. There is a need for a quick and robust method to assess data quality and sources of errors in DNA-microarray experiments. To this end, a novel and cost-effective val...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-6-77
更新日期:2005-05-20 00:00:00
abstract:BACKGROUND:Gene knockouts are a critical resource for functional genomics. In Arabidopsis, comprehensive knockout collections were generated by amplifying and sequencing genomic DNA flanking insertion mutants. These Flanking Sequence Tags (FSTs) map each mutant to a specific locus within the genome. In maize, FSTs have...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-116
更新日期:2007-05-09 00:00:00
abstract:BACKGROUND:Fruit peel colour is an important agronomic trait for fruit quality. Cytosine methylation plays an important role in gene regulation. Although the DNA methylation level of a single gene is important to affect the phenotype of mutation, there are large unknown of difference of the DNA methylation in plant and...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5499-2
更新日期:2019-02-07 00:00:00
abstract:BACKGROUND:In the model legume Medicago truncatula, the near saturation genome-wide Tnt1 insertion mutant population in ecotype R108 is a valuable tool in functional genomics studies. Forward genetic screens have identified many Tnt1 mutants defective in nodule development and symbiotic nitrogen fixation (SNF). However...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2452-5
更新日期:2016-02-27 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:Chronic renal disease (CKD) is characterized by complex changes in cell metabolism leading to an increased production of oxygen radicals, that, in turn has been suggested to play a key role in numerous clinical complications of this pathological condition. Several reports have focused on the identification o...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-388
更新日期:2009-08-21 00:00:00
abstract:BACKGROUND:Skeletal muscle mass can be markedly reduced through a process called atrophy, as a consequence of many diseases or critical physiological and environmental situations. Atrophy is characterised by loss of contractile proteins and reduction of fiber volume. Although in the last decade the molecular aspects un...
journal_title:BMC genomics
pub_type: 杂志文章,meta分析
doi:10.1186/1471-2164-9-630
更新日期:2008-12-23 00:00:00
abstract:BACKGROUND:Engineered nanomaterials may release nanosized residues, by degradation, throughout their life cycle. These residues may be a threat for living organisms. They may be ingested by humans through food and water. Although the toxicity of pristine CeO2 nanoparticles (NPs) has been documented, there is a lack of ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-700
更新日期:2014-08-21 00:00:00
abstract:BACKGROUND:Genetic resistance in cattle is considered a suitable way to control tick burden and its consequent losses for livestock production. Exploring tick-resistant (R) and tick-susceptible (S) hosts, we investigated the genetic mechanisms underlying the variation of Braford resistance to tick infestation. Skin bio...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6360-3
更新日期:2019-12-19 00:00:00
abstract:BACKGROUND:Myostatin, a muscle-specific member of the Transforming Growth Factor beta family, negatively regulates muscle development. Double-muscled (DM) cattle have a loss-of-function mutation in their myostatin gene responsible for the hypermuscular phenotype. Thus, these animals are a good model for understanding t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-63
更新日期:2007-03-01 00:00:00
abstract:BACKGROUND:Over the last decade, emerging research methods, such as comparative genomic analysis and phylogenetic study, have yielded new insights into genotypes and phenotypes of closely related bacterial strains. Several findings have revealed that genomic structural variations (SVs), including gene gain/loss, gene d...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1259-0
更新日期:2015-02-14 00:00:00
abstract:BACKGROUND:Thymoma is a heterogeneous group of tumors in biology and clinical behavior. Even though thymoma is divided into five subgroups following the World Health Organization classification, the nature of the disease is mixed within the subgroups. RESULTS:We investigated the molecular characteristics of genetic ch...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-305
更新日期:2007-09-03 00:00:00
abstract:BACKGROUND:Prokaryotic translation initiation involves the proper docking, anchoring, and accommodation of mRNA to the 30S ribosomal subunit. Three initiation factors (IF1, IF2, and IF3) and some ribosomal proteins mediate the assembly and activation of the translation initiation complex. Although the interaction betwe...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1808-6
更新日期:2015-08-14 00:00:00
abstract:BACKGROUND:Cryptic unstable transcripts (CUTs) are a largely unexplored class of nuclear exosome degraded, non-coding RNAs in budding yeast. It is highly debated whether CUT transcription has a functional role in the cell or whether CUTs represent noise in the yeast transcriptome. We sought to ascertain the extent of c...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2622-5
更新日期:2016-04-26 00:00:00
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:Because of the advent of high-throughput sequencing and the consequent reduction in the cost of sequencing, many organisms have been completely sequenced and most of their genes identified. It thus has become possible to represent whole genomes as ordered lists of gene identifiers and to study the rearrangem...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-S2-S15
更新日期:2008-09-16 00:00:00
abstract:BACKGROUND:In mammals, CEACAM1 and closely related members represent paired receptors with similar extracellular ligand-binding regions and cytoplasmic domains with opposing functions. Human CEACAM1 and CEACAM3 which have inhibitory ITIM/ITSM and activating ITAM-like motifs, respectively, in their cytoplasmic regions a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3279-9
更新日期:2016-11-16 00:00:00
abstract:BACKGROUND:Rich in genetic information and cost-effective to genotype, the Insertion-Deletion (InDel) molecular marker system is an important tool for studies in genetics, genomics and for marker-assisted breeding. Advent of next-generation sequencing (NGS) revolutionized the speed and throughput of sequence data gener...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2614-5
更新日期:2016-04-14 00:00:00
abstract:BACKGROUND:The human neuroblastoma cell line, SH-SY5Y, is a commonly used cell line in studies related to neurotoxicity, oxidative stress, and neurodegenerative diseases. Although this cell line is often used as a cellular model for Parkinson's disease, the relevance of this cellular model in the context of Parkinson's...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1154
更新日期:2014-12-20 00:00:00
abstract:BACKGROUND:Aging is affected by genetic and environmental factors, and cigarette smoking is strongly associated with accumulation of senescent cells. In this study, we wanted to identify genes that may potentially be beneficial for cell survival in response to cigarette smoke and thereby may contribute to development o...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5409-z
更新日期:2019-01-09 00:00:00
abstract:BACKGROUND:Skin and its mucus are known to be the first barrier of defence against any external stressors. In fish, skin wounds frequently appear as a result of intensive culture and also some diseases have skin ulcers as external clinical signs. However, there is no information about the changes produced by the wounds...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4349-3
更新日期:2017-12-02 00:00:00
abstract:BACKGROUND:An underlying tenet of the epigenetic code hypothesis is the existence of protein domains that can recognize various chromatin structures. To date, two major candidates have emerged: (i) the bromodomain, which can recognize certain acetylation marks and (ii) the chromodomain, which can recognize certain meth...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-6
更新日期:2006-01-16 00:00:00
abstract:BACKGROUND:Petal nectar spurs, which facilitate pollination through animal attraction and pollen placement, represent a key innovation promoting diversification in the genus Aquilegia (Ranunculaceae). Identifying the genetic components that contribute to the development of these three-dimensional structures will inform...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6002-9
更新日期:2019-08-22 00:00:00
abstract::As gene expression profile data from DNA microarrays accumulate rapidly, there is a natural need to compare data across labs and platforms. Comparisons of microarray data can be quite challenging due to data complexity and variability. Different labs may adopt different technology platforms. One may ask about the degr...
journal_title:BMC genomics
pub_type: 杂志文章,多中心研究
doi:10.1186/1471-2164-6-71
更新日期:2005-05-11 00:00:00
abstract:BACKGROUND:Evolutionary theory indicates that the dynamics of aging in the soma and reproductive tissues may be distinct. This difference arises from the fact that only the germline lineage establishes future generations. In the soma, changes in the landscape of heterochromatin have been proposed to have an important r...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5668-3
更新日期:2019-04-23 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) regulate the expression of target genes by mediating gene silencing in both plants and animals. The miRNA targets have been extensively investigated in Arabidopsis and rice using computational prediction, experimental validation by overexpression in transgenic plants, and by degradome or P...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-310
更新日期:2012-07-16 00:00:00
abstract:BACKGROUND:Cytoplasmic male sterility (CMS) is an inability to produce functional pollen that is caused by mutation of the mitochondrial genome. Comparative analyses of mitochondrial genomes of lines with and without CMS in several species have revealed structural differences between genomes, including extensive rearra...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-561
更新日期:2014-07-04 00:00:00
abstract:BACKGROUND:Next generation sequencing (NGS) has become a universal practice in modern molecular biology. As the throughput of sequencing experiments increases, the preparation of conventional multiplexed libraries becomes more labor intensive. Conventional library preparation typically requires quality control (QC) tes...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6481-8
更新日期:2020-01-28 00:00:00
abstract:BACKGROUND:Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici, is a costly global disease that burdens farmers with yield loss and high fungicide expenses. This sophisticated biotrophic parasite infiltrates wheat leaves and develops infection structures inside host cells, appropriating nutrients while sup...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1895-4
更新日期:2015-09-21 00:00:00
abstract:BACKGROUND:The pattern of point mutation is important for studying mutational mechanisms, genome evolution, and diseases. Previous studies of mutation direction were largely based on substitution data from a limited number of loci. To date, there is no genome-wide analysis of mutation direction or methylation-dependent...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-316
更新日期:2006-12-13 00:00:00