Coriander(Coriandrum sativum L.),also known as cilantro,is a globally important vegetable and spice crop.Its genome and that of carrot are models for studying the evolution of the Apiaceae family.Here,we developed the...Coriander(Coriandrum sativum L.),also known as cilantro,is a globally important vegetable and spice crop.Its genome and that of carrot are models for studying the evolution of the Apiaceae family.Here,we developed the Coriander Genomics Database(CGDB,http://cgdb.bio2db.com/)to collect,store,and integrate the genomic,transcriptomic,metabolic,functional annotation,and repeat sequence data of coriander and carrot to serve as a central online platform for Apiaceae and other related plants.Using these data sets in the CGDB,we intriguingly found that seven transcription factor(TF)families showed significantly greater numbers of members in the coriander genome than in the carrot genome.The highest ratio of the numbers of MADS TFs between coriander and carrot reached 3.15,followed by those for tubby protein(TUB)and heat shock factors.As a demonstration of CGDB applications,we identified 17 TUB family genes and conducted systematic comparative and evolutionary analyses.RNA-seq data deposited in the CGDB also suggest dose compensation effects of gene expression in coriander.CGDB allows bulk downloading,significance searches,genome browser analyses,and BLAST searches for comparisons between coriander and other plants regarding genomics,gene families,gene collinearity,gene expression,and the metabolome.A detailed user manual and contact information are also available to provide support to the scientific research community and address scientific questions.CGDB will be continuously updated,and new data will be integrated for comparative and functional genomic analysis in Apiaceae and other related plants.展开更多
Cucurbitaceae is one of the most important plant families distributed worldwide.Transcription factors(TFs)regulate plant growth at the transcription level.Here,we performed a systematic analysis of 42641 TFs from 63 f...Cucurbitaceae is one of the most important plant families distributed worldwide.Transcription factors(TFs)regulate plant growth at the transcription level.Here,we performed a systematic analysis of 42641 TFs from 63 families in 14 Cucurbitaceae and 10 non-cucurbit species.Whole-genome duplication(WGD)was the dominant event type in almost all Cucurbitaceae plants.The TF families were divided into 1210 orthogroups(OGs),of which,112 were unique to Cucurbitaceae.Although the loss of several gene families was detected in Cucurbitaceae,the gene families expanded in five species that experienced a WGD event comparing with grape.Our findings revealed that the recent WGD events that had occurred in Cucurbitaceae played important roles in the expansion of most TF families.The functional enrichment analysis of the genes that significantly expanded or contracted uncovered five gene families,AUX/IAA,NAC,NBS,HB,and NF-YB.Finally,we conducted a comprehensive analysis of the TCP gene family and identified 16 tendril-related(TEN)genes in 11 Cucurbitaceae species.Interestingly,the characteristic sequence changed from CNNFYFP to CNNFYLP in the TEN gene(Bhi06M000087)of Benincasa hispida.Furthermore,we identified a new characteristic sequence,YNN,which could be used for TEN gene exploitation in Cucurbitaceae.In conclusion,this study will serve as a reference for studying the relationship between gene family evolution and genome duplication.Moreover,it will provide rich genetic resources for functional Cucurbitaceae studies in the future.展开更多
Water lilies are not only highly favored aquatic ornamental plants with cultural and economic importance but they also occupy a critical evolutionary space that is crucial for understanding the origin and early evolut...Water lilies are not only highly favored aquatic ornamental plants with cultural and economic importance but they also occupy a critical evolutionary space that is crucial for understanding the origin and early evolutionary trajectory of flowering plants.The birth and rapid radiation of flowering plants has interested many scientists and was considered‘an abominable mystery’by Charles Darwin.In searching for the angiosperm evolutionary origin and its underlying mechanisms,the genome of Amborella has shed some light on the molecular features of one of the basal angiosperm lineages;however,little is known regarding the genetics and genomics of another basal angiosperm lineage,namely,the water lily.In this study,we reviewed current molecular research and note that water lily research has entered the genomic era.We propose that the genome of the water lily is critical for studying the contentious relationship of basal angiosperms and Darwin’s‘abominable mystery’.Four pantropical water lilies,especially the recently sequenced Nymphaea colorata,have characteristics such as small size,rapid growth rate and numerous seeds and can act as the best model for understanding the origin of angiosperms.The water lily genome is also valuable for revealing the genetics of ornamental traits and will largely accelerate the molecular breeding of water lilies.展开更多
Sugarcane is a prominent source of sugar and ethanol production.Genetic analysis for trait improvement of sugarcane is greatly hindered by its complex genome,long breeding cycle,and recalcitrance to genetic transforma...Sugarcane is a prominent source of sugar and ethanol production.Genetic analysis for trait improvement of sugarcane is greatly hindered by its complex genome,long breeding cycle,and recalcitrance to genetic transformation.The protoplast-based transient transformation system is a versatile and convenient tool for in vivo functional gene analysis;however,quick and effective transformation systems are still lacking for sugarcane.Here,we developed an efficient protoplast-based transformation system by optimizing conditions of protoplasts isolation and PEG-mediated transformation in S.spontaneum.The yield of viable protoplasts was approximately 1.26×107 per gram of leaf material,and the transformation efficiency of 80.19%could be achieved under the optimized condition.Furthermore,using this approach,the nuclear localization of an ABI5-like bZIPs transcription factor was validated,and the promoter activity of several putative DNase I hypersensitive sites(DHSs)was assessed.The results indicated this system can be conveniently applied to protein subcellular localization and promoter activity assays.A highly efficient S.spontaneum mesophyll cell protoplast isolation and transient transformation method was developed,and it shall be suitable for in vivo functional gene analysis in sugarcane.展开更多
Congenital contractural arachnodactyly(CCA,OMIM:121050),also known as Beals syndrome,belongs to a group of rare autosomal dominant(AD)diseases of connective tissue(Maslen et al.,1997).People with CCA share many distin...Congenital contractural arachnodactyly(CCA,OMIM:121050),also known as Beals syndrome,belongs to a group of rare autosomal dominant(AD)diseases of connective tissue(Maslen et al.,1997).People with CCA share many distinguishing features,such as arachnodactyly,camp tod actyly,multiple joint contractures(especially finger,elbow,and knee joints),crumpled ears,scoliosis,pectus deformities,and muscular hypoplasia(Jurko et al.,2013).It exhibits no specific geographic or ethnic predilection(Frederic et al.,2009).展开更多
Sugarcane has a large,complex,polyploid genome that has hindered the progress of genomic research and molecular marker-assisted selection.The user-friendly SSR markers have attracted considerable attention owing to th...Sugarcane has a large,complex,polyploid genome that has hindered the progress of genomic research and molecular marker-assisted selection.The user-friendly SSR markers have attracted considerable attention owing to their ideal genetic attributes.However,these markers were not characterized and developed at the genome-wide scale due to the previously lacking high-quality chromosome-level assembled sugarcane genomes.In this present study,744305and 361638 candidate SSRs were identified from the genomes of S.officinarum and S.spontaneum,respectively.We verified the reliability of the predicted SSRs by using 1200 interspecific SSR primer pairs to detect polymorphisms among 11 representative accessions of Saccharum,including S.spontaneum,S.officinarum,S.robustum,and modern sugarcane hybrid.The results showed that 660 SSR markers displayed interspecific polymorphisms among these accessions.Furthermore,100 SSRs were randomly selected to detect the genetic diversity for 39 representative Saccharum accessions.A total of 320 alleles were generated using 100 polymorphic primers,with each marker ranging from two to seven alleles.The genetic diversity analysis revealed that these accessions were distributed in four main groups,including group I(14 S.spontaneum accessions),group II(two S.officinarum accessions),group III(18 modern sugarcane hybrid accessions),and group IV(five S.robustum accessions).Experimental verification supported the reliability of the SSR markers based on genome-wide predictions.The development of a large number of SSR markers based on wet experiments is valuable for genetic studies,including genetic linkage maps,comparative genome analysis,genome-wide association studies,and marker-assisted selection in Saccharum.展开更多
Colorectal cancer (CRC) accounts for approximately 10% of newly diagnosed cancer cases and cancer-related deaths worldwide~1. The identification of molecular subtypes of CRCs has significantly advanced treatment strat...Colorectal cancer (CRC) accounts for approximately 10% of newly diagnosed cancer cases and cancer-related deaths worldwide~1. The identification of molecular subtypes of CRCs has significantly advanced treatment strategies,including targeted therapy and immunotherapy.展开更多
Pineapple occupies an important phylogenetic position as its reference genome is a model for studying the evolution the Bromeliaceae family and the crassulacean acid metabolism(CAM)photosynthesis.Here,we developed a p...Pineapple occupies an important phylogenetic position as its reference genome is a model for studying the evolution the Bromeliaceae family and the crassulacean acid metabolism(CAM)photosynthesis.Here,we developed a pineapple genomics database(PGD,http://pineapple.angiosperms.org/pineapple/html/index.html)as a central online platform for storing and integrating genomic,transcriptomic,function annotation and genetic marker data for pineapple(Ananas comosus(L.)Merr.).The PGD currently hosts significant search tools and available datasets for researchers to study comparative genomics,gene expression,gene co-expression molecular marker,and gene annotation of A.comosus(L).PGD also performed a series of additional pages for a genomic browser that visualizes genomic data interactively,bulk data download,a detailed user manual,and data integration information.PGD was developed with the capacity to integrate future data resources,and will be used as a long-term and open access database to facilitate the study of the biology,distribution,and the evolution of pineapple and the relative plant species.An email-based helpdesk is also available to offer support with the website and requests of specific datasets from the research community.展开更多
Bacteriophages are viruses that attack bacteria and kill them through the lytic replication cycle. Many studies have reported that phages are more specific to bacteria than antibiotics are; thus, phage therapy has man...Bacteriophages are viruses that attack bacteria and kill them through the lytic replication cycle. Many studies have reported that phages are more specific to bacteria than antibiotics are; thus, phage therapy has many poten- tial applications in human medicine, with the advantage of having few side effects （Keen, 2012）. Investigating the mechanisms of bacteria-killing phages will therefore aid in the development of antibacterial drugs.展开更多
Current clinicopathologic indicators are insufficient to distinguish the small percentage of aggressive prostate cancer （PCa） from the vast majority of indolent disease at diagnosis, leading to overtreatment of PCa....Current clinicopathologic indicators are insufficient to distinguish the small percentage of aggressive prostate cancer （PCa） from the vast majority of indolent disease at diagnosis, leading to overtreatment of PCa. A recent study reported and confirmed a strong association of PCa-specific mortality with somatic DNA copy number alterations （CNAs） in primary pro- state tumors.展开更多
Chromosomal rearrangements(CRs)often cause phenotypic variations.Although several major rearrangements have been identified in Triticeae,a comprehensive study of the order,timing,and breakpoints of CRs has not been co...Chromosomal rearrangements(CRs)often cause phenotypic variations.Although several major rearrangements have been identified in Triticeae,a comprehensive study of the order,timing,and breakpoints of CRs has not been conducted.Here,we reconstruct high-quality ancestral genomes for the most recent common ancestor(MRCA)of the Triticeae,and the MRCA of the wheat lineage(Triticum and Aegilops).The protogenes of MRCA of the Triticeae and the wheat lineage are 22,894 and 29,060,respectively,which were arranged in their ancestral order.By partitioning modern Triticeae chromosomes into sets of syntenic regions and linking each to the corresponding protochromosomes,we revisit the rye chromosome structural evolution and propose alternative evolutionary routes.The previously identified 4L/5L reciprocal translocation in rye and Triticum urartu is found to have occurred independently and is unlikely to be the result of chromosomal introgression following distant hybridization.We also clarify that the 4AL/7BS translocation in tetraploid wheat was a bidirectional rather than unidirectional translocation event.Lastly,we identify several breakpoints in protochromosomes that independently reoccur following Triticeae evolution,representing potential CR hotspots.This study demonstrates that these reconstructed ancestral genomes can serve as special comparative references and facilitate a better understanding of the evolution of structural rearrangements in Triticeae.展开更多
Hepatocellular carcinoma is difficult to treat,primarilybecause the underlying molecular mechanisms drivingclinical outcome are still poorly understood.Growingevidence suggests that the tissue microenvironmenthas a ro...Hepatocellular carcinoma is difficult to treat,primarilybecause the underlying molecular mechanisms drivingclinical outcome are still poorly understood.Growingevidence suggests that the tissue microenvironmenthas a role in the biological behavior of the tumor.Themain clinical issue is to identify the best target fortherapeutic approaches.Here,we discuss the hypothesis that the entire tissue microenvironment might beconsidered as a biological target.However,the tissuemicroenvironment consists of several cellular and biochemical components,each of which displays a distinctbiological activity.We discuss the major components ofthis environment and consider how they may interactto promote tumor/host crosstalk.展开更多
Tea plants(Camellia sinensis)are commercially cultivated in>60 countries,and their fresh leaves are processed into tea,which is the most widely consumed beverage in the world.Although several chromosome-level tea p...Tea plants(Camellia sinensis)are commercially cultivated in>60 countries,and their fresh leaves are processed into tea,which is the most widely consumed beverage in the world.Although several chromosome-level tea plant genomes have been published,they collapsed the two haplotypes and ignored a large number of allelic variations that may underlie important biological functions in this species.Here,we present a phased chromosome-scale assembly for an elite oolong tea cultivar,"Huangdan",that is well known for its high levels of aroma.Based on the two sets of haplotype genome data,we identi fi ed numerous genetic variations and a substantial proportion of allelic imbalance related to important traits,including aroma-and stress-related alleles.Comparative genomics revealed extensive structural variations as well as expansion of some gene families,such as terpene synthases(TPSs),that likely contribute to the high-aroma characteristics of the backbone parent,underlying the molecular basis for the biosynthesis of aroma-related chemicals in oolong tea.Our results uncovered the genetic basis of special features of this oolong tea cultivar,providing fundamental genomic resources to study evolution and domestication for the economically important tea crop.展开更多
The ripening of papaya is a physiological and metabolic process associated with accumulation of carotenoids,alternation of flesh color and flavor,which depending on genotype and external factors such as light and horm...The ripening of papaya is a physiological and metabolic process associated with accumulation of carotenoids,alternation of flesh color and flavor,which depending on genotype and external factors such as light and hormone.Transcription factors regulating carotenoid biosynthesis have not been analyzed during papaya fruit ripening.RNA-Seq experiments were implemented using different ripening stages of papaya fruit from two papaya varieties.Cis-elements in lycopeneβ-cyclase genes(CpCYC-B and CpLCY-B)were identified,and followed by genome-wide analysis to identify transcription factors binding to these cis-elements,resulting in the identification of CpbHLH1 and CpbHLH2,two bHLH genes.The expressions of CpbHLH1/2 were changed during fruit development,coupled with transcript increase of carotenoid biosynthesis-related genes including CpCYC-B,CpLCY-B,CpPDS2,CpZDS,CpLCY-E,and CpCHY-B.Yeast onehybrid(Y1H)and transient expression assay revealed that CpbHLH1/2 could bind to the promoters of CpCYC-B and CpLCY-B,and regulate their transcriptions.In response to strong light,the results of elevated expression of carotenoid biosynthesis-related genes and the changed expression of CpbHLH1/2 indicated that CpbHLH1/2 were involved in light-mediated mechanisms of regulating critical genes in the carotenoid biosynthesis pathway.Collectively,our findings demonstrated several TF family members participating in the regulation of carotenoid genes and proved that CpbHLH1 and CpbHLH2 individually regulated the transcription of lycopeneβ-cyclase genes(CpCYC-B and CpLCY-B).This study yielded novel findings on regulatory mechanism of carotenoid biosynthesis during papaya fruit ripening.展开更多
Cold stress profoundly affects plant growth and development and is a key factor affecting the geographic distribution and evolution of plants.Plants have evolved adaptive mechanisms to cope with cold stress.Here,throu...Cold stress profoundly affects plant growth and development and is a key factor affecting the geographic distribution and evolution of plants.Plants have evolved adaptive mechanisms to cope with cold stress.Here,through the genomic analysis of Arabidopsis,three Brassica species and 17 other representative species,we found that both cold-related genes(CRGs)and their collinearity were preferentially retained after polyploidization followed by genome instability,while genome-wide gene sets exhibited a variety of other expansion mechanisms.The coldrelated regulatory network was increased in Brassicaceae genomes,which were recursively affected by polyploidization.By combining our findings regarding the selective retention of CRGs from this ecological genomics study with the available knowledge of cold-induced chromosome doubling,we hypothesize that cold stress may have contributed to the success of polyploid plants through both increasing polyploidization and selectively maintaining CRGs during evolution.This hypothesis requires further biological and ecological exploration to obtain solid supporting evidence,which will potentially contribute to understanding the generation of polyploids and to the field of ecological genomics.展开更多
The expanded outer seed coat and the rigid inner seed coat of pomegranate seeds,both affect the sensory qualities of the fruit and its acceptability to consumers.Pomegranate seeds are also an appealing model for the s...The expanded outer seed coat and the rigid inner seed coat of pomegranate seeds,both affect the sensory qualities of the fruit and its acceptability to consumers.Pomegranate seeds are also an appealing model for the study of seed coat differentiation and development.We conducted nontarget metabolic profiling to detect metabolites that contribute to the morphological differentiation of the seed coats along with transcriptomic profiling to unravel the genetic mechanisms underlying this process.Comparisons of metabolites in the lignin biosynthetic pathway accumulating in seed coat layers at different developmental stages revealed that monolignols,including coniferyl alcohol and sinapyl alcohol,greatly accumulated in inner seed coats and monolignol glucosides greatly accumulated in outer seed coats.Strong expression of genes involved in monolignol biosynthesis and transport might explain the spatial patterns of biosynthesis and accumulation of these metabolites.Hemicellulose constituents and flavonoids in particular accumulated in the inner seed coat,and candidate genes that might be involved in their accumulation were also identified.Genes encoding transcription factors regulating monolignol,cellulose,and hemicellulose metabolism were chosen by coexpression analysis.These results provide insights into metabolic factors influencing seed coat differentiation and a reference for studying seed coat developmental biology and pomegranate genetic improvement.展开更多
Reciprocal translocation is a chromosomal structural abnormal- ity that arises when two non-homologous chromosomes rearrange and attach with each other, an incidence that occurs in about 1/500 to 1/625 newborns （Mack...Reciprocal translocation is a chromosomal structural abnormal- ity that arises when two non-homologous chromosomes rearrange and attach with each other, an incidence that occurs in about 1/500 to 1/625 newborns （Mackie and Scriven, 2002）. This event typically does not lead to any significant loss of genetic material, thus recip- rocal translocation carriers do not exhibit any severe abnormal phenotypes （Scriven et al., 1998; Zhang et al., 2016）.展开更多
Jute(Corchorus spp.)is a member of the Malvaceae family,which comprises more than 100 species.The systematic positions of jute species have remained unsettled.Chloroplasts are maternally inherited and their genomes ar...Jute(Corchorus spp.)is a member of the Malvaceae family,which comprises more than 100 species.The systematic positions of jute species have remained unsettled.Chloroplasts are maternally inherited and their genomes are widely used for plant phylogenetic studies.In the present study,the chloroplast genomes of Corchorus capsularis and C.olitorius were assembled,with sizes of respectively 161,088 and 161,766 bp.Both genomes contained 112 unique genes(78 protein-coding,four rRNA,and 30 tRNA genes).Four regionswith high variation between the two species were located in single-copy rather than inverted-repeat regions.A total of 66 simple sequence repeats(SSRs)were identified in the C.capsularis chloroplast genome and 56 in that of C.olitorius.Comparison of the two chloroplast genome sequences permitted the evaluation of nucleotide variation including 2417 single-nucleotide polymorphisms sites and 294 insertion or deletion sites,of which one marker(cpInDel 205)could discriminate the two jute species.Comparison of the C.capsularis and C.olitorius chloroplast genomeswith those of other species in theMalvaceae revealed breakpoints in the accD locus,which is involved in fatty acid synthesis,in C.capsularis and C.olitorius.This finding suggests that genes from the chloroplast genomemight have been transferred to the nuclear genome in some Corchorus species.This hypothesis was supported by synteny analysis of the accD region among the nuclear,chloroplast,and mitochondrial genomes.To our knowledge,this is the first report of the assembled chloroplast genome sequences of C.capsularis and C.olitorius.C.capsularis and C.olitorius are closely related to Gossypium species and there are abundant microstructure variations between these two genera.These results will expand our understanding of the systematics of species in the Malvaceae.展开更多
Flower development plays vital role in horticultural plants.Post-transcriptional regulation via small RNAs is important for plant flower development.To uncover post-transcriptional regulatory networks during the flowe...Flower development plays vital role in horticultural plants.Post-transcriptional regulation via small RNAs is important for plant flower development.To uncover post-transcriptional regulatory networks during the flower development in Dimocarpus longan Lour.‘Shixia’,an economically important fruit crop in subtropical regions,we collected and analyzed sRNA deep-sequencing datasets and degradome libraries Apart from identifying miRNAs and phased siRNA generating loci(PHAS loci),120 hairpin loci,producing abundant sRNAs,were identified by in-house protocols.Our results suggested that 56 miRNA-target pairs,2221-nt-PHAS loci,and 111 hairpin loci are involved in posttranscriptional gene silencing during longan reproductive development.Lineage-specific or species-specific post-transcriptional regulatory modules have been unveiled,including miR482-PHAS and miRN15.miR482-PHAS might be involved in longan flower development beyond their conserved roles in plant defense,and miRN15 is a novel miRNA likely associated with a hairpin locus(HPL-056)to regulate strigolactone receptor gene DWARF14(D14)and the biogenesis of phasiRNAs from D14.These small RNAs are enriched in flower buds,suggesting they are likely involved in post-transcriptional regulatory networks essential for longan flower development via the strigolactone signaling pathway.展开更多
基金supported by the National Natural Science Foundation of China(31801856 to X.S.)the Hebei Province Higher Education Youth Talents Program(BJ2018016 to X.S.)+1 种基金China-Hebei 100 Scholars Supporting Project(E2013100003 to X.W.)the Natural Science Foundation of Hebei(C2017209103 to X.S.).
文摘Coriander(Coriandrum sativum L.),also known as cilantro,is a globally important vegetable and spice crop.Its genome and that of carrot are models for studying the evolution of the Apiaceae family.Here,we developed the Coriander Genomics Database(CGDB,http://cgdb.bio2db.com/)to collect,store,and integrate the genomic,transcriptomic,metabolic,functional annotation,and repeat sequence data of coriander and carrot to serve as a central online platform for Apiaceae and other related plants.Using these data sets in the CGDB,we intriguingly found that seven transcription factor(TF)families showed significantly greater numbers of members in the coriander genome than in the carrot genome.The highest ratio of the numbers of MADS TFs between coriander and carrot reached 3.15,followed by those for tubby protein(TUB)and heat shock factors.As a demonstration of CGDB applications,we identified 17 TUB family genes and conducted systematic comparative and evolutionary analyses.RNA-seq data deposited in the CGDB also suggest dose compensation effects of gene expression in coriander.CGDB allows bulk downloading,significance searches,genome browser analyses,and BLAST searches for comparisons between coriander and other plants regarding genomics,gene families,gene collinearity,gene expression,and the metabolome.A detailed user manual and contact information are also available to provide support to the scientific research community and address scientific questions.CGDB will be continuously updated,and new data will be integrated for comparative and functional genomic analysis in Apiaceae and other related plants.
基金supported by the Natural Science Foundation of Hebei(Grant No.C2021209005)National Natural Science Foundation of China(Grant No.32172583)+1 种基金the Natural Science Foundation for Distinguished Young Scholar of Hebei Province(Grant No.C2022209010)the China Postdoctoral Science Foundation(Grant Nos.2020M673188,2021T140097).
文摘Cucurbitaceae is one of the most important plant families distributed worldwide.Transcription factors(TFs)regulate plant growth at the transcription level.Here,we performed a systematic analysis of 42641 TFs from 63 families in 14 Cucurbitaceae and 10 non-cucurbit species.Whole-genome duplication(WGD)was the dominant event type in almost all Cucurbitaceae plants.The TF families were divided into 1210 orthogroups(OGs),of which,112 were unique to Cucurbitaceae.Although the loss of several gene families was detected in Cucurbitaceae,the gene families expanded in five species that experienced a WGD event comparing with grape.Our findings revealed that the recent WGD events that had occurred in Cucurbitaceae played important roles in the expansion of most TF families.The functional enrichment analysis of the genes that significantly expanded or contracted uncovered five gene families,AUX/IAA,NAC,NBS,HB,and NF-YB.Finally,we conducted a comprehensive analysis of the TCP gene family and identified 16 tendril-related(TEN)genes in 11 Cucurbitaceae species.Interestingly,the characteristic sequence changed from CNNFYFP to CNNFYLP in the TEN gene(Bhi06M000087)of Benincasa hispida.Furthermore,we identified a new characteristic sequence,YNN,which could be used for TEN gene exploitation in Cucurbitaceae.In conclusion,this study will serve as a reference for studying the relationship between gene family evolution and genome duplication.Moreover,it will provide rich genetic resources for functional Cucurbitaceae studies in the future.
基金This work was supported by the National Natural Science Foundation of China(81502437)a start-up fund from the Fujian Agriculture and Forestry University to LZ We acknowledge Dr Xianxian Yu from Xuchang University for providing the N.colorata picture in Figure 1.
文摘Water lilies are not only highly favored aquatic ornamental plants with cultural and economic importance but they also occupy a critical evolutionary space that is crucial for understanding the origin and early evolutionary trajectory of flowering plants.The birth and rapid radiation of flowering plants has interested many scientists and was considered‘an abominable mystery’by Charles Darwin.In searching for the angiosperm evolutionary origin and its underlying mechanisms,the genome of Amborella has shed some light on the molecular features of one of the basal angiosperm lineages;however,little is known regarding the genetics and genomics of another basal angiosperm lineage,namely,the water lily.In this study,we reviewed current molecular research and note that water lily research has entered the genomic era.We propose that the genome of the water lily is critical for studying the contentious relationship of basal angiosperms and Darwin’s‘abominable mystery’.Four pantropical water lilies,especially the recently sequenced Nymphaea colorata,have characteristics such as small size,rapid growth rate and numerous seeds and can act as the best model for understanding the origin of angiosperms.The water lily genome is also valuable for revealing the genetics of ornamental traits and will largely accelerate the molecular breeding of water lilies.
基金funded by the National Natural Science Foundation of China(3190020451 and 31771862)。
文摘Sugarcane is a prominent source of sugar and ethanol production.Genetic analysis for trait improvement of sugarcane is greatly hindered by its complex genome,long breeding cycle,and recalcitrance to genetic transformation.The protoplast-based transient transformation system is a versatile and convenient tool for in vivo functional gene analysis;however,quick and effective transformation systems are still lacking for sugarcane.Here,we developed an efficient protoplast-based transformation system by optimizing conditions of protoplasts isolation and PEG-mediated transformation in S.spontaneum.The yield of viable protoplasts was approximately 1.26×107 per gram of leaf material,and the transformation efficiency of 80.19%could be achieved under the optimized condition.Furthermore,using this approach,the nuclear localization of an ABI5-like bZIPs transcription factor was validated,and the promoter activity of several putative DNase I hypersensitive sites(DHSs)was assessed.The results indicated this system can be conveniently applied to protein subcellular localization and promoter activity assays.A highly efficient S.spontaneum mesophyll cell protoplast isolation and transient transformation method was developed,and it shall be suitable for in vivo functional gene analysis in sugarcane.
基金supported by the National High Technology Research and Development Program(Nos.2018YFC1002904,2018YFC1004000 and 2017YFA0103801)。
文摘Congenital contractural arachnodactyly(CCA,OMIM:121050),also known as Beals syndrome,belongs to a group of rare autosomal dominant(AD)diseases of connective tissue(Maslen et al.,1997).People with CCA share many distinguishing features,such as arachnodactyly,camp tod actyly,multiple joint contractures(especially finger,elbow,and knee joints),crumpled ears,scoliosis,pectus deformities,and muscular hypoplasia(Jurko et al.,2013).It exhibits no specific geographic or ethnic predilection(Frederic et al.,2009).
基金supported by the National Key Research and Development Program of China(2021YFF1000101-5)the Science and Technology Planting Project of Guangdong Province,China(2019B020238001)+2 种基金the Natural Science Foundation of Fujian Province,China(2019J05066)the National Natural Science Foundation of China(41906096)the Guangdong Laboratory for Lingnan Modern Agriculture and the State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources,China。
文摘Sugarcane has a large,complex,polyploid genome that has hindered the progress of genomic research and molecular marker-assisted selection.The user-friendly SSR markers have attracted considerable attention owing to their ideal genetic attributes.However,these markers were not characterized and developed at the genome-wide scale due to the previously lacking high-quality chromosome-level assembled sugarcane genomes.In this present study,744305and 361638 candidate SSRs were identified from the genomes of S.officinarum and S.spontaneum,respectively.We verified the reliability of the predicted SSRs by using 1200 interspecific SSR primer pairs to detect polymorphisms among 11 representative accessions of Saccharum,including S.spontaneum,S.officinarum,S.robustum,and modern sugarcane hybrid.The results showed that 660 SSR markers displayed interspecific polymorphisms among these accessions.Furthermore,100 SSRs were randomly selected to detect the genetic diversity for 39 representative Saccharum accessions.A total of 320 alleles were generated using 100 polymorphic primers,with each marker ranging from two to seven alleles.The genetic diversity analysis revealed that these accessions were distributed in four main groups,including group I(14 S.spontaneum accessions),group II(two S.officinarum accessions),group III(18 modern sugarcane hybrid accessions),and group IV(five S.robustum accessions).Experimental verification supported the reliability of the SSR markers based on genome-wide predictions.The development of a large number of SSR markers based on wet experiments is valuable for genetic studies,including genetic linkage maps,comparative genome analysis,genome-wide association studies,and marker-assisted selection in Saccharum.
基金supported by grants from the National Natural Science Foundation of China (Grant No.81972702)the Beijing Nova Program (Grant No. 2022029)。
文摘Colorectal cancer (CRC) accounts for approximately 10% of newly diagnosed cancer cases and cancer-related deaths worldwide~1. The identification of molecular subtypes of CRCs has significantly advanced treatment strategies,including targeted therapy and immunotherapy.
基金The authors would like to thank Irene Lavagi for editing the language.The study was supported by grants from the 863 program(2013AA102604),NSFC(31201260)Program for New Century Excellent Talents in Fujian Province and Science and Technology Major Project of Fujian Province(2016NZ0001).
文摘Pineapple occupies an important phylogenetic position as its reference genome is a model for studying the evolution the Bromeliaceae family and the crassulacean acid metabolism(CAM)photosynthesis.Here,we developed a pineapple genomics database(PGD,http://pineapple.angiosperms.org/pineapple/html/index.html)as a central online platform for storing and integrating genomic,transcriptomic,function annotation and genetic marker data for pineapple(Ananas comosus(L.)Merr.).The PGD currently hosts significant search tools and available datasets for researchers to study comparative genomics,gene expression,gene co-expression molecular marker,and gene annotation of A.comosus(L).PGD also performed a series of additional pages for a genomic browser that visualizes genomic data interactively,bulk data download,a detailed user manual,and data integration information.PGD was developed with the capacity to integrate future data resources,and will be used as a long-term and open access database to facilitate the study of the biology,distribution,and the evolution of pineapple and the relative plant species.An email-based helpdesk is also available to offer support with the website and requests of specific datasets from the research community.
基金supported by the National Nature Scientific Foundation of China(No.61301260)the Applied Basic Research Program of Sichuan Province(No.2015JY0100 and LZ-LY-45)+3 种基金the Scientific Research Foundation of the Education Department of Sichuan Province(11ZB122)the Nature Scientific Foundation of Hebei Province(No.C2013209105)the Fundamental Research Funds for the Central Universities of China(No.ZYGX2015J144,ZYGX2015Z006)Program for the Top Young Innovative Talents of Higher Learning Institutions of Hebei Province(No.BJ2014028)
文摘Bacteriophages are viruses that attack bacteria and kill them through the lytic replication cycle. Many studies have reported that phages are more specific to bacteria than antibiotics are; thus, phage therapy has many poten- tial applications in human medicine, with the advantage of having few side effects （Keen, 2012）. Investigating the mechanisms of bacteria-killing phages will therefore aid in the development of antibacterial drugs.
文摘Current clinicopathologic indicators are insufficient to distinguish the small percentage of aggressive prostate cancer （PCa） from the vast majority of indolent disease at diagnosis, leading to overtreatment of PCa. A recent study reported and confirmed a strong association of PCa-specific mortality with somatic DNA copy number alterations （CNAs） in primary pro- state tumors.
基金CAs Youth Interdisciplinary Team(JCTD-2022-06)the National Nature Science Foundation of China(31870209).
文摘Chromosomal rearrangements(CRs)often cause phenotypic variations.Although several major rearrangements have been identified in Triticeae,a comprehensive study of the order,timing,and breakpoints of CRs has not been conducted.Here,we reconstruct high-quality ancestral genomes for the most recent common ancestor(MRCA)of the Triticeae,and the MRCA of the wheat lineage(Triticum and Aegilops).The protogenes of MRCA of the Triticeae and the wheat lineage are 22,894 and 29,060,respectively,which were arranged in their ancestral order.By partitioning modern Triticeae chromosomes into sets of syntenic regions and linking each to the corresponding protochromosomes,we revisit the rye chromosome structural evolution and propose alternative evolutionary routes.The previously identified 4L/5L reciprocal translocation in rye and Triticum urartu is found to have occurred independently and is unlikely to be the result of chromosomal introgression following distant hybridization.We also clarify that the 4AL/7BS translocation in tetraploid wheat was a bidirectional rather than unidirectional translocation event.Lastly,we identify several breakpoints in protochromosomes that independently reoccur following Triticeae evolution,representing potential CR hotspots.This study demonstrates that these reconstructed ancestral genomes can serve as special comparative references and facilitate a better understanding of the evolution of structural rearrangements in Triticeae.
基金Supported by EU-Marie Curie Initial Training Network(ITN),FP7-PEOPLE-2012-ITN 2012,Grant Agreement No.316549
文摘Hepatocellular carcinoma is difficult to treat,primarilybecause the underlying molecular mechanisms drivingclinical outcome are still poorly understood.Growingevidence suggests that the tissue microenvironmenthas a role in the biological behavior of the tumor.Themain clinical issue is to identify the best target fortherapeutic approaches.Here,we discuss the hypothesis that the entire tissue microenvironment might beconsidered as a biological target.However,the tissuemicroenvironment consists of several cellular and biochemical components,each of which displays a distinctbiological activity.We discuss the major components ofthis environment and consider how they may interactto promote tumor/host crosstalk.
基金This research was funded by the Fujian Province"2011 Collaborative Innovation Center",the Chinese Oolong Tea Industry Innovation Center special project(J 2015-75)the National Natural Science Foundation of China(31701874)+3 种基金the Major Special Project of Scientific and Technological Innovation on Anxi Tea(AX2021001)the Earmarked Fund for the China Agriculture Research System(CARS-19)the Scientific Research Foundation of the Graduate School of Fujian Agriculture and Forestry University(324-1122yb060)the Scientific Research Foundation of Horticulture College of Fujian Agriculture and Forestry University(2018B02).
文摘Tea plants(Camellia sinensis)are commercially cultivated in>60 countries,and their fresh leaves are processed into tea,which is the most widely consumed beverage in the world.Although several chromosome-level tea plant genomes have been published,they collapsed the two haplotypes and ignored a large number of allelic variations that may underlie important biological functions in this species.Here,we present a phased chromosome-scale assembly for an elite oolong tea cultivar,"Huangdan",that is well known for its high levels of aroma.Based on the two sets of haplotype genome data,we identi fi ed numerous genetic variations and a substantial proportion of allelic imbalance related to important traits,including aroma-and stress-related alleles.Comparative genomics revealed extensive structural variations as well as expansion of some gene families,such as terpene synthases(TPSs),that likely contribute to the high-aroma characteristics of the backbone parent,underlying the molecular basis for the biosynthesis of aroma-related chemicals in oolong tea.Our results uncovered the genetic basis of special features of this oolong tea cultivar,providing fundamental genomic resources to study evolution and domestication for the economically important tea crop.
基金supported by the grant 2015N20002-1 from the Department of Science and Technology of Fujian Province,US National Science Foundation(NSF)Plant Genome Research Program Award DBI-1546890the National Natural Science Foundation of China(Grant No.31701889).
文摘The ripening of papaya is a physiological and metabolic process associated with accumulation of carotenoids,alternation of flesh color and flavor,which depending on genotype and external factors such as light and hormone.Transcription factors regulating carotenoid biosynthesis have not been analyzed during papaya fruit ripening.RNA-Seq experiments were implemented using different ripening stages of papaya fruit from two papaya varieties.Cis-elements in lycopeneβ-cyclase genes(CpCYC-B and CpLCY-B)were identified,and followed by genome-wide analysis to identify transcription factors binding to these cis-elements,resulting in the identification of CpbHLH1 and CpbHLH2,two bHLH genes.The expressions of CpbHLH1/2 were changed during fruit development,coupled with transcript increase of carotenoid biosynthesis-related genes including CpCYC-B,CpLCY-B,CpPDS2,CpZDS,CpLCY-E,and CpCHY-B.Yeast onehybrid(Y1H)and transient expression assay revealed that CpbHLH1/2 could bind to the promoters of CpCYC-B and CpLCY-B,and regulate their transcriptions.In response to strong light,the results of elevated expression of carotenoid biosynthesis-related genes and the changed expression of CpbHLH1/2 indicated that CpbHLH1/2 were involved in light-mediated mechanisms of regulating critical genes in the carotenoid biosynthesis pathway.Collectively,our findings demonstrated several TF family members participating in the regulation of carotenoid genes and proved that CpbHLH1 and CpbHLH2 individually regulated the transcription of lycopeneβ-cyclase genes(CpCYC-B and CpLCY-B).This study yielded novel findings on regulatory mechanism of carotenoid biosynthesis during papaya fruit ripening.
基金supported by the National Natural Science Foundation of China(31801856 to X.S.,2016YFD0101001 to X.W.)the Hebei Province Higher Education Youth Talents Program(BJ2018016 to X.S.)the Natural Science Foundation of Hebei(C2017209103 to X.S.).
文摘Cold stress profoundly affects plant growth and development and is a key factor affecting the geographic distribution and evolution of plants.Plants have evolved adaptive mechanisms to cope with cold stress.Here,through the genomic analysis of Arabidopsis,three Brassica species and 17 other representative species,we found that both cold-related genes(CRGs)and their collinearity were preferentially retained after polyploidization followed by genome instability,while genome-wide gene sets exhibited a variety of other expansion mechanisms.The coldrelated regulatory network was increased in Brassicaceae genomes,which were recursively affected by polyploidization.By combining our findings regarding the selective retention of CRGs from this ecological genomics study with the available knowledge of cold-induced chromosome doubling,we hypothesize that cold stress may have contributed to the success of polyploid plants through both increasing polyploidization and selectively maintaining CRGs during evolution.This hypothesis requires further biological and ecological exploration to obtain solid supporting evidence,which will potentially contribute to understanding the generation of polyploids and to the field of ecological genomics.
基金supported by the Natural Science Foundation of Anhui Province(1708085MC85).
文摘The expanded outer seed coat and the rigid inner seed coat of pomegranate seeds,both affect the sensory qualities of the fruit and its acceptability to consumers.Pomegranate seeds are also an appealing model for the study of seed coat differentiation and development.We conducted nontarget metabolic profiling to detect metabolites that contribute to the morphological differentiation of the seed coats along with transcriptomic profiling to unravel the genetic mechanisms underlying this process.Comparisons of metabolites in the lignin biosynthetic pathway accumulating in seed coat layers at different developmental stages revealed that monolignols,including coniferyl alcohol and sinapyl alcohol,greatly accumulated in inner seed coats and monolignol glucosides greatly accumulated in outer seed coats.Strong expression of genes involved in monolignol biosynthesis and transport might explain the spatial patterns of biosynthesis and accumulation of these metabolites.Hemicellulose constituents and flavonoids in particular accumulated in the inner seed coat,and candidate genes that might be involved in their accumulation were also identified.Genes encoding transcription factors regulating monolignol,cellulose,and hemicellulose metabolism were chosen by coexpression analysis.These results provide insights into metabolic factors influencing seed coat differentiation and a reference for studying seed coat developmental biology and pomegranate genetic improvement.
基金supported by the National Natural Science Foundation of China (No. 31522034)Ministry of Science and Technology of China (2016YFC0900103)the National High Technology Research and Development Program Grant (2015AA020407)
文摘Reciprocal translocation is a chromosomal structural abnormal- ity that arises when two non-homologous chromosomes rearrange and attach with each other, an incidence that occurs in about 1/500 to 1/625 newborns （Mackie and Scriven, 2002）. This event typically does not lead to any significant loss of genetic material, thus recip- rocal translocation carriers do not exhibit any severe abnormal phenotypes （Scriven et al., 1998; Zhang et al., 2016）.
基金supported by the National Natural Science Foundation of China(31771369)the China Agriculture Research System for Crops of Bast and Leaf Fiber,China(nycytx-19-E06)。
文摘Jute(Corchorus spp.)is a member of the Malvaceae family,which comprises more than 100 species.The systematic positions of jute species have remained unsettled.Chloroplasts are maternally inherited and their genomes are widely used for plant phylogenetic studies.In the present study,the chloroplast genomes of Corchorus capsularis and C.olitorius were assembled,with sizes of respectively 161,088 and 161,766 bp.Both genomes contained 112 unique genes(78 protein-coding,four rRNA,and 30 tRNA genes).Four regionswith high variation between the two species were located in single-copy rather than inverted-repeat regions.A total of 66 simple sequence repeats(SSRs)were identified in the C.capsularis chloroplast genome and 56 in that of C.olitorius.Comparison of the two chloroplast genome sequences permitted the evaluation of nucleotide variation including 2417 single-nucleotide polymorphisms sites and 294 insertion or deletion sites,of which one marker(cpInDel 205)could discriminate the two jute species.Comparison of the C.capsularis and C.olitorius chloroplast genomeswith those of other species in theMalvaceae revealed breakpoints in the accD locus,which is involved in fatty acid synthesis,in C.capsularis and C.olitorius.This finding suggests that genes from the chloroplast genomemight have been transferred to the nuclear genome in some Corchorus species.This hypothesis was supported by synteny analysis of the accD region among the nuclear,chloroplast,and mitochondrial genomes.To our knowledge,this is the first report of the assembled chloroplast genome sequences of C.capsularis and C.olitorius.C.capsularis and C.olitorius are closely related to Gossypium species and there are abundant microstructure variations between these two genera.These results will expand our understanding of the systematics of species in the Malvaceae.
基金funded by the National Key Research and Developmental Program of China(Grant No.2018YFD1000104)supported by awards from the National Natural Science Foundation of China(Grant Nos.32002009 and 32072547)The Special Support Program of Guangdong Province(Grant No.2019TX05N193).
文摘Flower development plays vital role in horticultural plants.Post-transcriptional regulation via small RNAs is important for plant flower development.To uncover post-transcriptional regulatory networks during the flower development in Dimocarpus longan Lour.‘Shixia’,an economically important fruit crop in subtropical regions,we collected and analyzed sRNA deep-sequencing datasets and degradome libraries Apart from identifying miRNAs and phased siRNA generating loci(PHAS loci),120 hairpin loci,producing abundant sRNAs,were identified by in-house protocols.Our results suggested that 56 miRNA-target pairs,2221-nt-PHAS loci,and 111 hairpin loci are involved in posttranscriptional gene silencing during longan reproductive development.Lineage-specific or species-specific post-transcriptional regulatory modules have been unveiled,including miR482-PHAS and miRN15.miR482-PHAS might be involved in longan flower development beyond their conserved roles in plant defense,and miRN15 is a novel miRNA likely associated with a hairpin locus(HPL-056)to regulate strigolactone receptor gene DWARF14(D14)and the biogenesis of phasiRNAs from D14.These small RNAs are enriched in flower buds,suggesting they are likely involved in post-transcriptional regulatory networks essential for longan flower development via the strigolactone signaling pathway.
