Stomata play critical roles in gas exchange and immunity to pathogens.While many genes regulating early stomatal development up to the production of young guard cells(GCs)have been identified in Arabidopsis,much less ...Stomata play critical roles in gas exchange and immunity to pathogens.While many genes regulating early stomatal development up to the production of young guard cells(GCs)have been identified in Arabidopsis,much less is known about how young GCs develop into mature functional stomata.Here we perform a maturomics study on stomata,with“maturomics”defined as omics analysis of the maturation process of a tissue or organ.We develop an integrative scheme to analyze three public stomata-related single-cell RNAseq datasets and identify a list of 586 genes that are specifically up-regulated in all three datasets during stomatal maturation and function formation.The list,termed sc_586,is enriched with known regulators of stomatal maturation and functions.To validate the reliability of the dataset,we selected two candidate G2-like transcription factor genes,MYS1 and MYS2,to investigate their roles in stomata.These two genes redundantly regulate the size and hoop rigidity of mature GCs,and the mys1 mys2 double mutants cause mature GCs with severe defects in regulating their stomatal apertures.Taken together,our results provide a valuable list of genes for studying GC maturation and function formation.展开更多
The oxidative pentose phosphate(OPP)pathway provides metabolic intermediates for the shikimate pathway and directs carbon flow to the biosynthesis of aromatic amino acids(AAAs),which serve as basic protein building bl...The oxidative pentose phosphate(OPP)pathway provides metabolic intermediates for the shikimate pathway and directs carbon flow to the biosynthesis of aromatic amino acids(AAAs),which serve as basic protein building blocks and precursors of numerous metabolites essential for plant growth.However,genetic evidence linking the two pathways is largely unclear.In this study,we identified 6-phosphogluconate dehydrogenase 2(PGD2),the rate-limiting enzyme of the cytosolic OPP pathway,through suppressor screening of arogenate dehydrogenase 2(adh2)in Arabidopsis.Our data indicated that a single amino acid substitution at position 63(glutamic acid to lysine)of PGD2 enhanced its enzyme activity by facilitating the dissociation of products from the active site of PGD2,thus increasing the accumulation of AAAs and partially restoring the defective phenotype of adh2.Phylogenetic analysis indicated that the point mutation occurred in a well-conserved amino acid residue.Plants with different amino acids at this conserved site of PGDs confer diverse catalytic activities,thus exhibiting distinct AAAs producing capability.These findings uncover the genetic link between the OPP pathway and AAAs biosynthesis through PGD2.The gain-of-function point mutation of PGD2 identified here could be considered as a potential engineering target to alter the metabolic flux for the production of AAAs and downstream compounds.展开更多
Transcription factors(TFs)regulate cellular activities by controlling gene expression,but a predictive model describing how TFs quantitatively modulate human transcriptomes is lacking.We construct a universal human ge...Transcription factors(TFs)regulate cellular activities by controlling gene expression,but a predictive model describing how TFs quantitatively modulate human transcriptomes is lacking.We construct a universal human gene expression predictor named EXPLICIT-Human and utilize it to decode transcriptional regulation.Using the expression of 1613 TFs,the predictor reconstitutes highly accurate transcriptomes for samples derived from a wide range of tissues and conditions.The broad applicability of the predictor indicates that it recapitulates the quantitative relationships between TFs and target genes ubiquitous across tissues.Significant interacting TF-target gene pairs are extracted from the predictor and enable downstream inference of TF regulators for diverse pathways involved in development,immunity,metabolism,and stress response.A detailed analysis of the hematopoiesis process reveals an atlas of key TFs regulating the development of different hematopoietic cell lineages,and a portion of these TFs are conserved between humans and mice.The results demonstrate that our method is capable of delineating the TFs responsible for fate determination.Compared to other existing tools,EXPLICIT-Human shows a better performance in recovering the correct TF regulators.展开更多
Single-cell RNA-sequencing datasets of Arabidopsis roots have been generated,but related comprehensive gene co-expression network analyses are lacking.We conducted a single-cell gene co-expression network analysis wit...Single-cell RNA-sequencing datasets of Arabidopsis roots have been generated,but related comprehensive gene co-expression network analyses are lacking.We conducted a single-cell gene co-expression network analysis with publicly available scRNA-seq datasets of Arabidopsis roots using a SingleCellGGM algorithm.The analysis identified 149 gene co-expression modules,which we considered to be gene expression programs(GEPs).By examining their spatiotemporal expression,we identified GEPs specifically expressed in major root cell types along their developmental trajectories.These GEPs define gene programs regulating root cell development at different stages and are enriched with relevant developmental regulators.As examples,a GEP specific for the quiescent center(QC)contains 20 genes regulating QC and stem cell niche homeostasis,and four GEPs are expressed in sieve elements(SEs)from early to late developmental stages,with the early-stage GEP containing 17 known SE developmental regulators.We also identified GEPs for metabolic pathways with cell-type-specific expression,suggesting the existence of cell-type-specific metabolism in roots.Using the GEPs,we discovered and verified a columellaspecific gene,NRL27,as a regulator of the auxin-related root gravitropism response.Our analysis thus systematically reveals GEPs that regulate Arabidopsis root development and metabolism and provides ample resources for root biology studies.展开更多
Soybean was domesticated in China and has become one of the most important oilseed crops. Due to bottlenecks in their introduction and dissemination, soybeans from different geographic areas exhibit extensive genetic ...Soybean was domesticated in China and has become one of the most important oilseed crops. Due to bottlenecks in their introduction and dissemination, soybeans from different geographic areas exhibit extensive genetic diversity. Asia is the largest soybean market; therefore, a high-quality soybean reference genome from this area is critical for soybean research and breeding.Here, we report the de novo assembly and sequence analysis of a Chinese soybean genome for "Zhonghuang 13" by a combination of SMRT, Hi-C and optical mapping data. The assembled genome size is 1.025 Gb with a contig N50 of 3.46 Mb and a scaffold N50 of 51.87 Mb. Comparisons between this genome and the previously reported reference genome(cv. Williams82) uncovered more than 250,000 structure variations. A total of 52,051 protein coding genes and 36,429 transposable elements were annotated for this genome, and a gene co-expression network including 39,967 genes was also established. This high quality Chinese soybean genome and its sequence analysis will provide valuable information for soybean improvement in the future.展开更多
Protein kinases regulate virtually all cellular processes,but it remains challenging to determine the functions of all protein kinases,collectively called the“kinome”,in any species.We developed a computational appr...Protein kinases regulate virtually all cellular processes,but it remains challenging to determine the functions of all protein kinases,collectively called the“kinome”,in any species.We developed a computational approach called EXPLICIT-Kinase to predict the functions of the Arabidopsis kinome.Because the activities of many kinases can be regulated transcriptionally,their gene expression patterns provide clues to their functions.A universal gene expression predictor for Arabidopsis was constructed to predict the expression of 30,172 nonkinase genes based on the expression of 994 kinases.The model reconstituted highly accurate transcriptomes for diverse Arabidopsis samples.It identified the significant kinases as predictor kinases for predicting the expression of Arabidopsis genes and pathways.Strikingly,these predictor kinases were often regulators of related pathways,as exemplified by those involved in cytokinesis,tissue development,and stress responses.Comparative analyses revealed that portions of these predictor kinases are shared and conserved between Arabidopsis and maize.As an example,we identified a conserved predictor kinase,RAF6,from a stomatal movement module.We verified that RAF6 regulates stomatal closure.It can directly interact with SLAC1,a key anion channel for stomatal closure,and modulate its channel activity.Our approach enables a systematic dissection of the functions of the Arabidopsis kinome.展开更多
基金supported by grants from the Strategic Priority Research Program of the Chinese Academy of Science(XDA24010303)the National Natural Science Foundation of China(31770268)+1 种基金the Fundamental Research Funds for the Central Universities(WK2070000091)the University of Science and Technology of China(Start-up fund to S.M.)。
文摘Stomata play critical roles in gas exchange and immunity to pathogens.While many genes regulating early stomatal development up to the production of young guard cells(GCs)have been identified in Arabidopsis,much less is known about how young GCs develop into mature functional stomata.Here we perform a maturomics study on stomata,with“maturomics”defined as omics analysis of the maturation process of a tissue or organ.We develop an integrative scheme to analyze three public stomata-related single-cell RNAseq datasets and identify a list of 586 genes that are specifically up-regulated in all three datasets during stomatal maturation and function formation.The list,termed sc_586,is enriched with known regulators of stomatal maturation and functions.To validate the reliability of the dataset,we selected two candidate G2-like transcription factor genes,MYS1 and MYS2,to investigate their roles in stomata.These two genes redundantly regulate the size and hoop rigidity of mature GCs,and the mys1 mys2 double mutants cause mature GCs with severe defects in regulating their stomatal apertures.Taken together,our results provide a valuable list of genes for studying GC maturation and function formation.
基金supported by the National Key Research and Development Program of China(2019YFA0903900)the National Natural Science Foundation of China(32300233)+1 种基金Guangdong Provincial Key Laboratory of Synthetic Genomics(2023B1212060054)Shenzhen Key Laboratory of Synthetic Genomics(ZDSYS201802061806209).
文摘The oxidative pentose phosphate(OPP)pathway provides metabolic intermediates for the shikimate pathway and directs carbon flow to the biosynthesis of aromatic amino acids(AAAs),which serve as basic protein building blocks and precursors of numerous metabolites essential for plant growth.However,genetic evidence linking the two pathways is largely unclear.In this study,we identified 6-phosphogluconate dehydrogenase 2(PGD2),the rate-limiting enzyme of the cytosolic OPP pathway,through suppressor screening of arogenate dehydrogenase 2(adh2)in Arabidopsis.Our data indicated that a single amino acid substitution at position 63(glutamic acid to lysine)of PGD2 enhanced its enzyme activity by facilitating the dissociation of products from the active site of PGD2,thus increasing the accumulation of AAAs and partially restoring the defective phenotype of adh2.Phylogenetic analysis indicated that the point mutation occurred in a well-conserved amino acid residue.Plants with different amino acids at this conserved site of PGDs confer diverse catalytic activities,thus exhibiting distinct AAAs producing capability.These findings uncover the genetic link between the OPP pathway and AAAs biosynthesis through PGD2.The gain-of-function point mutation of PGD2 identified here could be considered as a potential engineering target to alter the metabolic flux for the production of AAAs and downstream compounds.
基金supported by grants from the National Natural Science Foundation of China(31770268)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA24010303)+1 种基金the Fundamental Research Funds for the Central Universities(WK2070000091)University of Science and Technology of China(Start-up fund to S.M.).
文摘Transcription factors(TFs)regulate cellular activities by controlling gene expression,but a predictive model describing how TFs quantitatively modulate human transcriptomes is lacking.We construct a universal human gene expression predictor named EXPLICIT-Human and utilize it to decode transcriptional regulation.Using the expression of 1613 TFs,the predictor reconstitutes highly accurate transcriptomes for samples derived from a wide range of tissues and conditions.The broad applicability of the predictor indicates that it recapitulates the quantitative relationships between TFs and target genes ubiquitous across tissues.Significant interacting TF-target gene pairs are extracted from the predictor and enable downstream inference of TF regulators for diverse pathways involved in development,immunity,metabolism,and stress response.A detailed analysis of the hematopoiesis process reveals an atlas of key TFs regulating the development of different hematopoietic cell lineages,and a portion of these TFs are conserved between humans and mice.The results demonstrate that our method is capable of delineating the TFs responsible for fate determination.Compared to other existing tools,EXPLICIT-Human shows a better performance in recovering the correct TF regulators.
基金supported by grants from the Strategic Priority Research Program of the Chinese Academy of Science(XDA24010303)the National Natural Science Foundation of China(31770268)+1 种基金the Fundamental Research Funds for the Central Universities(WK2070000091)the University of Science and Technology of China(start-up fund to S.M.)。
文摘Single-cell RNA-sequencing datasets of Arabidopsis roots have been generated,but related comprehensive gene co-expression network analyses are lacking.We conducted a single-cell gene co-expression network analysis with publicly available scRNA-seq datasets of Arabidopsis roots using a SingleCellGGM algorithm.The analysis identified 149 gene co-expression modules,which we considered to be gene expression programs(GEPs).By examining their spatiotemporal expression,we identified GEPs specifically expressed in major root cell types along their developmental trajectories.These GEPs define gene programs regulating root cell development at different stages and are enriched with relevant developmental regulators.As examples,a GEP specific for the quiescent center(QC)contains 20 genes regulating QC and stem cell niche homeostasis,and four GEPs are expressed in sieve elements(SEs)from early to late developmental stages,with the early-stage GEP containing 17 known SE developmental regulators.We also identified GEPs for metabolic pathways with cell-type-specific expression,suggesting the existence of cell-type-specific metabolism in roots.Using the GEPs,we discovered and verified a columellaspecific gene,NRL27,as a regulator of the auxin-related root gravitropism response.Our analysis thus systematically reveals GEPs that regulate Arabidopsis root development and metabolism and provides ample resources for root biology studies.
基金supported by the National Natural Science Foundation of China (91531304, 31525018, 31370266, and 31788103)the “Strategic Priority Research Program” of the Chinese Academy of Sciences (XDA08000000)the State Key Laboratory of Plant Cell and Chromosome Engineering (PCCE-KF-2017-03)
文摘Soybean was domesticated in China and has become one of the most important oilseed crops. Due to bottlenecks in their introduction and dissemination, soybeans from different geographic areas exhibit extensive genetic diversity. Asia is the largest soybean market; therefore, a high-quality soybean reference genome from this area is critical for soybean research and breeding.Here, we report the de novo assembly and sequence analysis of a Chinese soybean genome for "Zhonghuang 13" by a combination of SMRT, Hi-C and optical mapping data. The assembled genome size is 1.025 Gb with a contig N50 of 3.46 Mb and a scaffold N50 of 51.87 Mb. Comparisons between this genome and the previously reported reference genome(cv. Williams82) uncovered more than 250,000 structure variations. A total of 52,051 protein coding genes and 36,429 transposable elements were annotated for this genome, and a gene co-expression network including 39,967 genes was also established. This high quality Chinese soybean genome and its sequence analysis will provide valuable information for soybean improvement in the future.
基金supported by grants from the National Natural Science Foundation of China(31770268)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA24010303)+1 种基金the Fundamental Research Funds for the Central Universities(WK2070000091)University of Science and Technology of China(Start-up fund to S.M.)。
文摘Protein kinases regulate virtually all cellular processes,but it remains challenging to determine the functions of all protein kinases,collectively called the“kinome”,in any species.We developed a computational approach called EXPLICIT-Kinase to predict the functions of the Arabidopsis kinome.Because the activities of many kinases can be regulated transcriptionally,their gene expression patterns provide clues to their functions.A universal gene expression predictor for Arabidopsis was constructed to predict the expression of 30,172 nonkinase genes based on the expression of 994 kinases.The model reconstituted highly accurate transcriptomes for diverse Arabidopsis samples.It identified the significant kinases as predictor kinases for predicting the expression of Arabidopsis genes and pathways.Strikingly,these predictor kinases were often regulators of related pathways,as exemplified by those involved in cytokinesis,tissue development,and stress responses.Comparative analyses revealed that portions of these predictor kinases are shared and conserved between Arabidopsis and maize.As an example,we identified a conserved predictor kinase,RAF6,from a stomatal movement module.We verified that RAF6 regulates stomatal closure.It can directly interact with SLAC1,a key anion channel for stomatal closure,and modulate its channel activity.Our approach enables a systematic dissection of the functions of the Arabidopsis kinome.
