Abstract Almost all plants in the genus Populus are dioecious (i.e. trees either male or female), but it is unknown whether dioecy evolved a common ancestor independently different subgenera. Here, we sequence small peritelomeric X- and Y-linked regions of P. deltoides chromosome XIX. Two genes present only region. One duplication non-Y-linked, female-specifically expressed response regulator, which produces siRNAs that block this gene’s expression, repressing femaleness. The other an...

Although organellar genomes (including chloroplast and mitochondrial genomes) are smaller than nuclear in size gene number, very important for the investigation of plant evolution molecular ecology mechanisms. Few studies have focused on horticultural plants. Approximately 1193 199 land plants available National Center Biotechnology Information (NCBI), which only 39 from In this paper, we report an innovative efficient method high-quality genome assembly next-generation sequencing (NGS)...

Collaborative filtering is one of the most important algorithms applied in e-commerce recommendation systems. The conventional calculations similarities are inefficient, which suffers from data sparsity and poor prediction quality problems. In order to overcome limitations, a new collaborative algorithm based on item clustering global similarity proposed. Firstly, K-MEANS cluster items into several classes users' ratings items, local user calculated each cluster. addition, factor overlap...

Salix suchowensis is an early-flowering shrub willow that provides a desirable system for studies on the basic biology of woody plants. The current reference genome S. was assembled with 454 sequencing reads. Here, we report chromosome-scale assembly generated by combining PacBio Hi-C technologies. obtained assemblies covered total length 356 Mb. contig N50 these 263,908 bp, which ~65-fold higher than reported previously. contiguity and completeness were significantly improved. By applying...

In order to overcome the limitations of data sparsity and inaccurate similarity in personalized recommendation systems, a new collaborative filtering algorithm by using items categories interestingness measure is proposed. this algorithm, first matrix constructed calculating item-item category distance, then analyzes correlation degree different measure, last an improved proposed combining information with utilizing conditional probability method as standard measure. Experimental results...

Background . In order to understand the colocalization of genetic loci amongst species, synteny and collinearity analysis is a frequent task in comparative genomics research. However many software packages are not effective visualizing results. Problems include lack graphic visualization, simple representation, or inextensible format outputs. Moreover, higher throughput sequencing technology requires resolution image output. Implementation To fill this gap, paper publishes VGSC, Vector Graph...

The phytohormone auxin plays a pivotal role in the regulation of plant growth and development, including vascular differentiation tree growth. auxin/indole-3-acetic acid (Aux/IAA) response transcription factor (ARF) genes are key components signaling. To gain more insight into functional features Aux/IAA ARF during these processes, we identified 38 AUX/IAA 34 genome Salix suchowensis characterized their gene structures, conserved domains, encoded amino compositions. Phylogenetic analysis...

Populus (poplars) and Salix (willows) are sister genera in the Salicaceae family that arise from a common tetraploid ancestor. The karyotypes of these two lineages distinguished by major interchromosomal some minor intrachromosomal rearrangements, but which one is evolutionarily more primitive remains debatable. In this study, we compare selection pressure acting on paralogous genes resulting salicoid duplication (PGRS) within between genomes lineages. Purifying was determined to act...

Cytokinins have vital effects on various plant development-related processes. Type-A response regulators (RRs) are among the most important in cytokinin signaling pathway. Specifically, RR genes primary cytokinin-responsive genes, encode negative of signaling. Similar sex-determining mechanisms involving a type-A homolog recently been identified sister genera Populus and Salix. Here, we aimed to identify characterize gene family members deltoides. On basis conserved receiver domain...

Plant mitochondrial (mt) genomes possess several complex features, including a variable size, dynamic genome structure, and complicated patterns of gene loss gain throughout evolutionary history. Studies plant mt can, therefore, provide unique insights into organelle evolution. We assembled the complete Salix purpurea L. by screening genomic sequence reads generated Roche-454 pyrosequencing platform. The pseudo-molecule obtained has typical circular structure 598,970 bp long, with an overall...

The complete mitochondrial genome of Medicago truncatula (M. truncatula) was reported in this study. (mitogenome) assembled to 271 618 nt. mitogenome contains 31 protein-coding genes, three rRNA genes and 16 tRNAs. overall base composition the descending order is A: 27.21%, C: 22.61%, G: 22.78% T: 27.40%, G + C content 45.39%. Additionally, 30 exons 17 introns were identified eight nine tandem repeats with period size from 10 nt 33 Phylogenetic analysis shows that M. evolutionarily closest...

Labile sex expression is frequently observed in dioecious plants, but the underlying genetic mechanism remains largely unknown. Sex plasticity also many Populus species. Here we carried out a systematic study on maleness-promoting gene, MSL, detected deltoides genome. Our results showed that both strands of MSL contained multiple cis-activating elements, which generated long non-coding RNAs (lncRNAs) promoting maleness. Although female P. did not have male-specific large number partial...

Identification of the particular genes in an R supercluster underlying resistance to rust fungus Melampsora larici-populina poplar genome remains challenging. Based on de novo assembly Populus deltoides genome, all detected major genetic loci conferring M. were confined a 3.5-Mb region chromosome 19. The transcriptomes resistant and susceptible genotypes sequenced for timespan from 0 168 hours postinoculation. By mapping differentially expressed target genomic region, we identified two...

Streptococcus mutans is generally considered to be the principal aetiological agent for dental caries. Phenotypic variation in strains often associated with differences gene content, so isolation of DNA fragments from these genes or regions illuminating. The S. 9‐1 and 9‐2, which both colonized same oral cavity, were selected after screening possession suspected virulence traits. Genomic strain was used as tester, that 9‐2 driver. Suppression subtractive hybridization (SSH) applied between...

The complete nucleotide sequences of the mitochondrial (mt) genome an extremophile species Thellungiella parvula (T. parvula) have been determined with lengths 255,773 bp. T. mt is a circular sequence and contains 32 protein-coding genes, 19 tRNA three ribosomal RNA genes 11.5% coding sequence. base composition 27.5% A, T, 22.7% C, 22.3% G in descending order shows slight bias 55% AT. Fifty-three repeats were identified parvula, including 24 direct repeats, 28 tandem (TRs), one palindromic...

The effects of heavy metals mercury and lead on microbial biomass carbon nitrogen in soil were studied. results indicate that all show their toxic nitrogen, while the toxicity mercury, is much larger than lead. As to Mercury, critical content which resulted significant reduction 0.6 mg/kg soil, for 0.8 mg/kg•soil. lead, 150 mg/kg•soil carbon, 100 nitrogen. For when contents respectively between 0.6-1.2 150- 200 mg/kg•soil, had a sudden increasing, worthwhile phenomenon study future.

Abstract Plant sex determining systems and chromosomes are often evolutionarily young. Here, we present the early stage of chromosome in a fully dioecious plant, P. deltoides , by separate sequences physically small X- Y-linked regions. Intriguingly, two Y genes absent from X counterpart. One gene represses female structures producing siRNAs that block expression necessary for development structures, via RNA-directed DNA methylation siRNA-guided mRNA cleavage. The other generates long...

Elucidating the genetic factors underlying long-term biological processes remains challenging since relevant genes and their effects may vary across different developmental stages. In this study, we carried out a large-scale field trial of progeny an F1 full-sib pedigree Salix suchowensis measured plant height ground diameter periodically over time course 240 days. With obtained data, characterized growth rhythms performed time-sequential analyses quantitative trait loci dynamic plants. The...

Gene expression profiling data provide useful information for the investigation of biological function and process. However, identifying a specific pattern from extensive time series gene is not an easy task. Clustering, popular method, often used to classify similar genes, however, genes with 'desirable' or 'user-defined' cannot be efficiently detected by clustering methods. To address these limitations, we developed online tool called GEsture. Users can draw, graph curve using mouse...