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Landscape of cell heterogeneity and evolutionary trajectory in ulcerative colitis-associated colon cancer revealed by single-cell RNA sequencing 认领 引用 被引量：5
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作者 Quan Wang Zhu Wang +6 位作者 Zhen Zhang Wei Zhang Mengmeng Zhang Zhanlong Shen Yingjiang Ye Kewei Jiang Shan Wang 《Chinese Journal of Cancer Research》 SCIE CAS CSCD 2021年第2期271-288,共18页
Objective:The goal of this study was to get preliminary insight on the intra-tumor heterogeneity in colitisassociated cancer(CAC)and to reveal a potential evolutionary trajectory from ulcerative colitis(UC)to CAC at t... Objective:The goal of this study was to get preliminary insight on the intra-tumor heterogeneity in colitisassociated cancer(CAC)and to reveal a potential evolutionary trajectory from ulcerative colitis(UC)to CAC at the single-cell level.Methods:Fresh samples of tumor tissues and adjacent UC tissues from a CAC patient with pT3N1M0 stage cancer were examined by single-cell RNA sequencing(scRNA-seq).Data from The Cancer Genome Atlas(TCGA)and The Human Protein Atlas were used to confirm the different expression levels in normal and tumor tissues and to determine their relationships with patient prognosis.Results:Ultimately,4,777 single-cell transcriptomes(1,220 genes per cell)were examined,of which 2,250(47%)and 2,527(53%)originated from tumor and adjacent UC tissues,respectively.We defined the composition of cancer-associated stromal cells and identified six cell clusters,including myeloid,T and B cells,fibroblasts,endothelial and epithelial cells.Notable pathways and transcription factors involved in these cell clusters were analyzed and described.Moreover,the precise cellular composition and developmental trajectory from UC to UCassociated colon cancer were graphed,and it was predicted that CD74,CLCA1,and DPEP1 played a potential role in disease progression.Conclusions:scRNA-seq technology revealed intra-tumor cell heterogeneity in UC-associated colon cancer,and might provide a promising direction to identify novel potential therapeutic targets in the evolution from UC to CAC. 展开更多
关键词 Ulcerative colitis-associated colon cancer single-cell RNA sequencing cell heterogeneity evolutionary trajectory
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Evolutionary history mediates adaptation through shaping genetic variance 认领 引用 被引量：1
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作者 Jia-Xu Han Zhuang-Dong Bai Rui-Wu Wang 《Journal of Systematics and Evolution》 SCIE CSCD 2025年第4期910-921,共12页
Organisms exhibit diverse responses when exposed to novel environments,and successful adaptation depends on aligning evolutionary histories with these new conditions.Reusing standing genetic variation is a critical me... Organisms exhibit diverse responses when exposed to novel environments,and successful adaptation depends on aligning evolutionary histories with these new conditions.Reusing standing genetic variation is a critical mechanism for this adaptation process.Using an extended Fisher's geometric model,we conducted simulations of evolving populations to investigate how evolutionary histories influence adaptation to novel environments.Our results highlight that distinct evolutionary histories produce varying patterns of genetic variance within populations.When organisms return to previously experienced environments,they exhibit enhanced performance and rapid adaptation.This supports the validity of the strategy commonly employed in ecological restoration to revert habitats to their original state.Moreover,small deviations of the greatest genetic variance direction from the optimum are beneficial for both fitness and fitness increase.A small genetic variance size is advantageous for fitness but impedes fitness increase.A short distance to the optimum and a sharp genetic variance shape are beneficial for fitness but have no significant effects on fitness increase.Our findings underscore the crucial role of evolutionary histories in shaping genetic variance and evolutionary potential when adapting to a new optimum.These results contribute to an evolutionary understanding of the factors underlying the disparate responses of phenotypically similar species to environmental change. 展开更多
关键词 direction of greatest genetic variance evolutionary trajectories individual based simulations rapid environment change
SWEET transporters in Dendrobium species:molecular insights into the regulation of polysaccharide biosynthesis 认领 引用
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作者 Dongxiao Li Peijun Lu +12 位作者 Fulai Li Qi Qi Zhenqin Lai Jie Li Zaihua Wang Zhihao Hong Zejun Ren Yutong Lin Jiaqi Zeng Huixian Mai Jiaqi Tian Hong-Bin Wang Hong-Lei Jin 《Medicinal Plant Biology》 2025年第1期119-130,共12页
Dendrobium,a large genus in the orchid family,is globally valued for its medicinal and ornamental properties.However,Dendrobium species exhibit significant variations in their phenotypic traits,chemical compositions,a... Dendrobium,a large genus in the orchid family,is globally valued for its medicinal and ornamental properties.However,Dendrobium species exhibit significant variations in their phenotypic traits,chemical compositions,and contents of bioactive compounds,particularly polysaccharides,which are a key determinant of quality.This study employed comparative genomics to investigate the evolutionary trajectories of four Dendrobium species with distinct polysaccharide profiles and phenotypic characteristics to identify putative genomic loci controlling polysaccharide biosynthesis.The analysis revealed differential evolutionary patterns potentially associated with polysaccharide accumulation.The SWEET gene family was systematically characterized,encoding sugar transporters implicated in polysaccharide metabolism,across Dendrobium species.Promoter analysis demonstrated that SWEET genes predominantly contain abiotic stress-responsive cis-acting elements.Using D.officinale as a model,SWEET gene expression dynamics were investigated through transcriptomic profiling and RT-qPCR validation.Heatmap analysis revealed tissue-specific expression patterns and differential responses to environmental stress factors(high light,cold,and salinity)and phytohormones.Integrated expression profiling identified six candidate genes(SWEET1,8,13,15,17,and 24)as potential key regulators of the quality formation mechanism of D.officinale.These six genes were silenced via virus-induced gene silencing.Polysaccharide accumulation was significantly reduced in all silenced lines,with a 14%–22%decrease observed across lines.Silencing DoSWEET1,8,13,17,and 24 had the most pronounced effects on polysaccharide contents.This study enhances the understanding of the mechanisms underlying quality formation in medicinal plants and provides critical genetic resources for the improvement and breeding of Dendrobium species. 展开更多
关键词 evolutionary trajectories dendrobium species sweet transporters polysaccharide biosynthesis bioactive compoundsparticularly phenotypic characteristics comparative genomics polysaccharide profiles
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From germplasm diversity to genetic design:strategies for photoperiod adaptation in rice 认领 引用
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作者 Leina Zhou Yinyin Liu +4 位作者 Salinda Sandamal Yuhang Zhang Asanka Tennakoon Qian Qian Xiaoming Zheng 《Seed Biology》 2025年第1期63-72,共10页
Rice(Oryza sativa L.)serves as a model for understanding how domestication and ecological adaptation together shape the global distribution of crops.Originating in tropical and subtropical regions characterized by sho... Rice(Oryza sativa L.)serves as a model for understanding how domestication and ecological adaptation together shape the global distribution of crops.Originating in tropical and subtropical regions characterized by short-day photoperiods and high temperatures,rice has undergone thousands of years of human selection and environmental shaping.These processes have enabled its cultivation across a broad range of latitudes,climates,and photoperiod conditions.A key driver of this ecological plasticity is the genetic reprogramming of heading date regulation.This review focuses on the genetic network underlying photoperiodic control of heading date(HD),with a focus on the evolutionary trajectories of major regulators,including Heading date 1(Hd1),Grains Height Date 7(Ghd7),Days to heading 8(DTH8),Early heading date 1(Ehd1)and Heading date 3a(Hd3a)/RICE FLOWERING LOCUS T 1(RFT1).The expansion of rice from tropical short-day to temperate long-day regions has been facilitated by loss-of-function mutations,expression divergence,and complex allelic combinations.Specific allele assemblies have also contributed to the divergence between indica and japonica subspecies,as well as to latitudinal adaptation.Despite the existence of over 780,000 germplasm accessions,a large portion of this germplasm diversity remains untapped.To bridge this gap,a conceptual framework for global adaptation that integrates multi-omics data,artificial intelligence(AI)-assisted modeling,and synthetic biology,is composed to reengineer heading date regulation.This review envisions a forward-looking breeding strategy that unites germplasm utilization,mechanistic understanding,and predictive design to develop rice varieties optimized for complex and variable agricultural environments. 展开更多
关键词 human selection environmental shapingthese rice evolutionary trajectories photoperiod adaptation heading date regulation ecological plasticity germplasm diversity genetic design
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Advancing plant phylogenetics and evolution through genomic data bursts and methodological innovations 认领 引用
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作者 Dayu Wu Kangshan Mao 《Journal of Systematics and Evolution》 SCIE CSCD 2025年第4期781-787,共7页
1 Introduction.Understanding the origins and evolutionary trajectories of biodiversity,along with their spatiotemporal patterns,is a long-standing theme in biology(Kapli et al.,2020).Phylogenetics,reconstructing evolu... 1 Introduction.Understanding the origins and evolutionary trajectories of biodiversity,along with their spatiotemporal patterns,is a long-standing theme in biology(Kapli et al.,2020).Phylogenetics,reconstructing evolutionary relationships among organisms based on molecular,morphological,and other biological data,acts as a cornerstone of biodiversity studies(Hill et al.,2025). 展开更多
关键词 methodological innovations biodiversity evolutionary trajectories origins evolutionary trajectories spatiotemporal patterns phylogenetics genomic data
Large-scale analyses of heat shock transcription factors and database construction based on whole-genome genes in horticultural and representative plants 认领 引用 被引量：10
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作者 Tong Yu Yun Bai +9 位作者 Zhuo Liu Zhiyuan Wang Qihang Yang Tong Wu Shuyan Feng Yu Zhang Shaoqin Shen Qiang Li Liqiang Gu Xiaoming Song 《Horticulture Research》 SCIE CSCD 2022年第1期1841-1858,共18页
Heat shock transcription factor(Hsf)plays a critical role in regulating heat resistance.Here,2950 Hsf family genes were identified from 111 horticultural and representative plants.More Hsf genes were detected in highe... Heat shock transcription factor(Hsf)plays a critical role in regulating heat resistance.Here,2950 Hsf family genes were identified from 111 horticultural and representative plants.More Hsf genes were detected in higher plants than in lower plants.Based on all Hsf genes,we constructed a phylogenetic tree,which indicated that Hsf genes of each branch evolved independently after species differentiation.Furthermore,we uncovered the evolutionary trajectories of Hsf genes by motif analysis.There were only six motifs(M1-M6)in lower plants,and then four novel motifs(M7-M10)appeared in higher plants.However,the motifs of some Hsf genes were lost in higher plants,indicating that Hsf genes have undergone sequence variation during their evolution.The number of Hsf genes lost was greater than the number of genes that were duplicated after whole-genome duplication in higher plants.The heat response network was constructed using 24 Hsf genes and 2421 downstream and 222 upstream genes of Arabidopsis.Further enrichment analysis revealed that Hsf genes and other transcription factors interacted with each other in the response to heat stress.Global expression maps were illustrated for Hsf genes under various abiotic and biotic stresses and several developmental stages in Arabidopsis.Syntenic and phylogenetic analyses were conducted using Hsf genes of Arabidopsis and the pan-genome of 18 Brassica rapa accessions.We also performed expression pattern analysis of Hsf and six Hsp family genes using expression values from different tissues and heat treatments in B.rapa.The interaction network between the Hsf and Hsp gene families was constructed in B.rapa,and several core genes were detected in the network.Finally,we constructed an Hsf database(http://gffzz157ef08c3ef94ea8hpqkn5nvqxqf56xpf.ffgz.tsg.suse.edu.cn)for researchers to retrieve Hsf gene family information.Therefore,our study will provide rich resources for the study of the evolution and function of Hsf genes. 展开更多
关键词 heat shock transcription factor hsf plays phylogenetic treewhich horticultural representative plantsmore evolutionary trajectories motif analysisthere hsf genes hsf geneswe regulating heat resistancehere
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A near-complete genome assembly of the allotetrapolyploid Cenchrus fungigraminus(JUJUNCAO)provides insights into its evolution and C4 photosynthesis 认领 引用 被引量：9
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作者 Huakun Zheng Baiyu Wang +17 位作者 Xiuting Hua Ruiting Gao Yuhao Wang Zixin Zhang Yixing Zhang Jing Mei Yongji Huang Yumin Huang Hui Lin Xingtan Zhang Dongmei Lin Siren Lan Zhongjian Liu Guodong Lu Zonghua Wang Ray Ming Jisen Zhang Zhanxi Lin 《Plant Communications》 SCIE CSCD 2023年第5期324-341,共18页
JUJUNCAO(Cenchrus fungigraminus;2n=4x=28)is a Cenchrus grass with the highest biomass production among cultivated plants,and it can be used for mushroom cultivation,animal feed,and biofuel production.Here,we report a ... JUJUNCAO(Cenchrus fungigraminus;2n=4x=28)is a Cenchrus grass with the highest biomass production among cultivated plants,and it can be used for mushroom cultivation,animal feed,and biofuel production.Here,we report a nearly complete genome assembly of JUJUNCAO and reveal that JUJUNCAO is an allopolyploid that originated2.7 million years ago(mya).Its genome consists of two subgenomes,and subgenome A shares high collinear synteny with pearl millet.We also investigated the genome evolution of JUJUNCAO and suggest that the ancestral karyotype of Cenchrus split into the A and B ancestral karyotypes of JUJUNCAO.Comparative transcriptome and DNA methylome analyses revealed functional divergence of homeologous gene pairs between the two subgenomes,which was a further indication of asymmetric DNA methylation.The three types of centromeric repeat in the JUJUNCAO genome(CEN137,CEN148,and CEN156)may have evolved independently within each subgenome,with some introgressions of CEN156 from the B to the A subgenome.We investigated the photosynthetic characteristics of JUJUNCAO,revealing its typical C4 Kranz anatomy and high photosynthetic efficiency.NADP-ME and PEPCK appear to cooperate in the major C4 decarboxylation reaction of JUJUNCAO,which is different from other C4 photosynthetic subtypes and may contribute to its high photosynthetic efficiency and biomass yield.Taken together,our results provide insights into the highly efficient photosynthetic mechanism of JUJUNCAO and provide a valuable reference genome for future genetic and evolutionary studies,as well as genetic improvement of Cenchrus grasses. 展开更多
关键词 genome assembly allotetrapolyploid centromere architecture evolutionary trajectory photosynthetic efficiency Cenchrus grass
Medullary thyroid cancer:single-cell transcriptome and tumor evolution 认领 引用
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作者 Li-feng Wang Wen-wen Zhou +3 位作者 Fang Yuan Kai-wen Fu Yongpeng He Rui Chen 《Holistic Integrative Oncology》 2024年第1期252-261,共10页
Background Medullary thyroid cancer(MTC)is a rare neuroendocrine tumor that originates from the parafollicular C cells of thyroid gland.Understanding the fundamental pathophysiology of MTC is essential for clinical ma... Background Medullary thyroid cancer(MTC)is a rare neuroendocrine tumor that originates from the parafollicular C cells of thyroid gland.Understanding the fundamental pathophysiology of MTC is essential for clinical manage-ment.Single-cell RNA sequencing(scRNA-seq)technology is a powerful tool for identifying distinct cell types,offering a new biological foundation for comprehending the MTC ecosystem and developing precise treatment.Methods Formalin fixed and paraffin-embedded(FFPE)samples of primary and adjacent non-cancerous tissues of three MTC cases were collected,and single-cell transcriptome data of MTC were obtained by using scRNA-seq technology.Annotated cell subpopulations were categorized and functionally enriched by principal component analysis,differential gene expression,and cell clustering analysis,to explore the biological process of tumor evolution that may be involved in each cell subpopulation.The copy number variation(CNV)profile was used to distinguish the malignancy of parafollicular thyroid cells,and the evolutionary trajectories of normal cells and tumor cells were revealed by the proposed time series analysis.The highly expressed genes in each cell subpopulation were analyzed by the FindAllMarker function of Seurat software,and verified by immunohistochemistry and fluorescence in situ hybridization.The prognostic value of specific cell subtypes was validated using large-scale public datasets.Results A total of 32,544 cells were obtained from the MTC tissue samples and 11,751 cells from the adjacent non-cancerous samples,which were classified into 7 heterogenous subpopulations by using R package of Seurat mod-ule.Copy number variations(CNVs)were significantly higher in tumor tissues than in adjacent non-tumor samples,predominantly enriched in subtypes C2 and C4.In addition,the pseudo-time for trajectory analysis suggested that the evolution of MTC tumor cells might begin with the C2 subtype,then transition to the early cancer sub-group C3,and further differentiate into four major malignant cell subpopulations C0,C1,C5 and C6.Survival analysis of a thyroid cancer cohort using the TCGA dataset revealed that high expression of genes linked to the C0 subcluster was correlated with poorer overall survival compared to low expression.Immunohistochemical staining showed that MAP3K4 was highly expressed in MTC tissues compared to adjacent non-cancerous tissues.Fluorescence in situ hybridization also confirmed the amplification of these two genes in MTC samples.Conclusions By conducting scRNA-seq on FFPE samples,we mapped the single-cell transcriptome of MTC,uncov-ering the tumor heterogeneity and unique biological features of each cellular subpopulation.The biological roles of identified tumor cell subpopulations such as C0 and C3 subtypes of parafollicular cells suggested the potential to discover new therapeutic targets and biomarkers for MTC,providing valuable insights for future translational and clinical research. 展开更多
关键词 Single-cell transcriptome sequencing Medullary thyroid carcinoma Tumor evolutionary trajectory Formalin fixed and paraffin-embedded samples Heterogeneity
Evolution of modern river systems:an assessment of‘landscape memory’in Indian river systems 认领 引用
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作者 Vikrant Jain Sonam +2 位作者 Ajit Singh Rajiv Sinha S.K.Tandon 《Episodes》 SCIE 2020年第1期535-551,共17页
Every river basin is characterised by an evolutionary history,which may be analysed at different time scales.This study provides a geological and geomorphic history of different river basins of India at different time... Every river basin is characterised by an evolutionary history,which may be analysed at different time scales.This study provides a geological and geomorphic history of different river basins of India at different time scales ranging from millions of years to millennial time scales.The river basins in India are divided into six different groups on the basis of different tectono-climatic settings and geomorphic characteristics.The evolutionary trajectories in the past strongly govern the modern day geomorphic characteristics and processes in a river basin.The basin scale data compiled in this paper highlights the role of geological inheritance and‘landscape memory’in the evolution of river systems of India. 展开更多
关键词 landscape memory Indian river systems evolutionary historywhich modern river systems river basin river basins evolutionary trajectories evolution
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