Amborella trichopoda(Amborellaceae;hereafter simply Amborella)(Fig.1A)is a shrub endemic to New Caledonia in the Southwest Pacific that represents the sole sister species of all other extant angiosperms(Qiu et al.,199...Amborella trichopoda(Amborellaceae;hereafter simply Amborella)(Fig.1A)is a shrub endemic to New Caledonia in the Southwest Pacific that represents the sole sister species of all other extant angiosperms(Qiu et al.,1999;One Thousand Plant Transcriptomes Initiative,2019).Due to its unique phylogenetic status,it holds tremendous interest for botanists.The nuclear and mitochondrial genomes of Amborella were first published in 2013,providing valuable resources for studies on genome and gene family evolution,phylogenomics,and flower development,despite the fact that the assembly is heavily fragmented(Amborella Genome Project,2013;Rice et al.,2013).In 2024,a haplotype-resolved Amborella genome assembly was published,showing significant improvement in quality and completeness(Carey et al.,2024).展开更多
Ginger(Zingiber officinale)is one of the most valued spice plants worldwide;it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance.Here,we present a hap...Ginger(Zingiber officinale)is one of the most valued spice plants worldwide;it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance.Here,we present a haplotype-resolved,chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb.Remarkable structural variation was identified between haplotypes,and two inversions larger than 15Mb on chromosome 4 may be associated with ginger infertility.We performed a comprehensive,spatiotemporal,genome-wide analysis of allelic expression patterns,revealing that most alleles are coordinately expressed.The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements,greater coding sequence divergence,more relaxed selection pressure,and more transcription factor binding site differences.We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis.Our allele-aware assembly provides a powerful platform for future functional genomics,molecular breeding,and genome editing in ginger.展开更多
Introduction In the global context, urban planning is undergoing a series of unprecedented transformations. These are reflected in several key aspects: the ongoing transition of global urbanization processes and plann...Introduction In the global context, urban planning is undergoing a series of unprecedented transformations. These are reflected in several key aspects: the ongoing transition of global urbanization processes and planning paradigms;the reconstruction of planning and design methodologies driven by digital technologies;the reshaping of planning governance through multi-stakeholder participation;the evolution of planning decisions under the influence of climate change;the emergence of innovative planning theories fostered by interdisciplinary integration.展开更多
Plants possess remarkable regenerative abilities to form de novo vasculature after damage and in response to pathogens that invade and withdraw nutrients.To identify common factors that affect vascular formation upon ...Plants possess remarkable regenerative abilities to form de novo vasculature after damage and in response to pathogens that invade and withdraw nutrients.To identify common factors that affect vascular formation upon stress,we searched for Arabidopsis thaliana genes differentially expressed upon Agrobacterium infection,nematode infection,and plant grafting.One such gene is cell wall-related and highly induced by all three stresses,which we named ENHANCED XYLEM AND GRAFTING1(EXG1),since its mutations promote ectopic xylem formation in a vascular cell induction system and enhance graft formation.Further observations revealed that exg1 mutants show inhibited cambium development and callus formation but enhanced tissue attachment,syncytium size,phloem reconnection,and xylem formation.Given that bras-sinosteroids also promote xylem differentiation,we analyzed brassinosteroid-related genes and found that mutations in RLP44 encoding a receptor-like protein cause similar regeneration-related phenotypes as mu-tations in EXG1.Like EXG1,RLP44 expression is also induced by grafting and wounding.Mutations in EXG1 and RLP44 affect the expression of many genes in common,including those related to cell walls and genes important for vascular regeneration.Our results suggest that EXG1 integrates information from wounding or pathogen stress and functions with RLP44 to suppress vascular differentiation during regeneration and healing.展开更多
The white poplar(Populus alba) is widely distributed in Central Asia and Europe. There are natural populations of white poplar in Irtysh River basin in China. It also can be cultivated and grown well in northern China...The white poplar(Populus alba) is widely distributed in Central Asia and Europe. There are natural populations of white poplar in Irtysh River basin in China. It also can be cultivated and grown well in northern China. In this study, we sequenced the genome of P. alba by single-molecule real-time technology. De novo assembly of P. alba had a genome size of 415.99 Mb with a contig N50 of 1.18 Mb. A total of 32,963 protein-coding genes were identified. 45.16% of the genome was annotated as repetitive elements. Genome evolution analysis revealed that divergence between P. alba and Populus trichocarpa(black cottonwood)occurred ～5.0 Mya(3.0, 7.1). Fourfold synonymous third-codon transversion(4 DTV) and synonymous substitution rate(ks)distributions supported the occurrence of the salicoid WGD event(～ 65 Mya). Twelve natural populations of P. alba in the Irtysh River basin in China were sequenced to explore the genetic diversity. Average pooled heterozygosity value of P. alba populations was 0.170±0.014, which was lower than that in Italy(0.271±0.051) and Hungary(0.264±0.054). Tajima's D values showed a negative distribution, which might signify an excess of low frequency polymorphisms and a bottleneck with later expansion of P.alba populations examined.展开更多
At12Cys-1 （At5g64400） and At12Cys-2 （At5g09570） are two closely related isogenes that encode small, twin cysteine proteins, typically located in mitochondria. At12Cys-2 transcript is induced in a variety of mutant...At12Cys-1 （At5g64400） and At12Cys-2 （At5g09570） are two closely related isogenes that encode small, twin cysteine proteins, typically located in mitochondria. At12Cys-2 transcript is induced in a variety of mutants with disrupted mitochondrial proteins, but an increase in At12Cys protein is only detected in mutants with reduced mitochondrial complex I abundance. Induction of At12Cys protein in mutants that lack mitochondrial complex I is accompanied by At12Cys protein located in mitochondria, chloroplasts, and the cytosoh Biochemical analyses revealed that even single gene deletions, i.e., At12cys-1 orAtl2cys-2, have an effect on mitochondrial and chloroplast functions. However, only double mutants, i.e., At12cys-1：At12cys.2, affect the abundance of protein and mRNA transcripts encoding translation elongation factors as well as rRNA abundance. Blue native PAGE showed that At12Cys co-migrated with mitochondrial supercomplex I ＋ lU. Likewise, deletion of both At12cys-1 and At12cys-2 genes, but not single gene deletions, results in enhanced tolerance to drought and light stress and increased anti-oxidant capacity. The induction and multiple localization of At12Cys upon a reduction in complex I abundance provides a mechanism to specifically signal mitochondrial dysfunction to the cytosol and then beyond to other organelles in the cell.展开更多
Charles Chen(Chen Zhanxiang)was one of the founders and pioneers of China’s modern urban planning.He used to be the Chief Engineer in the Construction Administration Department of the Government of Republic of China....Charles Chen(Chen Zhanxiang)was one of the founders and pioneers of China’s modern urban planning.He used to be the Chief Engineer in the Construction Administration Department of the Government of Republic of China.He was mostly known through the'Liang&Chen Proposal,'a Plan for the New Civic Center submitted to the newly inaugurated Municipal Government of展开更多
Dear Editor, Photorespiration reduces plant carbon assimilation by an estimated 25%-50% of net CO2 assimilation in typical C3 plants （Roussel and Igamberdiev, 2011）. It results from the oxygenase activity of Rubisc...Dear Editor, Photorespiration reduces plant carbon assimilation by an estimated 25%-50% of net CO2 assimilation in typical C3 plants （Roussel and Igamberdiev, 2011）. It results from the oxygenase activity of Rubisco giving rise to phosphogly- colate. Subsequent photorespiratory metabolism involves decarboxylation of glycine in the mitochondrion and reduc- tion of hydroxypyruvate, usually assumed to occur in the peroxisome. Recent research in Arabidopsis has highlighted possible alternative sites of hydroxypyruvate reductase （HPR） activity （Figure 1A）. In addition to the accepted reduction by peroxisomal HPR1, Timm et al. （2008） identified cytosolic HPR2 and a putative chloroplast HPR3 （Timm et al., 2011）. For HPR2 or HPR3 to function in photorespiration, hydroxypyru- vate would first need to pass from the peroxisome into the cytosol. Another potential fate for hydroxypyruvate is its non-enzymic （NE） decarboxylation by reaction with hydrogen peroxide as previously suggested by experiments performed on isolated peroxisomes （Walton and Butt, 1981）.展开更多
Introduction On Apr.15-16,2023,the 2022 Annual Conference of the Housing and Community Planning Committee of the Urban Planning Society of China(UPSC)was successfully held at the Chongqing Planning Exhibition Gallery,...Introduction On Apr.15-16,2023,the 2022 Annual Conference of the Housing and Community Planning Committee of the Urban Planning Society of China(UPSC)was successfully held at the Chongqing Planning Exhibition Gallery,Chongqing.The conference was hosted by the Housing and Community Planning Committee of the UPSC.展开更多
Two homologous plastocyanin isoforms are encoded by the genes PETE1 and PETE2 in the nuclear genome of Arabidopsis thaliana. The PETE2 transcript is expressed at considerably higher levels and the PETE2 protein is the...Two homologous plastocyanin isoforms are encoded by the genes PETE1 and PETE2 in the nuclear genome of Arabidopsis thaliana. The PETE2 transcript is expressed at considerably higher levels and the PETE2 protein is the more abundant isoform. Null mutations in the PETE genes resulted in plants, designated pete1 and pete2, with decreased plastocyanin contents. However, despite reducing plastocyanin levels by over -90%, a pete2 null mutation on its own affects rates of photosynthesis and growth only slightly, whereas pete1 knockout plants, with about 60-80% of the wild-type plastocyanin level, did not show any alteration. Hence, plastocyanin concentration is not limiting for photosynthetic elec- tron flow under optimal growth conditions, perhaps implying other possible physiological roles for the protein. Indeed, plastocyanin has been proposed previously to cooperate with cytochrome C6A （Cyt C6A） in thylakoid redox reactions, but we find no evidence for a physical interaction between the two proteins, using interaction assays in yeast. We observed homodimerization of Cyt C6A in yeast interaction assays, but also Cyt C6A homodimers failed to interact with plastocyanin. Moreover, phenotypic analysis of atc6-1 pete1 and atc6-1 pete2 double mutants, each lacking Cyt C6A and one of the two piastocyanin-encoding genes, failed to reveal any genetic interaction. Overexpression of either PETE1 or PETE2 in the pete1 pete2 double knockout mutant background results in essentially wild-type photosynthetic performance, excluding the possibility that the two plastocyanin isoforms could have distinct functions in thylakoid electron flow.展开更多
基金supported by the National Natural Science Foundation of China(32270217,31970205,31770211)Metasequoia funding of Nanjing Forestry University to YY。
文摘Amborella trichopoda(Amborellaceae;hereafter simply Amborella)(Fig.1A)is a shrub endemic to New Caledonia in the Southwest Pacific that represents the sole sister species of all other extant angiosperms(Qiu et al.,1999;One Thousand Plant Transcriptomes Initiative,2019).Due to its unique phylogenetic status,it holds tremendous interest for botanists.The nuclear and mitochondrial genomes of Amborella were first published in 2013,providing valuable resources for studies on genome and gene family evolution,phylogenomics,and flower development,despite the fact that the assembly is heavily fragmented(Amborella Genome Project,2013;Rice et al.,2013).In 2024,a haplotype-resolved Amborella genome assembly was published,showing significant improvement in quality and completeness(Carey et al.,2024).
基金This study was supported by the Foundation for the Introduction of Talent of Pingdingshan University(PXY-BSQD2016009)the Key Research Project of Colleges and Universities of Henan Province(182102110132,172102110111)+6 种基金the National Natural Science Foundation(31600527)the Fundamental Research Funds for the Central Universities of Beijing Forestry University(2018BLCB08)the Project for the Construction of World Class Universities of Beijing Forestry University(2019XKJS0308)the Scientific Research Foundation for National Natural Science Fund(31600527)Z.L.is funded by a postdoctoral fellowship from the Special Research Fund of Ghent University(BOFPDO2018001701)Y.V.P.acknowledges fundings from the European Research Council(ERC)under the European Union’s Horizon 2020 research and innovation program(grant agreement No 833522)from Ghent University(Methusalem funding,BOF.MET.2021.0005.01).
文摘Ginger(Zingiber officinale)is one of the most valued spice plants worldwide;it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance.Here,we present a haplotype-resolved,chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb.Remarkable structural variation was identified between haplotypes,and two inversions larger than 15Mb on chromosome 4 may be associated with ginger infertility.We performed a comprehensive,spatiotemporal,genome-wide analysis of allelic expression patterns,revealing that most alleles are coordinately expressed.The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements,greater coding sequence divergence,more relaxed selection pressure,and more transcription factor binding site differences.We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis.Our allele-aware assembly provides a powerful platform for future functional genomics,molecular breeding,and genome editing in ginger.
文摘Introduction In the global context, urban planning is undergoing a series of unprecedented transformations. These are reflected in several key aspects: the ongoing transition of global urbanization processes and planning paradigms;the reconstruction of planning and design methodologies driven by digital technologies;the reshaping of planning governance through multi-stakeholder participation;the evolution of planning decisions under the influence of climate change;the emergence of innovative planning theories fostered by interdisciplinary integration.
基金S.M.and C.W.M.were supported by a Vetenskapsra det grant(2017-05122)A.Z.and C.W.M.were supported by a Wallenberg Academy Fellowship(2016-0274)+2 种基金F.A.,C.M.and C.W.M.were supported by a European Research Council starting grant(GRASP-805094)M.S.A.and P.M.were supported by a Vetenskapsra det grant(2019-05634)an MSCA Postdoctoral Fellowship(101066035-PREENER).
文摘Plants possess remarkable regenerative abilities to form de novo vasculature after damage and in response to pathogens that invade and withdraw nutrients.To identify common factors that affect vascular formation upon stress,we searched for Arabidopsis thaliana genes differentially expressed upon Agrobacterium infection,nematode infection,and plant grafting.One such gene is cell wall-related and highly induced by all three stresses,which we named ENHANCED XYLEM AND GRAFTING1(EXG1),since its mutations promote ectopic xylem formation in a vascular cell induction system and enhance graft formation.Further observations revealed that exg1 mutants show inhibited cambium development and callus formation but enhanced tissue attachment,syncytium size,phloem reconnection,and xylem formation.Given that bras-sinosteroids also promote xylem differentiation,we analyzed brassinosteroid-related genes and found that mutations in RLP44 encoding a receptor-like protein cause similar regeneration-related phenotypes as mu-tations in EXG1.Like EXG1,RLP44 expression is also induced by grafting and wounding.Mutations in EXG1 and RLP44 affect the expression of many genes in common,including those related to cell walls and genes important for vascular regeneration.Our results suggest that EXG1 integrates information from wounding or pathogen stress and functions with RLP44 to suppress vascular differentiation during regeneration and healing.
基金supported by the National Science Fund for Distinguished Young Scholars(31425006)Chinese Academy of Forestry(CAFYBB2018ZX001)
文摘The white poplar(Populus alba) is widely distributed in Central Asia and Europe. There are natural populations of white poplar in Irtysh River basin in China. It also can be cultivated and grown well in northern China. In this study, we sequenced the genome of P. alba by single-molecule real-time technology. De novo assembly of P. alba had a genome size of 415.99 Mb with a contig N50 of 1.18 Mb. A total of 32,963 protein-coding genes were identified. 45.16% of the genome was annotated as repetitive elements. Genome evolution analysis revealed that divergence between P. alba and Populus trichocarpa(black cottonwood)occurred ～5.0 Mya(3.0, 7.1). Fourfold synonymous third-codon transversion(4 DTV) and synonymous substitution rate(ks)distributions supported the occurrence of the salicoid WGD event(～ 65 Mya). Twelve natural populations of P. alba in the Irtysh River basin in China were sequenced to explore the genetic diversity. Average pooled heterozygosity value of P. alba populations was 0.170±0.014, which was lower than that in Italy(0.271±0.051) and Hungary(0.264±0.054). Tajima's D values showed a negative distribution, which might signify an excess of low frequency polymorphisms and a bottleneck with later expansion of P.alba populations examined.
文摘At12Cys-1 （At5g64400） and At12Cys-2 （At5g09570） are two closely related isogenes that encode small, twin cysteine proteins, typically located in mitochondria. At12Cys-2 transcript is induced in a variety of mutants with disrupted mitochondrial proteins, but an increase in At12Cys protein is only detected in mutants with reduced mitochondrial complex I abundance. Induction of At12Cys protein in mutants that lack mitochondrial complex I is accompanied by At12Cys protein located in mitochondria, chloroplasts, and the cytosoh Biochemical analyses revealed that even single gene deletions, i.e., At12cys-1 orAtl2cys-2, have an effect on mitochondrial and chloroplast functions. However, only double mutants, i.e., At12cys-1：At12cys.2, affect the abundance of protein and mRNA transcripts encoding translation elongation factors as well as rRNA abundance. Blue native PAGE showed that At12Cys co-migrated with mitochondrial supercomplex I ＋ lU. Likewise, deletion of both At12cys-1 and At12cys-2 genes, but not single gene deletions, results in enhanced tolerance to drought and light stress and increased anti-oxidant capacity. The induction and multiple localization of At12Cys upon a reduction in complex I abundance provides a mechanism to specifically signal mitochondrial dysfunction to the cytosol and then beyond to other organelles in the cell.
文摘Charles Chen(Chen Zhanxiang)was one of the founders and pioneers of China’s modern urban planning.He used to be the Chief Engineer in the Construction Administration Department of the Government of Republic of China.He was mostly known through the'Liang&Chen Proposal,'a Plan for the New Civic Center submitted to the newly inaugurated Municipal Government of
文摘Dear Editor, Photorespiration reduces plant carbon assimilation by an estimated 25%-50% of net CO2 assimilation in typical C3 plants （Roussel and Igamberdiev, 2011）. It results from the oxygenase activity of Rubisco giving rise to phosphogly- colate. Subsequent photorespiratory metabolism involves decarboxylation of glycine in the mitochondrion and reduc- tion of hydroxypyruvate, usually assumed to occur in the peroxisome. Recent research in Arabidopsis has highlighted possible alternative sites of hydroxypyruvate reductase （HPR） activity （Figure 1A）. In addition to the accepted reduction by peroxisomal HPR1, Timm et al. （2008） identified cytosolic HPR2 and a putative chloroplast HPR3 （Timm et al., 2011）. For HPR2 or HPR3 to function in photorespiration, hydroxypyru- vate would first need to pass from the peroxisome into the cytosol. Another potential fate for hydroxypyruvate is its non-enzymic （NE） decarboxylation by reaction with hydrogen peroxide as previously suggested by experiments performed on isolated peroxisomes （Walton and Butt, 1981）.
文摘Introduction On Apr.15-16,2023,the 2022 Annual Conference of the Housing and Community Planning Committee of the Urban Planning Society of China(UPSC)was successfully held at the Chongqing Planning Exhibition Gallery,Chongqing.The conference was hosted by the Housing and Community Planning Committee of the UPSC.
文摘Two homologous plastocyanin isoforms are encoded by the genes PETE1 and PETE2 in the nuclear genome of Arabidopsis thaliana. The PETE2 transcript is expressed at considerably higher levels and the PETE2 protein is the more abundant isoform. Null mutations in the PETE genes resulted in plants, designated pete1 and pete2, with decreased plastocyanin contents. However, despite reducing plastocyanin levels by over -90%, a pete2 null mutation on its own affects rates of photosynthesis and growth only slightly, whereas pete1 knockout plants, with about 60-80% of the wild-type plastocyanin level, did not show any alteration. Hence, plastocyanin concentration is not limiting for photosynthetic elec- tron flow under optimal growth conditions, perhaps implying other possible physiological roles for the protein. Indeed, plastocyanin has been proposed previously to cooperate with cytochrome C6A （Cyt C6A） in thylakoid redox reactions, but we find no evidence for a physical interaction between the two proteins, using interaction assays in yeast. We observed homodimerization of Cyt C6A in yeast interaction assays, but also Cyt C6A homodimers failed to interact with plastocyanin. Moreover, phenotypic analysis of atc6-1 pete1 and atc6-1 pete2 double mutants, each lacking Cyt C6A and one of the two piastocyanin-encoding genes, failed to reveal any genetic interaction. Overexpression of either PETE1 or PETE2 in the pete1 pete2 double knockout mutant background results in essentially wild-type photosynthetic performance, excluding the possibility that the two plastocyanin isoforms could have distinct functions in thylakoid electron flow.
