Poplar Genome Microarrays

2011 ◽  
pp. 112-127 ◽  
Author(s):  
Chung-Jui Tsai ◽  
Priya Ranjan ◽  
Stephen DiFazio ◽  
Gerald Tuskan ◽  
Virgil Johnson
Keyword(s):  
Poplar Genome

scholarly journals Genome-Wide Analysis of Multiple Organellar RNA Editing Factor Family in Poplar Reveals Evolution and Roles in Drought Stress

2019 ◽  
Vol 20 (6) ◽  
pp. 1425 ◽  
Author(s):  
Dongli Wang ◽  
Sen Meng ◽  
Wanlong Su ◽  
Yu Bao ◽  
Yingying Lu ◽  
...  
Keyword(s):  
Drought Stress ◽  
Rna Editing ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Structural Features ◽  
Specific Expression ◽  
Poplar Genome ◽  
Physiological Processes ◽  
Genome Wide

Poplar (Populus) is one of the most important woody plants worldwide. Drought, a primary abiotic stress, seriously affects poplar growth and development. Multiple organellar RNA editing factor (MORF) genes—pivotal factors in the RNA editosome in Arabidopsis thaliana—are indispensable for the regulation of various physiological processes, including organelle C-to-U RNA editing and plasmid development, as well as in the response to stresses. Although the poplar genome sequence has been released, little is known about MORF genes in poplar, especially those involved in the response to drought stress at the genome-wide level. In this study, we identified nine MORF genes in the Populus genome. Based on the structural features of MORF proteins and the topology of the phylogenetic tree, the P. trichocarpa (Ptr) MORF family members were classified into six groups (Groups I–VI). A microsynteny analysis indicated that two (22.2%) PtrMORF genes were tandemly duplicated and seven genes (77.8%) were segmentally duplicated. Based on the dN/dS ratios, purifying selection likely played a major role in the evolution of this family and contributed to functional divergence among PtrMORF genes. Moreover, analysis of qRT-PCR data revealed that PtrMORFs exhibited tissue- and treatment-specific expression patterns. PtrMORF genes in all group were involved in the stress response. These results provide a solid foundation for further analyses of the functions and molecular evolution of MORF genes in poplar, and, in particular, for improving the drought resistance of poplar by genetics manipulation.

scholarly journals Duplication of NRAMP3 gene in poplars generated two homologous transporters with distinct functions

2021 ◽  
Author(s):  
Mathieu Pottier ◽  
Van Anh Le Thi ◽  
Catherine Primard-Brisset ◽  
Jessica Marion ◽  
Michele Bianchi ◽  
...  
Keyword(s):  
Metal Binding ◽  
Secretory Pathway ◽  
Expression System ◽  
Purifying Selection ◽  
Confocal Imaging ◽  
Metal Transporters ◽  
Cell Transport ◽  
Poplar Genome ◽  
Metal Transporter ◽  
Golgi Network

ABSTRACTTransition metals are essential for a wealth of metabolic reactions, but their concentrations need to be tightly controlled across cells and cell compartments, as metal excess or imbalance has deleterious effects. Metal homeostasis is achieved by a combination of metal transport across membranes and metal binding to a variety of molecules. Gene duplication is a key process in evolution, as emergence of advantageous mutations on one of the copies can confer a new function. Here, we report that the poplar genome contains two paralogues encoding NRAMP3 metal transporters localized in tandem. All Populus species analyzed had two copies of NRAMP3, whereas only one could be identified in Salix species indicating that duplication occurred when the two genera separated. Both copies are under purifying selection and encode functional transporters, as shown by expression in the yeast heterologous expression system. However, genetic complementation revealed that only one of the paralogues has retained the original function in release of metals stored in the vacuole previously characterized in A. thaliana. Confocal imaging showed that the other copy has acquired a distinct localization to the Trans Golgi Network (TGN). Expression in poplar indicated that the copy of NRAMP3 localized on the TGN has a novel function in the control of cell-to-cell transport of manganese. This work provides a clear case of neo-functionalization through change in the subcellular localization of a metal transporter as well as evidence for the involvement of the secretory pathway in cell-to-cell transport of manganese.

Genome-Wide Identification and Characterization of the FAR1/FHY3 Family in Populus trichocarpa Torr. & Gray and Expression Analysis in Light Response

Forests ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1385
Author(s):  
Jiujun Du ◽  
Lei Zhang ◽  
Xiaolan Ge ◽  
Xiaodong Xiang ◽  
Demei Cao ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Higher Plants ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Light Response ◽  
Cis Acting ◽  
Poplar Genome ◽  
Genome Wide ◽  
Identification And Characterization

Light is an important environmental factor for plant growth, and in higher plants, phytochrome A (phyA) is the predominant far-red photoreceptor, involved in various photoresponses. The FAR1/FHY3 transcription factor family, derived from transposases, is able to regulate plant development in response to multiple photosensitizers phytochrome. In total, 51 PtrFRSs were identified in the poplar genome, and were divided into 4 subfamilies. Among them, 47 PtrFRSs are located on 17 chromosomes. Upstream cis-acting elements of the PtrFRS genes were classified into three categories: growth and metabolism, stress and hormone, and the hormone and stress categories contained most of the cis-acting elements. Analysis of the regulatory networks and expression patterns showed that most PtrFRSs responded to changes in light intensity and were involved in the regulation of phytochromes. In this study, 51 PtrFRSs were identified and comprehensively bioinformatically analyzed, and preliminary functional analysis and prediction of PtrFRSs was carried out.

scholarly journals Identification of RING-H2 Gene Candidates Related to Wood Formation in Poplar

Forests ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 698
Author(s):  
Guimin Tong ◽  
Hongmei Shen ◽  
Shenquan Cao ◽  
Wenjing Xu ◽  
Xujun Ma ◽  
...  
Keyword(s):  
Tandem Duplication ◽  
Populus Trichocarpa ◽  
Microarray Dataset ◽  
Wood Formation ◽  
Multiple Gene ◽  
Poplar Genome ◽  
Gene Expression Analyses ◽  
Genes Encoding ◽  
Duplication Events ◽  
Ubiquitin Ligase E3

RING-H2 genes, the most abundant RING-type genes encoding putative ubiquitin ligase E3, are involved in diverse biological processes. Whether RING-H2 genes are related to wood formation remains to be identified in trees. In this study, we identified 288 RING-H2 genes in Populus trichocarpa, and found that the segmental and tandem duplication events contributed to RING-H2 gene expansion. Microarray dataset (from Affymetrix poplar genome arrays) showed that 64 of the 249 RING-H2 genes were highly or preferentially expressed in stem xylem. According to the AspWood RNAseq dataset, the transcription levels of genes PtrRHH21, 33, 48, 69, 88, 93, 94, 121, 141, 166, 175, 192, 208, 214, 250 and 257 were significantly increased in the xylem ranging from the expanding xylem to the lignifying xylem, suggesting their association with wood formation. Promoter analyses revealed that most of the preferentially xylem-expressed RING-H2 genes possessed SNBE, TERE, M46RE, AC and SMRE cis-elements, which are involved in secondary cell wall biosynthesis and programmed cell death. Based on the promoter GUS-based analysis result, PtrRHH94 was indicated to be associated with wood formation in transgenic P. trichocarpa. Taken together, dozens of Populus RING-H2 gene candidates associated with wood formation have been identified based on multiple gene expression analyses.

Codon Usage Pattern of Metallothionein Genes in the Poplar Genome

2018 ◽  
Vol 13 (6) ◽  
pp. 617-624
Author(s):  
Junkai Zhi ◽  
Jian Zhang ◽  
Jian Li ◽  
Hao Zhang ◽  
Jichen Xu
Keyword(s):  
Codon Usage ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Poplar Genome

Genome-wide analyses of phenylpropanoid-related genes in Populus trichocarpa, Arabidopsis thaliana, and Oryza sativa: the Populus lignin toolbox and conservation and diversification of angiosperm gene familiesThis article is one of a selection of papers published in the Special Issue on Poplar Research in Canada.

2007 ◽  
Vol 85 (12) ◽  
pp. 1182-1201 ◽  
Author(s):  
Björn Hamberger ◽  
Margaret Ellis ◽  
Michael Friedmann ◽  
Clarice de Azevedo Souza ◽  
Brad Barbazuk ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Populus Trichocarpa ◽  
Rice Genome ◽  
Gene Families ◽  
Gene Family Evolution ◽  
Comparative Approach ◽  
Expression Data ◽  
Poplar Genome ◽  
Genes Encoding ◽  
Bona Fide

The completion of the Populus trichocarpa (Torr. & A. Gray) (poplar) genome sequence offers an opportunity to study complete genome families in a third fully sequenced angiosperm (after Arabidopsis and rice) and to conduct comparative genomics studies of angiosperm gene family evolution. We focussed on gene families encoding phenylpropanoid and phenylpropanoid-like enzymes, and identified and annotated the full set of genes encoding these and related enzymes in the poplar genome. We used a similar approach to identify an analogous set of genes from the rice genome and generated phylogenetic trees for nine phenylpropanoid gene families from aligned poplar, Arabidopsis, and rice predicted protein sequences. This enabled us to identify the likely full set of bona fide poplar lignin-related phenylpropanoid genes (poplar “lignification toolbox”) apparent within well-defined clades in all phylogenetic trees. Analysis of expression data for poplar genes confirmed and refined annotations of lignin-related genes, which generally showed high expression in wood-forming tissues. Expression data from both poplar and Arabidopsis were used to make inferences regarding biochemical and biological functions of phenylpropanoid-like genes with unknown functions. The comparative approach also provided insights into the evolution of angiosperm phenylpropanoid-like gene families, illustrating lineage-specific clades as well as ancient clades containing genes with apparent conserved function.

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