Abstract
BACKGROUND: Rop (RHO of plants) proteins are the plant-specific subfamily of RHO small GTP-binding proteins and act as a molecular switch to converge on a wide range of upstream signals and elicit downstream signaling cascades involving in modulating developmental processes and managing environmental stress. Although the function of Rops has been well studied in many plant species, the research conducting on Rops in potato is limited. RESULTS: In this work, a total of 11 Rop members were identified in the potato (Solanum tuberosum) genome. A comprehensive analysis encompassing their phylogenetic relationships, chromosomal locations, collinearity, conserved motifs, gene structures, cis-regulatory elements, tissue-specific expression profiles, and responses to biotic stress were undertaken. Phylogenetic and collinearity analyses suggested that 11 StRops were categorized into four groups, and five StRop genes (StRop6, StRop7, StRop8, StRop9 and StRop10) were incorporated in segmental duplication events. Synteny analysis indicated that five and eight StRop genes were orthologous to Arabidopsis (Arabidopsis thaliana) and tomato (Solanum lycopersicum), respectively. Tissue-specific expression analysis confirmed that StRops were widely expressed in various potato tissues, with variety-specific expression, implicating their multiple roles in growth and development in potato. The cis-regulatory elements related to stress response and hormone response were found in the promoters of StRop genes. Most StRops, including StRop2, StRop3, StRop8, StRop9, StRop10 and StRop11, were shown to be significantly differentially expressed in three different cultivars after infection with various pathogens (Phytophthora infestans, Fusarium oxysporum and Verticillium dahliae). Knock-down each of StRop3, StRop7 and StRop8 by virus induced gene silencing (VIGS) resulted in increased susceptibility of potato to pathogens P. infestans and V. dahliae, and transient silencing of StRop6 led to enhanced potato root colonization by V. dahliae, indicating their distinct roles in response to different pathogen challenges. CONCLUSIONS: The results unveil the structural characteristics of StRop genes, and provide the basic knowledge for further elucidating the gene functions of individual members in response to biotic stress.
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Claims 13
Claim · model-written summary
Eleven Rop members were identified in the potato genome.
- Taxon
- potato
Solanum tuberosume0 - Gene
- Rope0
- Outcome
- Rop memberse0
- Value
- 11e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a total of 11 Rop members were identified in the potato (Solanum tuberosum) genome”
Claim · model-written summary
The 11 StRops were placed in four phylogenetic groups.
- Taxon
- potatoSolanum tuberosumt0
- Gene
- StRopse0
- Outcome
- categorized into four groupse0
- Value
- four groupse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“11 StRops were categorized into four groups”
t0“potato (Solanum tuberosum L.)”
Claim · model-written summary
Five StRop genes were implicated in segmental duplication events.
- Taxon
- potatoSolanum tuberosumt0
- Gene
- StRop6, StRop7, StRop8, StRop9 and StRop10e0
- Outcome
- segmental duplication eventse0
- Value
- fivee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“five StRop genes (StRop6, StRop7, StRop8, StRop9 and StRop10) were incorporated in segmental duplication events”
t0“potato (Solanum tuberosum L.)”
Claim · model-written summary
Synteny indicated five StRop genes orthologous to Arabidopsis genes.
- Taxon
- potatoSolanum tuberosumt0
- Gene
- StRope0
- Outcome
- orthologous to Arabidopsis (Arabidopsis thaliana)e0
- Value
- fivee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“five and eight StRop genes were orthologous to Arabidopsis (Arabidopsis thaliana) and tomato (Solanum lycopersicum), respectively”
t0“potato (Solanum tuberosum L.)”
Claim · model-written summary
Synteny indicated eight StRop genes orthologous to tomato genes.
- Taxon
- potatoSolanum tuberosumt0
- Gene
- StRope0
- Outcome
- orthologous to Arabidopsis (Arabidopsis thaliana) and tomato (Solanum lycopersicum), respectivelye0
- Value
- eighte0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“five and eight StRop genes were orthologous to Arabidopsis (Arabidopsis thaliana) and tomato (Solanum lycopersicum), respectively”
t0“potato (Solanum tuberosum L.)”
Claim · model-written summary
StRops were widely expressed across potato tissues with variety-specific expression.
- Taxon
- potatoSolanum tuberosume0
- Organ / stage
- various potato tissuese0
- Gene
- StRopse0
- Outcome
- widely expressede0
- Qualifier
- variety-specific expressione0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“StRops were widely expressed in various potato tissues, with variety-specific expression”
Claim · model-written summary
Stress response cis-regulatory elements were found in promoters of StRop genes.
- Taxon
- potatoSolanum tuberosumt0
- Gene
- StRop genese0
- Outcome
- cis-regulatory elements related to stress responsee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The cis-regulatory elements related to stress response and hormone response were found in the promoters of StRop genes”
t0“potato (Solanum tuberosum L.)”
Claim · model-written summary
Hormone response cis-regulatory elements were found in promoters of StRop genes.
- Taxon
- potatoSolanum tuberosumt0
- Gene
- StRop genese0
- Outcome
- hormone responsee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The cis-regulatory elements related to stress response and hormone response were found in the promoters of StRop genes”
t0“potato (Solanum tuberosum L.)”
Claim · model-written summary
Most StRops were differentially expressed after pathogen infection in three potato cultivars.
- Taxon
- potatoSolanum tuberosumt0
- Material
- three different cultivarse0
- Treatment
- infection with various pathogense0
- Interactor
- Phytophthora infestans
Phytophthora infestanse0pathogen - Second interactor
- Fusarium oxysporum
_(Fusarium_oxysporum_f.sp._batatas)_1234227-PPT-Clemson_University.jpg?width=60)
Fusarium oxysporume0pathogen - Gene
- StRopse0
- Outcome
- differentially expressede0
- Qualifier
- Verticillium dahliaee0
Not reportedComparatorDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
_(Fusarium_oxysporum_f.sp._batatas)_1234227-PPT-Clemson_University.jpg?width=500)
Verbatim
e0“Most StRops, including StRop2, StRop3, StRop8, StRop9, StRop10 and StRop11, were shown to be significantly differentially expressed in three different cultivars after infection with various pathogens (Phytophthora infestans, Fusarium oxysporum and Verticillium dahliae)”
t0“potato (Solanum tuberosum L.)”
Claim · model-written summary
Silencing StRop3 increased potato susceptibility to P. infestans and V. dahliae.
- Taxon
- potatoSolanum tuberosume0
- Treatment
- virus induced gene silencing (VIGS)e0
- Interactor
- P. infestansPhytophthora infestanse0pathogen
- Second interactor
- V. dahliae
Verticillium dahliaee0pathogen - Gene
- StRop3e0
- Outcome
- susceptibility of potato to pathogens P. infestans and V. dahliaee0
- Direction
- increasede0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Knock-down each of StRop3, StRop7 and StRop8 by virus induced gene silencing (VIGS) resulted in increased susceptibility of potato to pathogens P. infestans and V. dahliae”
Claim · model-written summary
Silencing StRop7 increased potato susceptibility to P. infestans and V. dahliae.
- Taxon
- potatoSolanum tuberosume0
- Treatment
- virus induced gene silencing (VIGS)e0
- Interactor
- P. infestansPhytophthora infestanse0pathogen
- Second interactor
- V. dahliaeVerticillium dahliaee0pathogen
- Gene
- StRop7e0
- Outcome
- susceptibility of potato to pathogens P. infestans and V. dahliaee0
- Direction
- increasede0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Knock-down each of StRop3, StRop7 and StRop8 by virus induced gene silencing (VIGS) resulted in increased susceptibility of potato to pathogens P. infestans and V. dahliae”
Claim · model-written summary
Silencing StRop8 increased potato susceptibility to P. infestans and V. dahliae.
- Taxon
- potatoSolanum tuberosume0
- Treatment
- virus induced gene silencing (VIGS)e0
- Interactor
- P. infestansPhytophthora infestanse0pathogen
- Second interactor
- V. dahliaeVerticillium dahliaee0pathogen
- Gene
- StRop8e0
- Outcome
- susceptibility of potato to pathogens P. infestans and V. dahliaee0
- Direction
- increasede0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Knock-down each of StRop3, StRop7 and StRop8 by virus induced gene silencing (VIGS) resulted in increased susceptibility of potato to pathogens P. infestans and V. dahliae”
Claim · model-written summary
Transient StRop6 silencing enhanced V. dahliae colonization of potato roots.
- Taxon
- potatoSolanum tuberosume0
- Organ / stage
- roote0
- Treatment
- transient silencing of StRop6e0
- Interactor
- V. dahliaeVerticillium dahliaee0pathogen
- Gene
- StRop6e0
- Outcome
- potato root colonization by V. dahliaee0
- Direction
- enhancede0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“transient silencing of StRop6 led to enhanced potato root colonization by V. dahliae”
The same questions in other papers
loss of function · Phytophthora infestans · Solanum tuberosum (potato)Positive and negative results
14 papers in the same direction as this paper · 16 in the opposite direction
- positive
- positive
- positive
27 papers more in this group
See all 31 papers →loss of function · Verticillium dahliae · Solanum tuberosum (potato)Results agree
1 paper in the same direction as this paper
- no effect
Claims are grouped by organism, treatment and what was measured or targeted. A paper counts as positive when any of its claims in the group is positive.