Abstract Background MicroRNAs (miRNAs) play a critical role in post-transcriptional gene regulation and have been shown to control many genes involved various biological metabolic processes. There extensive studies discover miRNAs analyze their functions model plant species, such as Arabidopsis rice. Deep sequencing technologies facilitated identification of species-specific or lowly expressed well conserved highly plants. Results In this research, we used Solexa new microRNAs trifoliate...

The production and weathering processes of nanoparticles (NPs) introduce charged functional groups on their surface. Previous studies have found that the surface charge properties NPs play a critical role in toxic effects mechanisms are generally attributed to different accumulations transmembrane potentials. Currently, we still lack sufficient knowledge about effects, owing unique structures these polymers. In this study, positively (PS-NH2, 50 nm) at 0.05-0.5 μg mL-1 promoted proliferation...

Polyploidy provides evolutionary and morphological novelties in many plants some animals. However, the role of genome dosage composition gene expression changes remains poorly understood. Here, we generated a series resynthesized Arabidopsis tetraploids that contain 0–4 copies thaliana arenosa genomes investigated ploidy hybridity effects on expression. Allelic can be defined as dependent (expression levels correlate with dosages) or otherwise independent. show dosage-dependent genes...

Arabidopsis seed development involves maternal small interfering RNAs (siRNAs) that induce RNA-directed DNA methylation (RdDM) through the NRPD1 -mediated pathway. To investigate their biological functions, we characterized siRNAs in endosperm and coat were separated by laser-capture microdissection (LCM) reciprocal genetic crosses with an nrpd1 mutant. We also monitored spatial-temporal activity of pathway on using AGO4:GFP::AGO4 (promoter:GFP::protein) reporter promoter:GUS sensors...

MicroRNAs (miRNAs) are a class of non-coding RNA molecules which have significant gene regulation roles in organisms. The advent new high-throughput sequencing technologies has enabled the discovery novel miRNAs. Although there two recent reports on analysis small libraries from different organs wine grapevine varieties, was divergence number and kinds miRNAs sequenced these studies. More is still important for grapevine. In this study, total 130 conserved Vitis vinifera miRNA (Vv-miRNA)...

Abstract Summary: In plants, many trans-acting small interfering RNA (ta-siRNA) regulatory pathways have been identified as significant components of the gene networks involved in development, metabolism, responses to biotic and abiotic stresses DNA methylation at TAS locus. To obtain a more comprehensive understanding on nature ta-siRNA pathways, we developed freely accessible resource, tasiRNAdb, serve repository for sequences pathway-related microRNAs, TASs, ta-siRNAs targets, cascading...

Abstract Motivation: Trans-acting small interfering RNAs (ta-siRNAs) play an essential role in the regulation of plant gene expression, but relevant reports are still limited. Bioinformatic analyses indicate that many ta-siRNA-producing loci (TASs) present plants, implying existence as yet undiscovered ta-siRNAs and related regulatory pathways. To expand our knowledge these regulators, we applied high-throughput computational experimental methods to grapevine (Vitis vinifera L.). Results:...

Phenotypic variation within organisms is driven primarily by genetic diversity. However, there a growing appreciation that epigenetic variation, resulting from multitude of diverse chemical modifications to the DNA and chromatin, can have profound effects on phenotype. Heritable marks persist through meiosis be stably transmitted next generation, in transgenerational inheritance. Importantly, when changes occur near coding genes, affecting their transcriptional state, heritable result...

Background With the completion of genome sequencing projects for more than 30 plant species, large volumes sequences have been produced and stored in online databases. Advancements technologies reduced cost time whole enabling plants to be subjected sequencing. Despite this, sequence qualities multiple not evaluated. Methodology/Principal Finding Integrity accuracy were calculated evaluate quality 32 plants. The integrity a is presented by ratio chromosome size (or between scaffold size),...

The diversity of ericoid mycorrhizal fungi isolated from Rhododendron decorum Franch. in Yunnan, southwestern China, was examined for the first time. In total 300 hair-root samples were collected 13 R. individuals two adjacent wild population sites and one cultivated site. Two hundred eighteen slow-growing isolates obtained; ability some to form mycorrhiza tested vitro. One twenty-five formed hyphal structures morphologically corresponding mycorrhiza, these determined by morphological...

Abstract Background Dendrobium spp. comprise a group of tropical orchids with ornamental and medicinal value. are sensitive to low temperature, the underlying cold response regulatory mechanisms in this unclear. To understand how these plants respond stress, we compared transcriptomic responses cold-tolerant cultivar ‘Hongxing’ (HX) cold-sensitive ‘Sonia Hiasakul’ (SH) stress. Results Chemometric results showed that physiological SH later stages stress is similar HX throughout treatment....

Rhododendron Linnaeus (1753: 392) is one of the largest genera in family Ericaceae, which subject to much ongoing taxonomic debate. About 1,025 species are recognized; these distributed from northern temperate zone, throughout tropical Southeast Asia, northeastern Australia (Chamberlain et al. 1996). In China, there 571 classified 6 subgenera, 405 endemic (Fang 2005). Apart Xinjiang and Ningxia, Rhododendrons have been documented all other provinces (Ma 2014; Wu

The production of small RNAs (sRNAs) from phased positions set by microRNA-directed cleavage trans-acting-siRNA-producing locus (TAS) transcript has been characterized extensively; however, the sRNAs non-phased remains unknown. We report three cis-cleavages that occurred in TAS3 transcripts Vitis vinifera, combining high-throughput sRNA deep sequencing information with evolutional conservation and genome-wide RNA degradome analysis. can be deciphered to generate an orderly cascade, also...

miRNAs are important regulators of plant gene expression. To better characterize their functions, we applied high-throughput sequencing and degradome analyses to investigate three blueberry (Vaccinium ashei) tissues. A total 127 known 101 novel were identified. Moreover, 141 targets for 42 19 experimentally validated by sequencing. functional analysis these miRNA revealed they associated with diverse biological activities several pathways, e.g., anthocyanin biosynthesis cytokinin signal...

Cultivar identification is a key step to avoid the formation of homonyms and synonyms Ginkgo biloba.In this study, new approach based on combinational utilization polymorphic bands produced from 6 different random amplified DNA (RAPD) primers was developed for identifying 42 cultivars, manual cultivar diagram that consisted RAPD reported.To check reliability efficiency diagram, 5 randomly chosen cultivars were further tested, workability verified.This will be very helpful discrimination...

Background: Tobacco bacterial wilt caused by Ralstonia solanacearum is a devastating disease in Solanaceae crops and the pathogen notorious worldwide.Methodology: The phenotypic characterization of R. under various osmolytes pH environments were analyzed using biolog Phenotype Microarray system (PMs).Using PM plates 9 10, 192 different assays tested, including 96 environments.Results: Result presented that all four isolates exhibited similar fingerprints.They had wide range adaptabilities...

Endogenous small non-coding RNAs play pivotal roles in regulating gene expression eukaryotes. Many studies have investigated the function and molecular mechanism of microRNAs development disease various organisms via mRNA repression protein-coding genes. Recent findings indicate might trigger generation trans-acting interfering (ta-siRNAs). The interaction among different types RNA molecules reveals an even more complicated elaborate pattern regulation during than previously thought. We...

Abstract Stripe rust, caused by Puccinia striiformis f.sp. tritici ( Pst ), is one of the most widespread and destructive diseases wheat worldwide. Resistance breeding constantly pursued for decades to tackle variations prevalent races. Zhongliang 12 has strong resistance abiotic stresses, wide adaptability, higher stripe rust excellent biological characteristics. To identify gene(s) against was crossed with susceptible genotype Mingxian 169, F 1 , 2 : 3 BC progenies were tested Chinese race...

Abstract Background Current approaches for identifying transcriptional regulatory elements are mainly via the combination of two properties, evolutionary conservation and overrepresentation functional in promoters co-regulated genes. Despite development many motif detection algorithms, discovery conserved motifs a wide range phylogenetically related is still challenge, especially short embedded distantly gene or very closely promoters, situation that there not enough orthologous genes...

The Arabidopsis DEMETER (DME) DNA glycosylase demethylates the central cell genome prior to fertilization. This epigenetic reconfiguration of female gamete companion establishes gene imprinting in endosperm and is essential for seed viability. DME small genic-flanking transposons as well intergenic heterochromatin sequences, but how recruited these loci remains unknown. H1.2 was identified a DME-interacting protein yeast two-hybrid screen, maternal H1 loss affects methylation expression...