MiR1444a Is Involved in the Response of Populus trichocarpa to Zinc Stress

2012 ◽  
Vol 42 (10) ◽  
pp. 850-860 ◽  
Author(s):  
ShanFa LU ◽  
HaiYing WANG ◽  
LiChai YUAN ◽  
XiuNa CUI ◽  
XiangYun WU ◽  
...  
Keyword(s):  
Populus Trichocarpa ◽  
Zinc Stress

Betaines and free amino acids in salt stressed vitroplants and winter resting buds of Populus trichocarpa x deltoides

1991 ◽  
Vol 83 (1) ◽  
pp. 136-143 ◽  
Author(s):  
L. Bray ◽  
D. Chriqui ◽  
K. Gloux ◽  
D. Le Rudulier ◽  
M. Meyer ◽  
...  
Keyword(s):  
Amino Acids ◽  
Free Amino Acids ◽  
Free Amino ◽  
Populus Trichocarpa

PlncRNADB: A Repository of Plant lncRNAs and lncRNA-RBP Protein Interactions

2019 ◽  
Vol 14 (7) ◽  
pp. 621-627 ◽  
Author(s):  
Youhuang Bai ◽  
Xiaozhuan Dai ◽  
Tiantian Ye ◽  
Peijing Zhang ◽  
Xu Yan ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Populus Trichocarpa ◽  
Noncoding Rnas ◽  
Reference Database ◽  
Protein Coding ◽  
Arabidopsis Lyrata ◽  
User Friendly

Background: Long noncoding RNAs (lncRNAs) are endogenous noncoding RNAs, arbitrarily longer than 200 nucleotides, that play critical roles in diverse biological processes. LncRNAs exist in different genomes ranging from animals to plants. Objective: PlncRNADB is a searchable database of lncRNA sequences and annotation in plants. Methods: We built a pipeline for lncRNA prediction in plants, providing a convenient utility for users to quickly distinguish potential noncoding RNAs from protein-coding transcripts. Results: More than five thousand lncRNAs are collected from four plant species (Arabidopsis thaliana, Arabidopsis lyrata, Populus trichocarpa and Zea mays) in PlncRNADB. Moreover, our database provides the relationship between lncRNAs and various RNA-binding proteins (RBPs), which can be displayed through a user-friendly web interface. Conclusion: PlncRNADB can serve as a reference database to investigate the lncRNAs and their interaction with RNA-binding proteins in plants. The PlncRNADB is freely available at http://bis.zju.edu.cn/PlncRNADB/.

Codon Usage of Expansin Genes in Populus trichocarpa

2017 ◽  
Vol 12 (5) ◽  
Author(s):  
Jian Li ◽  
Haoyang Li ◽  
Junkai Zhi ◽  
Chuzhao Shen ◽  
Xuesong Yang ◽  
...  
Keyword(s):  
Codon Usage ◽  
Populus Trichocarpa

scholarly journals Structural characterization and duplication modes of pseudogenes in plants

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Flavia Mascagni ◽  
Gabriele Usai ◽  
Andrea Cavallini ◽  
Andrea Porceddu
Keyword(s):  
Evolutionary Rate ◽  
Populus Trichocarpa ◽  
Sequence Divergence ◽  
Strand Break ◽  
Whole Genome ◽  
Flanking Sequence ◽  
Plant Genomes ◽  
High Sequence Divergence ◽  
Flanking Regions

AbstractWe identified and characterized the pseudogene complements of five plant species: four dicots (Arabidopsis thaliana, Vitis vinifera, Populus trichocarpa and Phaseolus vulgaris) and one monocot (Oryza sativa). Retroposition was considered of modest importance for pseudogene formation in all investigated species except V. vinifera, which showed an unusually high number of retro-pseudogenes in non coding genic regions. By using a pipeline for the classification of sequence duplicates in plant genomes, we compared the relative importance of whole genome, tandem, proximal, transposed and dispersed duplication modes in the pseudo and functional gene complements. Pseudogenes showed higher tendencies than functional genes to genomic dispersion. Dispersed pseudogenes were prevalently fragmented and showed high sequence divergence at flanking regions. On the contrary, those deriving from whole genome duplication were proportionally less than expected based on observations on functional loci and showed higher levels of flanking sequence conservation than dispersed pseudogenes. Pseudogenes deriving from tandem and proximal duplications were in excess compared to functional loci, probably reflecting the high evolutionary rate associated with these duplication modes in plant genomes. These data are compatible with high rates of sequence turnover at neutral sites and double strand break repairs mediated duplication mechanisms.

scholarly journals A peroxisomal β-oxidative pathway contributes to the formation of C6–C1 aromatic volatiles in poplar

2021 ◽  
Author(s):  
Nathalie D Lackus ◽  
Axel Schmidt ◽  
Jonathan Gershenzon ◽  
Tobias G Köllner
Keyword(s):  
Cinnamic Acid ◽  
Aromatic Compounds ◽  
Populus Trichocarpa ◽  
Alternative Pathway ◽  
Gene Families ◽  
Defense Responses ◽  
In Planta ◽  
Black Cottonwood ◽  
Oxidative Pathway

AbstractBenzenoids (C6–C1 aromatic compounds) play important roles in plant defense and are often produced upon herbivory. Black cottonwood (Populus trichocarpa) produces a variety of volatile and nonvolatile benzenoids involved in various defense responses. However, their biosynthesis in poplar is mainly unresolved. We showed feeding of the poplar leaf beetle (Chrysomela populi) on P. trichocarpa leaves led to increased emission of the benzenoid volatiles benzaldehyde, benzylalcohol, and benzyl benzoate. The accumulation of salicinoids, a group of nonvolatile phenolic defense glycosides composed in part of benzenoid units, was hardly affected by beetle herbivory. In planta labeling experiments revealed that volatile and nonvolatile poplar benzenoids are produced from cinnamic acid (C6–C3). The biosynthesis of C6–C1 aromatic compounds from cinnamic acid has been described in petunia (Petunia hybrida) flowers where the pathway includes a peroxisomal-localized chain shortening sequence, involving cinnamate-CoA ligase (CNL), cinnamoyl-CoA hydratase/dehydrogenase (CHD), and 3-ketoacyl-CoA thiolase (KAT). Sequence and phylogenetic analysis enabled the identification of small CNL, CHD, and KAT gene families in P. trichocarpa. Heterologous expression of the candidate genes in Escherichia coli and characterization of purified proteins in vitro revealed enzymatic activities similar to those described in petunia flowers. RNA interference-mediated knockdown of the CNL subfamily in gray poplar (Populus x canescens) resulted in decreased emission of C6–C1 aromatic volatiles upon herbivory, while constitutively accumulating salicinoids were not affected. This indicates the peroxisomal β-oxidative pathway participates in the formation of volatile benzenoids. The chain shortening steps for salicinoids, however, likely employ an alternative pathway.

scholarly journals Functional Characterisation of the Poplar Atypical Aspartic Protease Gene PtAP66 in Wood Secondary Cell Wall Deposition

Forests ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1002
Author(s):  
Shenquan Cao ◽  
Cong Wang ◽  
Huanhuan Ji ◽  
Mengjie Guo ◽  
Jiyao Cheng ◽  
...  
Keyword(s):  
Cell Wall ◽  
Secondary Cell Wall ◽  
Fluorescent Protein ◽  
Secondary Xylem ◽  
Populus Trichocarpa ◽  
Wood Formation ◽  
Protease Gene ◽  
Cellulose Content ◽  
Transcription Analysis ◽  
Functional Characterisation

Secondary cell wall (SCW) deposition is an important process during wood formation. Although aspartic proteases (APs) have been reported to have regulatory roles in herbaceous plants, the involvement of atypical APs in SCW deposition in trees has not been reported. In this study, we characterised the Populus trichocarpa atypical AP gene PtAP66, which is involved in wood SCW deposition. Transcriptome data from the AspWood resource showed that in the secondary xylem of P. trichocarpa, PtAP66 transcripts increased from the vascular cambium to the xylem cell expansion region and maintained high levels in the SCW formation region. Fluorescent signals from transgenic Arabidopsis plant roots and transiently transformed P. trichocarpa leaf protoplasts strongly suggested that the PtAP66-fused fluorescent protein (PtAP66-GFP or PtAP66-YFP) localised in the plasma membrane. Compared with the wild-type plants, the Cas9/gRNA-induced PtAP66 mutants exhibited reduced SCW thickness of secondary xylem fibres, as suggested by the scanning electron microscopy (SEM) data. In addition, wood composition assays revealed that the cellulose content in the mutants decreased by 4.90–5.57%. Transcription analysis further showed that a loss of PtAP66 downregulated the expression of several SCW synthesis-related genes, including cellulose and hemicellulose synthesis enzyme-encoding genes. Altogether, these findings indicate that atypical PtAP66 plays an important role in SCW deposition during wood formation.

scholarly journals Genome-wide analysis of UGDH genes in Populus trichocarpa and responsiveness to nitrogen treatment

3 Biotech ◽  
2021 ◽  
Vol 11 (3) ◽  
Author(s):  
Shuang Zhang ◽  
Lina Cao ◽  
Xue Sun ◽  
Jiajie Yu ◽  
Xiuyue Xu ◽  
...  
Keyword(s):  
Populus Trichocarpa ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Nitrogen Treatment

scholarly journals Variation of growth and phenology traits in poplars planted in clonal trials in Northern Europe—implications for breeding

2021 ◽  
Author(s):  
Anneli Adler ◽  
Almir Karacic ◽  
Ann-Christin Rönnberg Wästljung ◽  
Ulf Johansson ◽  
Kaspars Liepins ◽  
...  
Keyword(s):  
Baltic Sea ◽  
Populus Trichocarpa ◽  
Selection Criterion ◽  
Volume Index ◽  
Northern Europe ◽  
Bud Burst ◽  
The Baltic Sea ◽  
European Climate ◽  
Baltic Sea Region ◽  
The Baltic

AbstractThe increased demand for wood to replace oil-based products with renewable products has lifted focus to the Baltic Sea region where the environment is favorable for woody biomass growth. The aim of this study was to estimate broad-sense heritabilities and genotype-by-environment (G×E) interactions in growth and phenology traits in six climatically different regions in Sweden and the Baltics. We tested the hypothesis that both bud burst and bud set have a significant effect on the early growth of selected poplar clones in Northern Europe. Provenance hybrids of Populus trichocarpa adapted to the Northern European climate were compared to reference clones with adaptation to the Central European climate. The volume index of stemwood was under low to medium genetic control with heritabilities from 0.22 to 0.75. Heritabilities for phenology traits varied between 0.31 and 0.91. Locally chosen elite clones were identified. G×E interactions were analyzed using pairwise comparisons of the trials. Three different breeding zones for poplars between the latitudes of 55° N and 60° N in the Baltic Sea Region were outlined. The studied provenance hybrids with origin from North America offer a great possibility to broaden the area with commercial poplar plantations in Northern Europe and further improve the collection of commercial clones to match local climates. We conclude that phenology is an important selection criterion after growth.

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