With the increasing number of sequenced species,phylogenetic profiling(PP)has become a powerful method to predict functional genes based on co-evolutionary information.However,its potential in plant genomics has not y...With the increasing number of sequenced species,phylogenetic profiling(PP)has become a powerful method to predict functional genes based on co-evolutionary information.However,its potential in plant genomics has not yet been fully explored.In this context,we combined the power of machine learning and PP to identify salt stress-related genes in a halophytic grass,Spartina alterniflora,using evolutionary information generated from 365 plant species.Our results showed that the genes highly co-evolved with known salt stress-related genes are enriched in biological processes of ion transport,detoxification and metabolic pathways.For ion transport,five identified genes coding two sodium and three potassium transporters were validated to be able to uptake Na?.In addition,we identified two orthologs of trichome-related AtR3-MYB genes,SaCPC1 and SaCPC2,which may be involved in salinity responses.Genes co-evolved with SaCPCs were enriched in functions related to the circadian rhythm and abiotic stress responses.Overall,this work demonstrates the feasibility of mining salt stress-related genes using evolutionary information,highlighting the potential of PP as a valuable tool for plant functional genomics.展开更多
The reverse construction and analysis of the networks of molecular interactions are essential for understanding their functions within cells. In this paper, a logic network model is constructed to investigate the comp...The reverse construction and analysis of the networks of molecular interactions are essential for understanding their functions within cells. In this paper, a logic network model is constructed to investigate the complicated regulation mechanism of shoot genes of Arabidopsis Thaliana in response to stimuli. The dynamics of the complicated logic network is analyzed, discussed, and simulated. The simulation results show that the logic network of the active genes of shoot eventually evolves into eleven attractors under the stimuli, including five 1-periodic and six 2-periodic attractors. Our work provides valuable reference and guidance for biologists to understand and explain Arabidopsis＇ response to external stimuli by experiments.展开更多
基金supported by the National Key R&D Program of China(2022YFF0711802)the Nanfan special project of the Chinese Academy of Agricultural Sciences(ZDXM2309)+1 种基金the National Natural Science Foundation of China(32022064)the Innovation Program of the Chinese Academy of Agricultural Sciences,the Alibaba Foundation,and the High-performance Computing Platform of YZBSTCACC.
文摘With the increasing number of sequenced species,phylogenetic profiling(PP)has become a powerful method to predict functional genes based on co-evolutionary information.However,its potential in plant genomics has not yet been fully explored.In this context,we combined the power of machine learning and PP to identify salt stress-related genes in a halophytic grass,Spartina alterniflora,using evolutionary information generated from 365 plant species.Our results showed that the genes highly co-evolved with known salt stress-related genes are enriched in biological processes of ion transport,detoxification and metabolic pathways.For ion transport,five identified genes coding two sodium and three potassium transporters were validated to be able to uptake Na?.In addition,we identified two orthologs of trichome-related AtR3-MYB genes,SaCPC1 and SaCPC2,which may be involved in salinity responses.Genes co-evolved with SaCPCs were enriched in functions related to the circadian rhythm and abiotic stress responses.Overall,this work demonstrates the feasibility of mining salt stress-related genes using evolutionary information,highlighting the potential of PP as a valuable tool for plant functional genomics.
基金This research is supported by the National Natural Science Foundation of China under Grant Nos. 60874036 and 60503002.
文摘The reverse construction and analysis of the networks of molecular interactions are essential for understanding their functions within cells. In this paper, a logic network model is constructed to investigate the complicated regulation mechanism of shoot genes of Arabidopsis Thaliana in response to stimuli. The dynamics of the complicated logic network is analyzed, discussed, and simulated. The simulation results show that the logic network of the active genes of shoot eventually evolves into eleven attractors under the stimuli, including five 1-periodic and six 2-periodic attractors. Our work provides valuable reference and guidance for biologists to understand and explain Arabidopsis＇ response to external stimuli by experiments.
