Soybean(Glycine max)is a vital foundation of global food security,providing a primary source of highquality protein and oil for human consumption and animal feed.The rising global population has significantly increase...Soybean(Glycine max)is a vital foundation of global food security,providing a primary source of highquality protein and oil for human consumption and animal feed.The rising global population has significantly increased the demand for soybeans,emphasizing the urgency of developing high-yield,stresstolerant,and nutritionally superior cultivars.The extensive collection of soybean germplasm resources—including wild relatives,landraces,and cultivars—represents a valuable reservoir of genetic diversity critical for breeding advancements.Recent breakthroughs in genomic technologies,particularly highthroughput sequencing and multi-omics approaches,have revolutionized the identification of key genes associated with essential agronomic traits within these resources.These innovations enable precise and strategic utilization of genetic diversity,empowering breeders to integrate traits that improve yield potential,resilience to biotic and abiotic stresses,and nutritional quality.This review highlights the critical role of genetic resources and omics-driven innovations in soybean breeding.It also offers insights into strategies for accelerating the development of elite soybean cultivars to meet the growing demands of global soybean production.展开更多
Increasing yield is one of the most important goals in crop breeding. Soybean （Glycine max L. Merr.）, one of the most economically important leguminous seed crops, provides the majority of plant proteins, and more t...Increasing yield is one of the most important goals in crop breeding. Soybean （Glycine max L. Merr.）, one of the most economically important leguminous seed crops, provides the majority of plant proteins, and more than a quarter of the world＇s food and animal feed （Graham and Vance, 2003）. The yield of soybean is finally determined by the number of seeds per unit area, which affected by many characters, such as height, branching number, photosynthesis, seed size, seed number. The number of seeds per pod is taken for one of the critical components that related to yield （You et al., 1995）.展开更多
Mobile Edge Computing(MEC)has become the most possible network architecture to realize the vision of interconnection of all things.By offloading compute-intensive or latency-sensitive applications to nearby small cell...Mobile Edge Computing(MEC)has become the most possible network architecture to realize the vision of interconnection of all things.By offloading compute-intensive or latency-sensitive applications to nearby small cell base stations(sBSs),the execution latency and device power consumption can be reduced on resource-constrained mobile devices.However,computation delay of Mobile Edge Network(MEN)tasks are neglected while the unloading decision-making is studied in depth.In this paper,we propose a workload allocation scheme which combines the task allocation optimization of mobile edge network with the actual user behavior activities to predict the task allocation of single user.We obtain the next possible location through the user's past location information,and receive the next access server according to the grid matrix.Furthermore,the next time task sequence is calculated on the base of the historical time task sequence,and the server is chosen to preload the task.In the experiments,the results demonstrate a high accuracy of our proposed model.展开更多
Leaf morphology varies substantially across plant species.In soybeans,the regulation of compound leaf development remains poorly characterized,despite its critical role in plant architecture.Some soybean cultivars hav...Leaf morphology varies substantially across plant species.In soybeans,the regulation of compound leaf development remains poorly characterized,despite its critical role in plant architecture.Some soybean cultivars have compound leaves with up to five leaflets,while most are trifoliolate.Using genetic mapping,we identified a gene behind the leaflet number variation as LF1,an AP2/ERF transcription factor.High expression levels of LF1were further observed in leaf primordium initiation sites,leaf primordia,and leaflet initiation domains.Transgenic overexpression of LF1 increased leaflet number.Further investigation revealed that LF1 regulates leaflet development through negative autoregulation via GCC-box ciselement binding.In addition to the role of LF1,the CRISPR-edited mutant of TEOSINTE-BRANCHED1/CYCLOIDEA/PCF3(GmTCP3)displayed serrated blade margins in juvenile leaves and increased compound leaflet numbers.Protein interaction assays confirmed LF1 binding affinity for GmTCP3.Furthermore,we demonstrate that LF1 induces the expression of GmLFY,a key regulator of leaflet development.Altogether,our findings establish LF1 as a central regulator of soybean leaflet morphogenesis and reveal its mechanistic interactions with GmTCP3 and LEAFY(GmLFY),offering novel mechanistic insights into the genetic control of compound leaf development.展开更多
The pathogenesis of benign prostatic hyperplasia(BPH)is commonly regarded as androgen-dependent.The first FDA-approved androgen-targeted medication for BPH,finasteride,achieves its therapeutic effect by selectively in...The pathogenesis of benign prostatic hyperplasia(BPH)is commonly regarded as androgen-dependent.The first FDA-approved androgen-targeted medication for BPH,finasteride,achieves its therapeutic effect by selectively inhibiting type II 5-alpha reductase(SRD5A2).This inhibition reduces the androgenic response by attenuating the interaction between dihydrotestosterone and androgen receptor(AR),ultimately leading to a reduction in prostate volume and alleviation of BPH-associated symptoms.However,it is noteworthy that non-response to finasteride may develop in certain BPH patients,1 indicating a potential inadvertent promotion of disease progression by this treatment.Nevertheless,the underlying mechanism remains elusive.Recent researches suggest that it may be associated with alterations within the prostate gland epithelia.2 Therefore,we designed this study to elucidate this phenomenon by employing spatial transcriptomic(ST)and single-cell RNA sequencing(scRNA-seq)(methods were described in Supplementary Materials in detail).Our findings will improve treatment adjustments by enabling a more accurate evaluation of patient's response to finasteride therapy,thus enhancing therapeutic outcomes.展开更多
Soybean is one of the most important crops globally,and its production must be significantly increased to meet increasing demand.Elucidating the genetic regulatory networks underlying soybean organ development is esse...Soybean is one of the most important crops globally,and its production must be significantly increased to meet increasing demand.Elucidating the genetic regulatory networks underlying soybean organ development is essential for breeding elite and resilient varieties to ensure increased soybean production under climate change.An integrated transcriptomic atlas that leverages multiple types of transcriptomics data can facilitate the characterization of temporal-spatial expression patterns of most organ developmentrelated genes and thereby help us to understand organ developmental processes.Here,we constructed a comprehensive,integrated transcriptomic atlas for soybeans,integrating bulk RNA sequencing(RNAseq)datasets from 314 samples across the soybean life cycle,along with single-nucleus RNA-seq and spatially enhanced resolution omics sequencing datasets from five organs:root,nodule,shoot apex,leaf,and stem.Investigating genes related to organ specificity,blade development,and nodule formation,we demonstrate that the atlas has robust power for exploring key genes involved in organ formation.In addition,we developed a user-friendly panoramic database for the transcriptomic atlas,enabling easy access and queries,which will serve as a valuable resource to significantly advance future soybean functional 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
Dear Editor,Soybean is one of the most important crops worldwide.A high-quality reference genome will facilitate its functional analysis and molecular breeding (Wang and Tian,2015).Previously,we de novo assembled a hi...Dear Editor,Soybean is one of the most important crops worldwide.A high-quality reference genome will facilitate its functional analysis and molecular breeding (Wang and Tian,2015).Previously,we de novo assembled a high-quality Chinese soybean genome Gmax_ZH13 (Shen et al.,2018,Yang and Huang,2018).However,due to technical limitations at the time when we generated Gmax_ZH13,a large number of small contigs were not anchored onto chromosomes.Therefore,we here build a new golden reference genome for Zhonghuang 13 consisting of 20 nearly complete chromosomes by adding more single-molecule real time (SMRT) sequencing reads.Furthermore,we add large RNA-seq and smRNA-seq datasets for improving the annotation of its protein coding genes.展开更多
Dear Editor,As one of the most important crops to supply the majority of plant oil and protein for the whole world,soybean is facing an increasing global demand.The reference genome of accession"Williams82"o...Dear Editor,As one of the most important crops to supply the majority of plant oil and protein for the whole world,soybean is facing an increasing global demand.The reference genome of accession"Williams82"opened the gate of genomics research in soybean(Schmutz et al.,2010).After that,vast multi-omics data were generated,thereby providing valuable resources for functional study and molecular breeding.Parts of these data have been collected in different soybean databases(see details in Supplemental Table 1),such as Soybase(Grant et al.,2010)and SoyKB(Joshi et al.,2012),which made valuable efforts to facilitate the wide utility of these data.Nevertheless,these existing databases poorly tackled multi-omics data integration and interactivity for soybean,provoking tremendous challenges for researchers to deal with these big omics data,particularly considering the unprecedented rate of data growth(Yang et al.,2021).Thus,constructing an integrated multi-omics database for soybean that provides a one-stop solution for big data mining with friendly interactivity is highly desired.展开更多
Soybean[Glycine max(L.)Merr.]is one of the most important,but a drought-sensitive,crops.Identifying the genes controlling drought tolerance is important in soybean breeding.Here,through a genome-wide association study...Soybean[Glycine max(L.)Merr.]is one of the most important,but a drought-sensitive,crops.Identifying the genes controlling drought tolerance is important in soybean breeding.Here,through a genome-wide association study,we identified one significant association locus,located on chromosome 8,which conferred drought tolerance variations in a natural soybean population.Allelic analysis and genetic validation demonstrated that GmACO1,encoding for a 1-aminocyclopropane-1-carboxylate oxidase,was the causal gene in this association locus,and positively regulated drought tolerance in soybean.Meanwhile,we determined that GmACO1 expression was reduced after rhizobial infection,and that GmACO1 negatively regulated soybean nodule formation.Overall,our findings provide insights into soybean cultivars for future breeding.展开更多
Gene innovation plays an essential role in trait evolution.Rhizobial symbioses,the most important N2-fixing agent in agricultural systems that exists mainly in Leguminosae,is one of the most attractive evolution event...Gene innovation plays an essential role in trait evolution.Rhizobial symbioses,the most important N2-fixing agent in agricultural systems that exists mainly in Leguminosae,is one of the most attractive evolution events.However,the gene innovations underlying Leguminosae root nodule symbiosis(RNS)remain largely unknown.Here,we investigated the gene gain event in Leguminosae RNS evolution through comprehensive phylogenomic analyses.We revealed that Leguminosae-gain genes were acquired by gene duplication and underwent a strong purifying selection.Kyoto Encyclopedia of Genes and Genomes analyses showed that the innovated genes were enriched in flavonoid biosynthesis pathways,particular downstream of chalcone synthase(CHS).Among them,Leguminosae-gain typeⅡchalcone isomerase(CHI)could be further divided into CHI1A and CHI1B clades,which resulted from the products of tandem duplication.Furthermore,the duplicated CHI genes exhibited exon–intron structural divergences evolved through exon/intron gain/loss and insertion/deletion.Knocking down CHI1B significantly reduced nodulation in Glycine max(soybean)and Medicago truncatula;whereas,knocking down its duplication gene CHI1A had no effect on nodulation.Therefore,Leguminosae-gain typeⅡCHI participated in RNS and the duplicated CHI1A and CHI1B genes exhibited RNS functional divergence.This study provides functional insights into Leguminosae-gain genetic innovation and sub-functionalization after gene duplication that contribute to the evolution and adaptation of RNS in Leguminosae.展开更多
Dear editor,Oxidative stress induced by reactive oxygen species(ROS)production plays a key role in tumor initiation and progression[1,2].Emerging evidence has shown that oxidative stress-related genes could be used as...Dear editor,Oxidative stress induced by reactive oxygen species(ROS)production plays a key role in tumor initiation and progression[1,2].Emerging evidence has shown that oxidative stress-related genes could be used as biomarkers for predicting the progression and prognosis of malignant tumors[3].Our previous study showed that the expression and genotypes of oxidative stress-related genes could be used for predicting the chemosensitivity and clinical outcomes of biliary tract cancer patients[4].展开更多
Cell typing is an important step in the single-cell RNA sequencing(scRNA-seq)analysis.Although some cell marker databases and cell typing tools have been proposed,limited roles are in prostate cell typing.Through lite...Cell typing is an important step in the single-cell RNA sequencing(scRNA-seq)analysis.Although some cell marker databases and cell typing tools have been proposed,limited roles are in prostate cell typing.Through literature review,we found prostate cell typing relied much on researchers'knowledge and experience,thus different markers were used to label the same cell type,leading to the divergences between studies,emphasizing the importance of a sound epistemological foundation for prostate cell typing in single-cell data.展开更多
基金supported by the National Key Research and Development Program of China(2022YFF1003301,2023YFF1000101,2022YFE0130200)the Taishan Scholars Program。
文摘Soybean(Glycine max)is a vital foundation of global food security,providing a primary source of highquality protein and oil for human consumption and animal feed.The rising global population has significantly increased the demand for soybeans,emphasizing the urgency of developing high-yield,stresstolerant,and nutritionally superior cultivars.The extensive collection of soybean germplasm resources—including wild relatives,landraces,and cultivars—represents a valuable reservoir of genetic diversity critical for breeding advancements.Recent breakthroughs in genomic technologies,particularly highthroughput sequencing and multi-omics approaches,have revolutionized the identification of key genes associated with essential agronomic traits within these resources.These innovations enable precise and strategic utilization of genetic diversity,empowering breeders to integrate traits that improve yield potential,resilience to biotic and abiotic stresses,and nutritional quality.This review highlights the critical role of genetic resources and omics-driven innovations in soybean breeding.It also offers insights into strategies for accelerating the development of elite soybean cultivars to meet the growing demands of global soybean production.
基金supported by the National Natural Science Foundation of China(Grant Nos.31271297 and 31222042) "One-hundred talents" Startup Funds from Chinese Academy of SciencesNational Key Basic Research Program(No. 2009CB 118402)
文摘Increasing yield is one of the most important goals in crop breeding. Soybean （Glycine max L. Merr.）, one of the most economically important leguminous seed crops, provides the majority of plant proteins, and more than a quarter of the world＇s food and animal feed （Graham and Vance, 2003）. The yield of soybean is finally determined by the number of seeds per unit area, which affected by many characters, such as height, branching number, photosynthesis, seed size, seed number. The number of seeds per pod is taken for one of the critical components that related to yield （You et al., 1995）.
基金This work is supported by the CETC Joint Advanced Research Foundation(No.6141B08020101)Major Special Science and Technology Project of Hainan Province(No.ZDKJ2019008).
文摘Mobile Edge Computing(MEC)has become the most possible network architecture to realize the vision of interconnection of all things.By offloading compute-intensive or latency-sensitive applications to nearby small cell base stations(sBSs),the execution latency and device power consumption can be reduced on resource-constrained mobile devices.However,computation delay of Mobile Edge Network(MEN)tasks are neglected while the unloading decision-making is studied in depth.In this paper,we propose a workload allocation scheme which combines the task allocation optimization of mobile edge network with the actual user behavior activities to predict the task allocation of single user.We obtain the next possible location through the user's past location information,and receive the next access server according to the grid matrix.Furthermore,the next time task sequence is calculated on the base of the historical time task sequence,and the server is chosen to preload the task.In the experiments,the results demonstrate a high accuracy of our proposed model.
基金supported by Biological Breeding-National Science and Technology Major Project(2023ZD04076)The Taishan Scholars Program+1 种基金the National Key Research and Development Program of China(grant no.2022YFD1201503,2023YFD1200600)the National Natural Science Foundation of China(grant nos.32272107)。
文摘Leaf morphology varies substantially across plant species.In soybeans,the regulation of compound leaf development remains poorly characterized,despite its critical role in plant architecture.Some soybean cultivars have compound leaves with up to five leaflets,while most are trifoliolate.Using genetic mapping,we identified a gene behind the leaflet number variation as LF1,an AP2/ERF transcription factor.High expression levels of LF1were further observed in leaf primordium initiation sites,leaf primordia,and leaflet initiation domains.Transgenic overexpression of LF1 increased leaflet number.Further investigation revealed that LF1 regulates leaflet development through negative autoregulation via GCC-box ciselement binding.In addition to the role of LF1,the CRISPR-edited mutant of TEOSINTE-BRANCHED1/CYCLOIDEA/PCF3(GmTCP3)displayed serrated blade margins in juvenile leaves and increased compound leaflet numbers.Protein interaction assays confirmed LF1 binding affinity for GmTCP3.Furthermore,we demonstrate that LF1 induces the expression of GmLFY,a key regulator of leaflet development.Altogether,our findings establish LF1 as a central regulator of soybean leaflet morphogenesis and reveal its mechanistic interactions with GmTCP3 and LEAFY(GmLFY),offering novel mechanistic insights into the genetic control of compound leaf development.
基金supported by the National Natural Science Foundation of China (No. 62101319)the Qingpu District Health Commission Discipline Talent Project of Shanghai, China (No. YY2023-3, TX2023-4)the Medical Discipline Construction Project of Pudong New Area Health System (Shanghai, China) (No. PYWgf2021-06).
文摘The pathogenesis of benign prostatic hyperplasia(BPH)is commonly regarded as androgen-dependent.The first FDA-approved androgen-targeted medication for BPH,finasteride,achieves its therapeutic effect by selectively inhibiting type II 5-alpha reductase(SRD5A2).This inhibition reduces the androgenic response by attenuating the interaction between dihydrotestosterone and androgen receptor(AR),ultimately leading to a reduction in prostate volume and alleviation of BPH-associated symptoms.However,it is noteworthy that non-response to finasteride may develop in certain BPH patients,1 indicating a potential inadvertent promotion of disease progression by this treatment.Nevertheless,the underlying mechanism remains elusive.Recent researches suggest that it may be associated with alterations within the prostate gland epithelia.2 Therefore,we designed this study to elucidate this phenomenon by employing spatial transcriptomic(ST)and single-cell RNA sequencing(scRNA-seq)(methods were described in Supplementary Materials in detail).Our findings will improve treatment adjustments by enabling a more accurate evaluation of patient's response to finasteride therapy,thus enhancing therapeutic outcomes.
基金supported by the National Natural Science Foundation of China(grant no.32388201)the National Key Research and Development Program of China(2022YFF1003301,and 2023YFF1000101)+1 种基金the Taishan Scholars Programthe Xplorer Prize.
文摘Soybean is one of the most important crops globally,and its production must be significantly increased to meet increasing demand.Elucidating the genetic regulatory networks underlying soybean organ development is essential for breeding elite and resilient varieties to ensure increased soybean production under climate change.An integrated transcriptomic atlas that leverages multiple types of transcriptomics data can facilitate the characterization of temporal-spatial expression patterns of most organ developmentrelated genes and thereby help us to understand organ developmental processes.Here,we constructed a comprehensive,integrated transcriptomic atlas for soybeans,integrating bulk RNA sequencing(RNAseq)datasets from 314 samples across the soybean life cycle,along with single-nucleus RNA-seq and spatially enhanced resolution omics sequencing datasets from five organs:root,nodule,shoot apex,leaf,and stem.Investigating genes related to organ specificity,blade development,and nodule formation,we demonstrate that the atlas has robust power for exploring key genes involved in organ formation.In addition,we developed a user-friendly panoramic database for the transcriptomic atlas,enabling easy access and queries,which will serve as a valuable resource to significantly advance future soybean functional 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 the National Key Research & Development Program of China (2017YFD0101305)National Natural Science Foundation of China (31525018, 31788103)the State Key Laboratory of Plant Cell and Chromosome Engineering (PCCE-KF2019-05)
文摘Dear Editor,Soybean is one of the most important crops worldwide.A high-quality reference genome will facilitate its functional analysis and molecular breeding (Wang and Tian,2015).Previously,we de novo assembled a high-quality Chinese soybean genome Gmax_ZH13 (Shen et al.,2018,Yang and Huang,2018).However,due to technical limitations at the time when we generated Gmax_ZH13,a large number of small contigs were not anchored onto chromosomes.Therefore,we here build a new golden reference genome for Zhonghuang 13 consisting of 20 nearly complete chromosomes by adding more single-molecule real time (SMRT) sequencing reads.Furthermore,we add large RNA-seq and smRNA-seq datasets for improving the annotation of its protein coding genes.
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA24000000,XDA19050302,and XDA24040201)the Science and Technology Innovation 2030-Major Project(2022ZD04017)+5 种基金the National Natural Science Foundation of China(32030021,32000475,and 32201775)the National Key Research and Development Program of China(2021YFF1001201)the Taishan Scholars Programthe Xplorer Prize Awardthe Youth Innovation Promotion Association of the Chinese Academy of Sciences(Y2021038)the China National Postdoctoral Program for innovative Talents(BX2021354).
文摘Dear Editor,As one of the most important crops to supply the majority of plant oil and protein for the whole world,soybean is facing an increasing global demand.The reference genome of accession"Williams82"opened the gate of genomics research in soybean(Schmutz et al.,2010).After that,vast multi-omics data were generated,thereby providing valuable resources for functional study and molecular breeding.Parts of these data have been collected in different soybean databases(see details in Supplemental Table 1),such as Soybase(Grant et al.,2010)and SoyKB(Joshi et al.,2012),which made valuable efforts to facilitate the wide utility of these data.Nevertheless,these existing databases poorly tackled multi-omics data integration and interactivity for soybean,provoking tremendous challenges for researchers to deal with these big omics data,particularly considering the unprecedented rate of data growth(Yang et al.,2021).Thus,constructing an integrated multi-omics database for soybean that provides a one-stop solution for big data mining with friendly interactivity is highly desired.
基金supported by the National Key Research and Development Program of China(2022YFD1201503)the National Natural Science Foundation of China(32341033,U22A20467)+1 种基金the Taishan Scholars Program,Hainan Seed Industry Laboratory(B21HJ0002,B23YQ1502)The GG project of the Xinjiang Production and Construction Corps,Provincial Special Fund for Science and Technology Innovation and Development of Agricultural Hightech Industrial Demonstration Area of the Yellow River Delta of Shandong Province(2022SZX15).
文摘Soybean[Glycine max(L.)Merr.]is one of the most important,but a drought-sensitive,crops.Identifying the genes controlling drought tolerance is important in soybean breeding.Here,through a genome-wide association study,we identified one significant association locus,located on chromosome 8,which conferred drought tolerance variations in a natural soybean population.Allelic analysis and genetic validation demonstrated that GmACO1,encoding for a 1-aminocyclopropane-1-carboxylate oxidase,was the causal gene in this association locus,and positively regulated drought tolerance in soybean.Meanwhile,we determined that GmACO1 expression was reduced after rhizobial infection,and that GmACO1 negatively regulated soybean nodule formation.Overall,our findings provide insights into soybean cultivars for future breeding.
基金The National Natural Science Foundation of China(grant nos.32388201,32300512 and U22A20467)“Strategic Priority Research Program”of the Chinese Academy of Sciences(grant no.XDA24030501)+1 种基金CAS Project for Young Scientists in Basic Research(YSBR-078)the Xplorer Prize。
文摘Gene innovation plays an essential role in trait evolution.Rhizobial symbioses,the most important N2-fixing agent in agricultural systems that exists mainly in Leguminosae,is one of the most attractive evolution events.However,the gene innovations underlying Leguminosae root nodule symbiosis(RNS)remain largely unknown.Here,we investigated the gene gain event in Leguminosae RNS evolution through comprehensive phylogenomic analyses.We revealed that Leguminosae-gain genes were acquired by gene duplication and underwent a strong purifying selection.Kyoto Encyclopedia of Genes and Genomes analyses showed that the innovated genes were enriched in flavonoid biosynthesis pathways,particular downstream of chalcone synthase(CHS).Among them,Leguminosae-gain typeⅡchalcone isomerase(CHI)could be further divided into CHI1A and CHI1B clades,which resulted from the products of tandem duplication.Furthermore,the duplicated CHI genes exhibited exon–intron structural divergences evolved through exon/intron gain/loss and insertion/deletion.Knocking down CHI1B significantly reduced nodulation in Glycine max(soybean)and Medicago truncatula;whereas,knocking down its duplication gene CHI1A had no effect on nodulation.Therefore,Leguminosae-gain typeⅡCHI participated in RNS and the duplicated CHI1A and CHI1B genes exhibited RNS functional divergence.This study provides functional insights into Leguminosae-gain genetic innovation and sub-functionalization after gene duplication that contribute to the evolution and adaptation of RNS in Leguminosae.
基金supported by grants from the National Natural Science Foundation of China(81970656).
文摘Dear editor,Oxidative stress induced by reactive oxygen species(ROS)production plays a key role in tumor initiation and progression[1,2].Emerging evidence has shown that oxidative stress-related genes could be used as biomarkers for predicting the progression and prognosis of malignant tumors[3].Our previous study showed that the expression and genotypes of oxidative stress-related genes could be used for predicting the chemosensitivity and clinical outcomes of biliary tract cancer patients[4].
基金supported by the National Natural Science Foundation of China,China (No.62101319,82170788)the Medical Discipline Construction Project of the Health System of Pudong New Area (China) (No.PYWgf2021-06).
文摘Cell typing is an important step in the single-cell RNA sequencing(scRNA-seq)analysis.Although some cell marker databases and cell typing tools have been proposed,limited roles are in prostate cell typing.Through literature review,we found prostate cell typing relied much on researchers'knowledge and experience,thus different markers were used to label the same cell type,leading to the divergences between studies,emphasizing the importance of a sound epistemological foundation for prostate cell typing in single-cell data.
