scholarly journals Comparative Functional Genomics of Salt Stress in Related Model and Cultivated Plants Identifies and Overcomes Limitations to Translational Genomics

PLoS ONE ◽  
2011 ◽  
Vol 6 (2) ◽  
pp. e17094 ◽  
Author(s):  
Diego H. Sanchez ◽  
Fernando L. Pieckenstain ◽  
Jedrzey Szymanski ◽  
Alexander Erban ◽  
Mariusz Bromke ◽  
...  
PLoS ONE ◽  
2010 ◽  
Vol 5 (7) ◽  
pp. e11847 ◽  
Author(s):  
Junya Fujimoto ◽  
Humam Kadara ◽  
Taoyan Men ◽  
Carolyn van Pelt ◽  
Dafna Lotan ◽  
...  

Biology ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 253 ◽  
Author(s):  
Petronia Carillo ◽  
Loredana F. Ciarmiello ◽  
Pasqualina Woodrow ◽  
Giandomenico Corrado ◽  
Pasquale Chiaiese ◽  
...  

Algal biomass, extracts, or derivatives have long been considered a valuable material to bring benefits to humans and cultivated plants. In the last decades, it became evident that algal formulations can induce multiple effects on crops (including an increase in biomass, yield, and quality), and that algal extracts contain a series of bioactive compounds and signaling molecules, in addition to mineral and organic nutrients. The need to reduce the non-renewable chemical input in agriculture has recently prompted an increase in the use of algal extracts as a plant biostimulant, also because of their ability to promote plant growth in suboptimal conditions such as saline environments is beneficial. In this article, we discuss some research areas that are critical for the implementation in agriculture of macro- and microalgae extracts as plant biostimulants. Specifically, we provide an overview of current knowledge and achievements about extraction methods, compositions, and action mechanisms of algal extracts, focusing on salt-stress tolerance. We also outline current limitations and possible research avenues. We conclude that the comparison and the integration of knowledge on the molecular and physiological response of plants to salt and to algal extracts should also guide the extraction procedures and application methods. The effects of algal biostimulants have been mainly investigated from an applied perspective, and the exploitation of different scientific disciplines is still much needed for the development of new sustainable strategies to increase crop tolerance to salt stress.


2014 ◽  
Vol 23 (22) ◽  
pp. 5524-5537 ◽  
Author(s):  
Vadim B. Fedorov ◽  
Anna V. Goropashnaya ◽  
Nathan C. Stewart ◽  
Øivind Tøien ◽  
Celia Chang ◽  
...  

Science ◽  
2011 ◽  
Vol 332 (6032) ◽  
pp. 930-936 ◽  
Author(s):  
N. Rhind ◽  
Z. Chen ◽  
M. Yassour ◽  
D. A. Thompson ◽  
B. J. Haas ◽  
...  

2021 ◽  
Author(s):  
Leila Fattel ◽  
Dennis Psaroudakis ◽  
Colleen F. Yanarella ◽  
Kevin Chiteri ◽  
Haley A. Dostalik ◽  
...  

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.


Genetics ◽  
2013 ◽  
Vol 195 (1) ◽  
pp. 275-287 ◽  
Author(s):  
Amy A. Caudy ◽  
Yuanfang Guan ◽  
Yue Jia ◽  
Christina Hansen ◽  
Chris DeSevo ◽  
...  

Sign in / Sign up

Export Citation Format

Share Document