scholarly journals Functional genomics: Probing plant gene function and expression with transposons

1998 ◽  
Vol 95 (5) ◽  
pp. 2021-2026 ◽  
Author(s):  
R. A. Martienssen
Keyword(s):  
Functional Genomics ◽  
Gene Function ◽  
Plant Gene

scholarly journals PhyloGenes: An online phylogenetics and functional genomics resource for plant gene function inference

Plant Direct ◽  
2020 ◽  
Vol 4 (12) ◽  
Author(s):  
Peifen Zhang ◽  
Tanya Z. Berardini ◽  
Dustin Ebert ◽  
Qian Li ◽  
Huaiyu Mi ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Gene Function ◽  
Plant Gene

Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function

2010 ◽  
Vol 5 (6) ◽  
pp. 1210-1227 ◽  
Author(s):  
Takayuki Tohge ◽  
Alisdair R Fernie
Keyword(s):  
Genetic Diversity ◽  
Gene Function ◽  
Plant Gene

scholarly journals Standardized genome-wide function prediction enables comparative functional genomics in plants: a new application area for Gene Ontologies

2021 ◽  
Author(s):  
Leila Fattel ◽  
Dennis Psaroudakis ◽  
Colleen F. Yanarella ◽  
Kevin Chiteri ◽  
Haley A. Dostalik ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Gene Function ◽  
Go Annotation ◽  
Functional Annotations ◽  
Genome Wide ◽  
Branch Support ◽  
Comparative Functional Genomics ◽  
Gene Ontologies ◽  
Established Species ◽  
Go Terms

BackgroundGenome-wide gene function annotations are useful for hypothesis generation and for prioritizing candidate genes responsible for phenotypes of interest. We functionally annotated the genes of 18 crop plant genomes across 14 species using the GOMAP pipeline.ResultsBy comparison to existing GO annotation datasets available for a subset of these genomes, GOMAP-generated datasets cover more genes, assign more GO terms, and produce datasets similar in quality (based on precision and recall metrics using existing gold standards as the basis for comparison). From there, we sought to determine whether the datasets could be used in tandem to carry out comparative functional genomics analyses. As a test of the idea and a proof of concept, we created parsimony and distance-based dendrograms of relatedness based on functions for all 18 genomes. These dendrograms were compared to well-established species-level phylogenies to determine whether trees derived through the analysis of gene function agree with known evolutionary histories, which they largely do. Where discrepancies were observed, we determined branch support based on jack-knifing then removed individual annotation sets by genome to identify the annotation sets causing errant relationships.ConclusionsBased on the results of these analyses, it is clear that for genome assembly and annotation products of similar quality, GOMAP-derived functional annotations used together across species do retain sufficient biological signal to recover known phylogenetic relationships, indicating that comparative functional genomics across species based on GO data hold promise as a tool for generating novel hypotheses about gene function and traits.

scholarly journals Transient Gene Expression is an Effective Experimental Tool for the Research into the Fine Mechanisms of Plant Gene Function: Advantages, Limitations, and Solutions

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1187
Author(s):  
Alexander A. Tyurin ◽  
Alexandra V. Suhorukova ◽  
Ksenia V. Kabardaeva ◽  
Irina V. Goldenkova-Pavlova
Keyword(s):  
Gene Expression ◽  
Transient Expression ◽  
Gene Function ◽  
Transient Gene Expression ◽  
Physiological Role ◽  
Gene Products ◽  
Plant Gene ◽  
Gene Functions ◽  
Insight Into

A large data array on plant gene expression accumulated thanks to comparative omic studies directs the efforts of researchers to the specific or fine effects of the target gene functions and, as a consequence, elaboration of relatively simple and concurrently effective approaches allowing for the insight into the physiological role of gene products. Numerous studies have convincingly demonstrated the efficacy of transient expression strategy for characterization of the plant gene functions. The review goals are (i) to consider the advantages and limitations of different plant systems and methods of transient expression used to find out the role of gene products; (ii) to summarize the current data on the use of the transient expression approaches for the insight into fine mechanisms underlying the gene function; and (iii) to outline the accomplishments in efficient transient expression of plant genes. In general, the review discusses the main and critical steps in each of the methods of transient gene expression in plants; areas of their application; main results obtained using plant objects; their contribution to our knowledge about the fine mechanisms of the plant gene functions underlying plant growth and development; and clarification of the mechanisms regulating complex metabolic pathways.

scholarly journals Functional genomics in the wild: a case study with paper wasps shows challenges and prospects for RNA interference in ecological systems

Genome ◽  
2018 ◽  
Vol 61 (4) ◽  
pp. 266-272 ◽  
Author(s):  
S.A. Weiner ◽  
A.G. Geffre ◽  
A.L. Toth
Keyword(s):  
Rna Interference ◽  
Functional Genomics ◽  
Gene Function ◽  
Ecological Model ◽  
Model Organisms ◽  
Natural Environments ◽  
Paper Wasps ◽  
Fatty Acid Binding ◽  
In The Wild

RNA interference (RNAi) is a useful tool to assess gene function by knocking down expression of a target gene and has been used successfully in domestic and laboratory organisms. However, the use of RNAi for functional genomics has not fully extended into ecological model organisms in natural environments. Assessment of gene function in the wild is important because gene function can be environmentally and context dependent. Here, we present a case study using RNAi to assess gene function in wild paper wasps Polistes metricus, to test roles for two candidate genes (NADH dehydrogenase (NADHdh) and retinoid and fatty acid binding protein (RfaBp)) in the development of reproductive castes. Previous studies have shown that these genes are upregulated in larvae that become queens compared to workers, but this pattern was reversed in the laboratory, making field-based studies necessary. We orally administered dsRNA to larvae in field colonies and found evidence of a short-term knockdown followed by a compensatory rebound in expression for RfaBp. We also observed the predicted worker-like decrease in lipid stores in NADHdh dsRNA treated wasps, suggesting a possible role for NADHdh in caste development. We discuss our results in the context of challenges for using RNAi for functional genomics in ecological model organisms in the field.

scholarly journals High-throughput Binary Vectors for Plant Gene Function Analysis

2007 ◽  
Vol 49 (4) ◽  
pp. 556-567 ◽  
Author(s):  
Zhi-Yong Lei ◽  
Ping Zhao ◽  
Min-Jie Cao ◽  
Rong Cui ◽  
Xi Chen ◽  
...  
Keyword(s):  
High Throughput ◽  
Gene Function ◽  
Function Analysis ◽  
Binary Vectors ◽  
Plant Gene ◽  
Gene Function Analysis

scholarly journals Metabolomics: Pandora's Box or Aladdin's Cave?

2003 ◽  
Vol 25 (1) ◽  
pp. 15-17 ◽  
Author(s):  
Kevin M. Brindle
Keyword(s):  
Functional Genomics ◽  
Small Molecule ◽  
Gene Function ◽  
Screening Tools ◽  
Massively Parallel ◽  
Cellular Phenotype ◽  
Gene Modification ◽  
Physiological Conditions ◽  
The Status

Functional genomics, the elucidation of gene function from studies of the effects of gene modification on cellular phenotype, has prompted the development of massively parallel and increasingly comprehensive screening tools for assessing the expression of mRNAs (transcriptomics) and proteins (proteomics). For a more complete description of the effects of changes in genotype or physiological conditions on cellular phenotype, we also need to define the status of a third class of biomolecules in the cell, the small-molecule metabolites. Study of the latter has been termed metabolomics and the metabolite complement the metabolome.

scholarly journals Special care is needed in applying phylogenetic comparative methods to gene trees with speciation and duplication nodes

2019 ◽  
Author(s):  
Tina Begum ◽  
Marc Robinson-Rechavi
Keyword(s):  
Functional Genomics ◽  
Gene Function ◽  
Evolutionary Biology ◽  
Tissue Specificity ◽  
Comparative Methods ◽  
Pairwise Comparisons ◽  
Phylogenetic Comparative Methods ◽  
Gene Trees ◽  
Time Calibration ◽  
Branch Lengths

AbstractHow gene function evolves is a central question of evolutionary biology. It can be investigated by comparing functional genomics results between species and between genes. Most comparative studies of functional genomics have used pairwise comparisons. Yet it has been shown that this can provide biased results, since genes, like species, are phylogenetically related. Phylogenetic comparative methods should allow to correct for this, but they depend on strong assumptions, including unbiased tree estimates relative to the hypothesis being tested. Such methods have recently been used to test the “ortholog conjecture”, the hypothesis that functional evolution is faster in paralogs than in orthologs. Whereas pairwise comparisons of tissue specificity (τ) provided support for the ortholog conjecture, phylogenetic independent contrasts did not. Our reanalysis on the same gene trees identified problems with the time calibration of duplication nodes. We find that the gene trees used suffer from important biases, due to the inclusion of trees with no duplication nodes, to the relative age of speciations and duplications, to systematic differences in branch lengths, and to non-Brownian motion of tissue-specificity on many trees. We find that incorrect implementation of phylogenetic method in empirical gene trees with duplications can be problematic. Controlling for biases allows to successfully use phylogenetic methods to study the evolution of gene function, and provides some support for the ortholog conjecture using three different phylogenetic approaches.

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