Garlic,an economically important vegetable,spice,and medicinal crop,produces highly enlarged bulbs and unique organosulfur compounds.Here,we report a chromosome-level genome assembly for garlic,with a total size of ap...Garlic,an economically important vegetable,spice,and medicinal crop,produces highly enlarged bulbs and unique organosulfur compounds.Here,we report a chromosome-level genome assembly for garlic,with a total size of approximately 16.24 Gb,as well as the annotation of 57561 predicted protein-coding genes,making garlic the first Allium species with a sequenced genome.Analysis of this garlic genome assembly reveals a recent burst of transposable elements,explaining the substantial expansion of the garlic genome.We examined the evolution of certain genes associated with the biosynthesis of allicin and inulin neoseries-type fructans,and provided new insights into the biosynthesis of these two compounds.Furthermore,a large-scale transcriptome was produced to characterize the expression patterns of garlic genes in different tissues and at various growth stages of enlarged bulbs.The reference genome and large-scale transcriptome data generated in this study provide valuable new resources for research on garlic biology and breeding.展开更多
Ferns and lycophytes have remarkably large genomes.However,little is known about how their genome size evolved in fern lineages.To explore the origins and evolution of chromosome numbers and genome size in ferns,we us...Ferns and lycophytes have remarkably large genomes.However,little is known about how their genome size evolved in fern lineages.To explore the origins and evolution of chromosome numbers and genome size in ferns,we used flow cytometry to measure the genomes of 240 species(255 samples)of extant ferns and lycophytes comprising 27 families and 72 genera,of which 228 species(242 samples)represent new reports.We analyzed correlations among genome size,spore size,chromosomal features,phylogeny,and habitat type preference within a phylogenetic framework.We also applied ANOVA and multinomial logistic regression analysis to preference of habitat type and genome size.Using the phylogeny,we conducted ancestral character reconstruction for habitat types and tested whether genome size changes simultaneously with shifts in habitat preference.We found that 2 C values had weak phylogenetic signal,whereas the base number of chromosomes(x)had a strong phylogenetic signal.Furthermore,our analyses revealed a positive correlation between genome size and chromosome traits,indicating that the base number of chromosomes(x),chromosome size,and polyploidization may be primary contributors to genome expansion in ferns and lycophytes.Genome sizes in different habitat types varied significantly and were significantly correlated with habitat types;specifically,multinomial logistic regression indicated that species with larger 2 C values were more likely to be epiphytes.Terrestrial habitat is inferred to be ancestral for both extant ferns and lycophytes,whereas transitions to other habitat types occurred as the major clades emerged.Shifts in habitat types appear be followed by periods of genomic stability.Based on these results,we inferred that habitat type changes and multiple whole-genome duplications have contributed to the formation of large genomes of ferns and their allies during their evolutionary history.展开更多
In this study, by analysis of genome structures of E. coli, the relationships between the genomic types of E. coli and the associated diseases were investigated. Samples of sputum, urine and other excretions from pati...In this study, by analysis of genome structures of E. coli, the relationships between the genomic types of E. coli and the associated diseases were investigated. Samples of sputum, urine and other excretions from patients with different infective diseases were collected. And 62 E. coli strains were isolated from these samples. Intact bacterial genomic DNA was cleaved with I-CeuI, separated by pulsed field gel electrophoresis and then typed on the basis of cleavage map. The results showed that 7 I-CeuI sites were found in all the genome structures of the 62 E. coli, indicating that there were 7 rrn operons in the genomes. The size of genome ranged from 4500 kb to 5000 kb. According to the genome structures, 62 E. coli strains were divided into 30 genome types. It was concluded that genome structures of E. coli isolated from the patients with different infective diseases varied to some extent, suggesting that some genome types of E. coli were closely related to some infective diseases.展开更多
Agrocybe cylindracea,an edible mushroom,is widely cultivated for its abundance of nutrients and flavor,and many of its metabolites are reported to have beneficial roles,such as medicinal effects on tumors and chronica...Agrocybe cylindracea,an edible mushroom,is widely cultivated for its abundance of nutrients and flavor,and many of its metabolites are reported to have beneficial roles,such as medicinal effects on tumors and chronical illnesses.However,the lack of genomic information has hindered further molecular studies on this fungus.Here,we present a genome assembly of A.cylindracea together with comparative genomics and pathway analyses of Agaricales species.The draft,generated from both next-generation sequencing(NGS)and single-molecule real-time(SMRT)sequencing platforms to overcome high genetic heterozygosity,is composed of a56.5 Mb sequence and 15,384 predicted genes.This mushroom possesses a complex reproductive system,including tetrapolar heterothallic and secondary homothallic mechanisms,and harbors several hydrolases and peptidases for gradual and effective degradation of various carbon sources.Our pathway analysis reveals complex processes involved in the biosynthesis of polysaccharides and other active substances,including B vitamins,unsaturated fatty acids,and N-acetylglucosamine.RNA-seq data show that A.cylindracea stipes tend to synthesize carbohydrate for carbon sequestration and energy storage,whereas pilei are more active in carbon utilization and unsaturated fatty acid biosynthesis.These results reflect diverse functions of the two anatomical structures of the fruiting body.Our comprehensive genomic and transcriptomic data,as well as preliminary comparative analyses,provide insights into the molecular details of the medicinal effects in terms of active compounds and nutrient components.展开更多
Angucyclinones are aromatic polyketides produced by type Ⅱ polyketide synthases（PKS） and are mainly found in terrestrial actinomycetes. To discover more angucyclinones from marine actinomycetes, a genomic DNA-based...Angucyclinones are aromatic polyketides produced by type Ⅱ polyketide synthases（PKS） and are mainly found in terrestrial actinomycetes. To discover more angucyclinones from marine actinomycetes, a genomic DNA-based PCR assay targeting type Ⅱ polyketide synthases was performed. Among the 167 marine actinomycetes strains screened, twelve strains were identified as the ＂positive＂ strains possessing type Ⅱ PKS-encoding genes based on the sequencing of PCR products. One of the 12 ＂positive＂ strains, Streptomyces sp. PKU-MA00218 was selected for the large-scale fermentation based on the HPLC and TLC analysis. Four angucyclinones, 6-deoxy-8-O-methylrabelomycin（1）, 8-O-methylrabelomycin（2）, 8-O-methyltetrangulol（3）, C-ring cleavage product of angucyclinone C（4）, were isolated and their structures were elucidated based on spectroscopic analyses. The isolation of angucyclinones 1–4 highlights the power of genome mining technologies based on biosynthetic knowledge in natural products discovery.展开更多
Background:Egg production is economically important in the meat-type chicken industry.To better understand the molecular genetic mechanism of egg production in meat-type chicken,genetic parameter estimation,genome-wid...Background:Egg production is economically important in the meat-type chicken industry.To better understand the molecular genetic mechanism of egg production in meat-type chicken,genetic parameter estimation,genome-wide association analyses combined with meta-analyses,Bayesian analyses,and selective sweep analyses were performed to screen single nucleotide polymorphisms(SNPs)and other genetic loci that were significantly associated with egg number traits in 11,279 chickens from seven material lines.Results:Yellow-feathered meat-type chickens laid 115 eggs at 43 weeks of age and white-feathered chickens laid 143 eggs at 60 weeks of age,with heritability ranging from 0.034–0.258.Based on meta-analyses and selective sweep analyses,one region(10.81–13.05 Mb)on chromosome Z was associated with egg number in all lines.Further analyses using the W2 line was also associated with the same region,and 29 SNPs were identified that significantly affected estimation of breeding value of egg numbers.The 29 SNPs were identified as having a significant effect on the egg number EBV in 3194 birds in line W2.There are 36 genes in the region,with glial cell derived neurotrophic factor,DAB adaptor protein 2,protein kinase AMP-activated catalytic subunit alpha 1,NAD kinase 2,mitochondrial,WD repeat domain 70,leukemia inhibitory factor receptor alpha,complement C6,and complement C7 identified as being potentially affecting to egg number.In addition,three SNPs(rs318154184,rs13769886,and rs313325646)associated with egg number were located on or near the prolactin receptor gene.Conclusion:Our study used genomic information from different chicken lines and populations to identify a genomic region(spanning 2.24 Mb)associated with egg number.Nine genes and 29 SNPs were identified as the most likely candidate genes and variations for egg production.These results contribute to the identification of candidate genes and variants for egg traits in poultry.展开更多
High myopia has long been highly prevalent worldwide with a largely yet unexplained genetic contribution.To identify novel susceptibility genes for axial length(AL)in highly myopic eyes,a genome-wide association study...High myopia has long been highly prevalent worldwide with a largely yet unexplained genetic contribution.To identify novel susceptibility genes for axial length(AL)in highly myopic eyes,a genome-wide association study(GWAS)was performed using the genomic dataset of 350 deep whole-genome sequencing data from highly myopic patients.Top single nucleotide polymorphisms(SNPs)were functionally annotated.Immunofluorescence staining,quantitative polymerase chain reaction,and western blot were performed using neural retina of form-deprived myopic mice.Enrichment analyses were further performed.We identified the four top SNPs and found that ADAM Metallopeptidase With Thrombospondin Type 1 Motif 16(ADAMTS16)and Phosphatidylinositol Glycan Anchor Biosynthesis Class Z(PIGZ)had the potential of clinical signifi-cance.Animal experiments confirmed that PIGZ expression could be observed and showed higher expression level in form-deprived mice,especially in the ganglion cell layer.The messenger RNA(mRNA)levels of both ADAMTS16 and PIGZ were significantly higher in the neural retina of form-deprived eyes(p=0.005 and 0.007 respectively),and both proteins showed significantly upregulated expression in the neural retina of deprived eyes(p=0.004 and 0.042,respectively).Enrichment analysis revealed a significant role of cellular adhesion and signal transduction in AL,and also several AL-related pathways including circadian entrainment and inflammatory mediator regulation of transient receptor potential channels were proposed.In conclusion,the current study identified four novel SNPs associated with AL in highly myopic eyes and confirmed that the expression of ADAMTS16 and PIGZ was significantly upregulated in neural retina of deprived eyes.Enrichment analyses provided novel insight into the etiology of high myopia and opened avenues for future research interest.展开更多
Restriction endonuclease analysis(REA),or restriction fragment length polymorphism(RFLP),was useful for identifying and determining the relatedness and putative identities of microbial strains(Tang et al.,1997)and for...Restriction endonuclease analysis(REA),or restriction fragment length polymorphism(RFLP),was useful for identifying and determining the relatedness and putative identities of microbial strains(Tang et al.,1997)and for characterizing and discriminating large numbers of samples inexpensively in the past。展开更多
基金supported by grants from the National Key R&D Program of China(2016YFD040024)the Agricultural Science and Technology Innovation Program of China(CAAS-ASTIP-lBFC)the National Natural Science Foundation of China(31772323,31871678,and 31972000).
文摘Garlic,an economically important vegetable,spice,and medicinal crop,produces highly enlarged bulbs and unique organosulfur compounds.Here,we report a chromosome-level genome assembly for garlic,with a total size of approximately 16.24 Gb,as well as the annotation of 57561 predicted protein-coding genes,making garlic the first Allium species with a sequenced genome.Analysis of this garlic genome assembly reveals a recent burst of transposable elements,explaining the substantial expansion of the garlic genome.We examined the evolution of certain genes associated with the biosynthesis of allicin and inulin neoseries-type fructans,and provided new insights into the biosynthesis of these two compounds.Furthermore,a large-scale transcriptome was produced to characterize the expression patterns of garlic genes in different tissues and at various growth stages of enlarged bulbs.The reference genome and large-scale transcriptome data generated in this study provide valuable new resources for research on garlic biology and breeding.
基金the National Natural Science Foundation of China(grant number 31870188,31800174,31700172,41571056)to Wang,Shen,Wang and XingShanghai Landscaping and City Appearance Administrative Bureau of China,Scientific Research Grants(G182411)to Yan+1 种基金the Strategic Priority Research Program of the Chinese Academy of Sciences(grant number XDA13020603,XDA13020500)to Chen and JianGuangdong Natural Science Foundation(grant number 2015A030308015)to Wang。
文摘Ferns and lycophytes have remarkably large genomes.However,little is known about how their genome size evolved in fern lineages.To explore the origins and evolution of chromosome numbers and genome size in ferns,we used flow cytometry to measure the genomes of 240 species(255 samples)of extant ferns and lycophytes comprising 27 families and 72 genera,of which 228 species(242 samples)represent new reports.We analyzed correlations among genome size,spore size,chromosomal features,phylogeny,and habitat type preference within a phylogenetic framework.We also applied ANOVA and multinomial logistic regression analysis to preference of habitat type and genome size.Using the phylogeny,we conducted ancestral character reconstruction for habitat types and tested whether genome size changes simultaneously with shifts in habitat preference.We found that 2 C values had weak phylogenetic signal,whereas the base number of chromosomes(x)had a strong phylogenetic signal.Furthermore,our analyses revealed a positive correlation between genome size and chromosome traits,indicating that the base number of chromosomes(x),chromosome size,and polyploidization may be primary contributors to genome expansion in ferns and lycophytes.Genome sizes in different habitat types varied significantly and were significantly correlated with habitat types;specifically,multinomial logistic regression indicated that species with larger 2 C values were more likely to be epiphytes.Terrestrial habitat is inferred to be ancestral for both extant ferns and lycophytes,whereas transitions to other habitat types occurred as the major clades emerged.Shifts in habitat types appear be followed by periods of genomic stability.Based on these results,we inferred that habitat type changes and multiple whole-genome duplications have contributed to the formation of large genomes of ferns and their allies during their evolutionary history.
文摘In this study, by analysis of genome structures of E. coli, the relationships between the genomic types of E. coli and the associated diseases were investigated. Samples of sputum, urine and other excretions from patients with different infective diseases were collected. And 62 E. coli strains were isolated from these samples. Intact bacterial genomic DNA was cleaved with I-CeuI, separated by pulsed field gel electrophoresis and then typed on the basis of cleavage map. The results showed that 7 I-CeuI sites were found in all the genome structures of the 62 E. coli, indicating that there were 7 rrn operons in the genomes. The size of genome ranged from 4500 kb to 5000 kb. According to the genome structures, 62 E. coli strains were divided into 30 genome types. It was concluded that genome structures of E. coli isolated from the patients with different infective diseases varied to some extent, suggesting that some genome types of E. coli were closely related to some infective diseases.
基金the project of “Cooperation with Localities and Industries”,Gansu,China(2012HZ-02)。
文摘Agrocybe cylindracea,an edible mushroom,is widely cultivated for its abundance of nutrients and flavor,and many of its metabolites are reported to have beneficial roles,such as medicinal effects on tumors and chronical illnesses.However,the lack of genomic information has hindered further molecular studies on this fungus.Here,we present a genome assembly of A.cylindracea together with comparative genomics and pathway analyses of Agaricales species.The draft,generated from both next-generation sequencing(NGS)and single-molecule real-time(SMRT)sequencing platforms to overcome high genetic heterozygosity,is composed of a56.5 Mb sequence and 15,384 predicted genes.This mushroom possesses a complex reproductive system,including tetrapolar heterothallic and secondary homothallic mechanisms,and harbors several hydrolases and peptidases for gradual and effective degradation of various carbon sources.Our pathway analysis reveals complex processes involved in the biosynthesis of polysaccharides and other active substances,including B vitamins,unsaturated fatty acids,and N-acetylglucosamine.RNA-seq data show that A.cylindracea stipes tend to synthesize carbohydrate for carbon sequestration and energy storage,whereas pilei are more active in carbon utilization and unsaturated fatty acid biosynthesis.These results reflect diverse functions of the two anatomical structures of the fruiting body.Our comprehensive genomic and transcriptomic data,as well as preliminary comparative analyses,provide insights into the molecular details of the medicinal effects in terms of active compounds and nutrient components.
基金National Natural Science Foundation of China(Grant No.81573326)
文摘Angucyclinones are aromatic polyketides produced by type Ⅱ polyketide synthases（PKS） and are mainly found in terrestrial actinomycetes. To discover more angucyclinones from marine actinomycetes, a genomic DNA-based PCR assay targeting type Ⅱ polyketide synthases was performed. Among the 167 marine actinomycetes strains screened, twelve strains were identified as the ＂positive＂ strains possessing type Ⅱ PKS-encoding genes based on the sequencing of PCR products. One of the 12 ＂positive＂ strains, Streptomyces sp. PKU-MA00218 was selected for the large-scale fermentation based on the HPLC and TLC analysis. Four angucyclinones, 6-deoxy-8-O-methylrabelomycin（1）, 8-O-methylrabelomycin（2）, 8-O-methyltetrangulol（3）, C-ring cleavage product of angucyclinone C（4）, were isolated and their structures were elucidated based on spectroscopic analyses. The isolation of angucyclinones 1–4 highlights the power of genome mining technologies based on biosynthetic knowledge in natural products discovery.
基金the Guangdong Provincial Key Research and Development Program(2020B02022002)the Shandong Agricultural Seed Improvement Project(2020LZGC013)the Technological Innovation Project of Chinese Academy of Agricultural Sciences(CAAS-ZDRW202005)。
文摘Background:Egg production is economically important in the meat-type chicken industry.To better understand the molecular genetic mechanism of egg production in meat-type chicken,genetic parameter estimation,genome-wide association analyses combined with meta-analyses,Bayesian analyses,and selective sweep analyses were performed to screen single nucleotide polymorphisms(SNPs)and other genetic loci that were significantly associated with egg number traits in 11,279 chickens from seven material lines.Results:Yellow-feathered meat-type chickens laid 115 eggs at 43 weeks of age and white-feathered chickens laid 143 eggs at 60 weeks of age,with heritability ranging from 0.034–0.258.Based on meta-analyses and selective sweep analyses,one region(10.81–13.05 Mb)on chromosome Z was associated with egg number in all lines.Further analyses using the W2 line was also associated with the same region,and 29 SNPs were identified that significantly affected estimation of breeding value of egg numbers.The 29 SNPs were identified as having a significant effect on the egg number EBV in 3194 birds in line W2.There are 36 genes in the region,with glial cell derived neurotrophic factor,DAB adaptor protein 2,protein kinase AMP-activated catalytic subunit alpha 1,NAD kinase 2,mitochondrial,WD repeat domain 70,leukemia inhibitory factor receptor alpha,complement C6,and complement C7 identified as being potentially affecting to egg number.In addition,three SNPs(rs318154184,rs13769886,and rs313325646)associated with egg number were located on or near the prolactin receptor gene.Conclusion:Our study used genomic information from different chicken lines and populations to identify a genomic region(spanning 2.24 Mb)associated with egg number.Nine genes and 29 SNPs were identified as the most likely candidate genes and variations for egg production.These results contribute to the identification of candidate genes and variants for egg traits in poultry.
基金Funding was provided by the National Natural Science Foundation of China,82122017:Xiangjia Zhu,81970780:Yi Lu,81870642:Xiangjia Zhu,81670835:Yi LuScience and Technology Innovation Plan of Shanghai Science and Technology Commission,19441900700:Xiangjia Zhu,21S31904900:Xiangjia Zhu+3 种基金Shanghai Hospital Development Center,SHDC12019X08:Xiangjia ZhuShanghai Shenkang Hospital Development Center,SHDC2020CR4078:Xiangjia ZhuDouble-E Plan of Eye&ENT Hospital,SYA202006:Xiangjia ZhuShanghai Municipal Key Clinical Specialty Program,shslczdzk01901:Xiangjia Zhu.
文摘High myopia has long been highly prevalent worldwide with a largely yet unexplained genetic contribution.To identify novel susceptibility genes for axial length(AL)in highly myopic eyes,a genome-wide association study(GWAS)was performed using the genomic dataset of 350 deep whole-genome sequencing data from highly myopic patients.Top single nucleotide polymorphisms(SNPs)were functionally annotated.Immunofluorescence staining,quantitative polymerase chain reaction,and western blot were performed using neural retina of form-deprived myopic mice.Enrichment analyses were further performed.We identified the four top SNPs and found that ADAM Metallopeptidase With Thrombospondin Type 1 Motif 16(ADAMTS16)and Phosphatidylinositol Glycan Anchor Biosynthesis Class Z(PIGZ)had the potential of clinical signifi-cance.Animal experiments confirmed that PIGZ expression could be observed and showed higher expression level in form-deprived mice,especially in the ganglion cell layer.The messenger RNA(mRNA)levels of both ADAMTS16 and PIGZ were significantly higher in the neural retina of form-deprived eyes(p=0.005 and 0.007 respectively),and both proteins showed significantly upregulated expression in the neural retina of deprived eyes(p=0.004 and 0.042,respectively).Enrichment analysis revealed a significant role of cellular adhesion and signal transduction in AL,and also several AL-related pathways including circadian entrainment and inflammatory mediator regulation of transient receptor potential channels were proposed.In conclusion,the current study identified four novel SNPs associated with AL in highly myopic eyes and confirmed that the expression of ADAMTS16 and PIGZ was significantly upregulated in neural retina of deprived eyes.Enrichment analyses provided novel insight into the etiology of high myopia and opened avenues for future research interest.
基金supported by the National Natural Science Foundation of China (31570155 and 31370199)"Young Top-notch Talents" of the Guangdong Province Special Support Program (2014)+3 种基金the Excellent Young Teacher Training Plan of Guangdong Province (Yq2013039)the Guangzhou Healthcare Collaborative Innovation Major Project (201400000002)funded by the China Scholarship Council (CSC No. 201508440056) as a Visiting Scholar (2015-2016)supported by a summer research grant to D.S. from the Office of the Vice President for Research at George Mason University
文摘Restriction endonuclease analysis(REA),or restriction fragment length polymorphism(RFLP),was useful for identifying and determining the relatedness and putative identities of microbial strains(Tang et al.,1997)and for characterizing and discriminating large numbers of samples inexpensively in the past。
