Lily(Lilium spp.) is an important ornamental flower, which is mainly propagated by bulbs. Cell wall invertases(CWINs), which catalyze the irreversibly conversion of sucrose into glucose and fructose in the extracellul...Lily(Lilium spp.) is an important ornamental flower, which is mainly propagated by bulbs. Cell wall invertases(CWINs), which catalyze the irreversibly conversion of sucrose into glucose and fructose in the extracellular space, are key enzymes participating in sucrose allocation in higher plants. Previous studies have shown that CWINs play an essential role in bulblet initiation process in bulbous crops, but the underlying molecular mechanism remains unclear. Here, a CWIN gene of Lilium brownii var. giganteum(Lbg) was identified and amplified from genomic DNA. Quantitative RT-PCR assays revealed that the expression level of LbgCWIN1 was highly upregulated exactly when the endogenous starch degraded in non-sucrose medium during in vitro bulblet initiation in Lbg. Phylogenetic relationship, motif, and domain analysis of LbgCWIN1 protein and CWINs in other plant species showed that all sequences of these CWIN proteins were highly conserved. The promoter sequence of LbgCWIN1 possessed a number of alpha-amylase-, phytohormone-, light-and stress-responsive cis-elements. Meanwhile, β-glucuronidase(GUS) assay showed that the 459 bp upstream fragment from the translational start site displayed maximal promoter activity. These results revealed that LbgCWIN1 might function in the process of in vitro bulblet initiation and be in the response to degradation of endogenous starch.展开更多
Rosa rugosa,commonly known as rugged rose,is a perennial ornamental shrub.It produces beautiful flowers with a mild fragrance and colorful seed pods.Unlike many other cultivated roses,R.rugosa adapts to a wide range o...Rosa rugosa,commonly known as rugged rose,is a perennial ornamental shrub.It produces beautiful flowers with a mild fragrance and colorful seed pods.Unlike many other cultivated roses,R.rugosa adapts to a wide range of habitat types and harsh environmental conditions such as salinity,alkaline,shade,drought,high humidity,and frigid temperatures.Here,we produced and analyzed a high-quality genome sequence for R.rugosa to understand its ecology,floral characteristics and evolution.PacBio HiFi reads were initially used to construct the draft genome of R.rugosa,and then Hi-C sequencing was applied to assemble the contigs into 7 chromosomes.We obtained a 382.6Mb genome encoding 39,704 protein-coding genes.The genome of R.rugosa appears to be conserved with no additional whole-genome duplication after the gamma whole-genome triplication(WGT),which occurred~100 million years ago in the ancestor of core eudicots.Based on a comparative analysis of the high-quality genome assembly of R.rugosa and other high-quality Rosaceae genomes,we found a unique large inverted segment in the Chinese rose R.chinensis and a retroposition in strawberry caused by post-WGT events.We also found that floral development-and stress response signaling-related gene modules were retained after the WGT.Two MADS-box genes involved in floral development and the stress-related transcription factors DREB2A-INTERACTING PROTEIN 2(DRIP2)and PEPTIDE TRANSPORTER 3(PTR3)were found to be positively selected in evolution,which may have contributed to the unique ability of this plant to adapt to harsh environments.In summary,the high-quality genome sequence of R.rugosa provides a map for genetic studies and molecular breeding of this plant and enables comparative genomic studies of Rosa in the near future.展开更多
Invertebrate species are a natural reservoir of viral genetic diversity,and invertebrate pests are widely distributed in crop fields.However,information on viruses infecting invertebrate pests of crops is limited.In t...Invertebrate species are a natural reservoir of viral genetic diversity,and invertebrate pests are widely distributed in crop fields.However,information on viruses infecting invertebrate pests of crops is limited.In this report,we describe the deep metatranscriptomic sequencing of 88 invertebrate samples covering all major invertebrate pests in rice fields.We identified 296 new RNA viruses and 13 known RNA viruses.These viruses clustered within 31 families,with many highly divergent viruses constituting potentially new families and genera.Of the identified viruses,13 RNA viruses clustered within the Fiersviridae family of bacteriophages,and 48 RNA viruses clustered within families and genera of mycoviruses.We detected known rice viruses in novel invertebrate hosts at high abundances.Furthermore,some novel RNA viruses have genome structures closely matching to known plant viruses and clustered within genera of several plant virus species.Fortyfive potential insect pathogenic RNA viruses were detected in invertebrate species.Our analysis revealed that host taxonomy plays a major role and geographical location plays an important role in structuring viral diversity.Cross-species transmission of RNA viruses was detected between invertebrate hosts.Newly identified viral genomes showed extensive variation for invertebrate viral families or genera.Together,the large-scale metatranscriptomic analysis greatly expands our understanding of RNA viruses in rice invertebrate species,the results provide valuable information for developing efficient strategies to manage insect pests and virus-mediated crop diseases.展开更多
Freezing tolerance is a significant trait in plants that grow in cold environments and survive through the winter.Apple(Malus domestica Borkh.)is a cold-tolerant fruit tree,and the cold tolerance of its bark is import...Freezing tolerance is a significant trait in plants that grow in cold environments and survive through the winter.Apple(Malus domestica Borkh.)is a cold-tolerant fruit tree,and the cold tolerance of its bark is important for its survival at low temperatures.However,little is known about the gene activity related to its freezing tolerance.To better understand the gene expression and regulation properties of freezing tolerance in dormant apple trees,we analyzed the transcriptomic divergences in the bark from 1-year-old branches of two apple cultivars,“Golden Delicious”(G)and“Jinhong”(H),which have different levels of cold resistance,under chilling and freezing treatments.“H”can safely overwinter below−30℃in extremely low-temperature regions,whereas“G”experiences severe freezing damage and death in similar environments.Based on 28 bark transcriptomes(from the epidermis,phloem,and cambium)from 1-year-old branches under seven temperature treatments(from 4 to−29°C),we identified 4173 and 7734 differentially expressed genes(DEGs)in“G”and“H”,respectively,between the chilling and freezing treatments.A gene coexpression network was constructed according to this expression information using weighted gene correlation network analysis(WGCNA),and seven biologically meaningful coexpression modules were identified from the network.The expression profiles of the genes from these modules suggested the gene regulatory pathways that are responsible for the chilling and freezing stress responses of“G”and/or“H.”Module 7 was probably related to freezing acclimation and freezing damage in“H”at the lower temperatures.This module contained more interconnected hub transcription factors(TFs)and cold-responsive genes(CORs).Modules 6 and 7 contained C-repeat binding factor(CBF)TFs,and many CBF-dependent homologs were identified as hub genes.We also found that some hub TFs had higher intramodular connectivity(KME)and gene significance(GS)than CBFs.Specifically,most hub TFs in modules 6 and 7 were activated at the beginning of the early freezing stress phase and maintained upregulated expression during the whole freezing stress period in“G”and“H”.The upregulation of DEGs related to methionine and carbohydrate biosynthetic processes in“H”under more severe freezing stress supported the maintenance of homeostasis in the cellular membrane.This study improves our understanding of the transcriptional regulation patterns underlying freezing tolerance in the bark of apple branches.展开更多
Starch is the predominant compound in bulb scales,and previous studies have shown that bulblet development is closely associated with starch enrichment.However,how starch synthesis affects bulbification at the molecul...Starch is the predominant compound in bulb scales,and previous studies have shown that bulblet development is closely associated with starch enrichment.However,how starch synthesis affects bulbification at the molecular level is unclear.In this study,we demonstrate that Lilium brownii var.giganteum,a wild lily with a giant bulb in nature,and L.brownii,the native species,have different starch levels and characteristics according to cytological and ultra-structural observations.We cloned the complete sequence of three key gene-encoding enzymes(LbgAGPS,LbgGBSS,and LbgSSⅢ)during starch synthesis by rapid amplification of 5’and 3’complementary DNA(cDNA)ends(RACE)technology.Bioinformatics analysis revealed that the proteins deduced by these genes contain the canonical conserved domains.Constructed phylogenetic trees confirmed the evolutionary relationships with proteins from other species,including monocotyledons and dicotyledons.The transcript levels of various tissues and time course samples obtained during bulblet development uncovered relatively high expression levels in bulblets and gradual increase expression accompanying bulblet growth.Moreover,a set of single nucleotide polymorphisms(SNPs)was discovered in the AGPS genes of four lily genotypes,and a purifying selection fashion was predicted according to the non-synonymous/synonymous(Ka/Ks)values.Taken together,our results suggested that key starch-synthesizing genes might play important roles in bulblet development and lead to distinctive phenotypes in bulblet size.展开更多
Plants belonging to the genus Taraxacum are widespread all over the world,which contain rubber-producing and non-rubberproducing species.However,the genomic basis underlying natural rubber(NR)biosynthesis still needs ...Plants belonging to the genus Taraxacum are widespread all over the world,which contain rubber-producing and non-rubberproducing species.However,the genomic basis underlying natural rubber(NR)biosynthesis still needs more investigation.Here,we presented high-quality genome assemblies of rubber-producing T.kok-saghyz TK1151 and non-rubber-producing T.mongolicum TM5.Comparative analyses uncovered a large number of genetic variations,including inversions,translocations,presence/absence variations,as well as considerable protein divergences between the two species.Two gene duplication events were found in these two Taraxacum species,including one common ancestral whole-genome triplication and one subsequent round of gene amplification.In genomes of both TK1151 and TM5,we identified the genes encoding for each step in the NR biosynthesis pathway and found that the SRPP and CPT gene families have experienced a more obvious expansion in TK1151 compared to TM5.This study will have large-ranging implications for the mechanism of NR biosynthesis and genetic improvement of NR-producing crops.展开更多
基金financially supported by the National Natural Science Foundation of China (Grant Nos.32101571,32002071)the Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding (Grant No.2021C02071-6)。
文摘Lily(Lilium spp.) is an important ornamental flower, which is mainly propagated by bulbs. Cell wall invertases(CWINs), which catalyze the irreversibly conversion of sucrose into glucose and fructose in the extracellular space, are key enzymes participating in sucrose allocation in higher plants. Previous studies have shown that CWINs play an essential role in bulblet initiation process in bulbous crops, but the underlying molecular mechanism remains unclear. Here, a CWIN gene of Lilium brownii var. giganteum(Lbg) was identified and amplified from genomic DNA. Quantitative RT-PCR assays revealed that the expression level of LbgCWIN1 was highly upregulated exactly when the endogenous starch degraded in non-sucrose medium during in vitro bulblet initiation in Lbg. Phylogenetic relationship, motif, and domain analysis of LbgCWIN1 protein and CWINs in other plant species showed that all sequences of these CWIN proteins were highly conserved. The promoter sequence of LbgCWIN1 possessed a number of alpha-amylase-, phytohormone-, light-and stress-responsive cis-elements. Meanwhile, β-glucuronidase(GUS) assay showed that the 459 bp upstream fragment from the translational start site displayed maximal promoter activity. These results revealed that LbgCWIN1 might function in the process of in vitro bulblet initiation and be in the response to degradation of endogenous starch.
基金F.C.acknowledges funding from the National Natural Science Foundation of China(31801898)This work is supported by the high-performance computing platform of the Bioinformatics Center,Nanjing Agricultural UniversityThis work is supported by the Fundamental Funds for the Central Universities,NJAU(KYXJ202004)。
文摘Rosa rugosa,commonly known as rugged rose,is a perennial ornamental shrub.It produces beautiful flowers with a mild fragrance and colorful seed pods.Unlike many other cultivated roses,R.rugosa adapts to a wide range of habitat types and harsh environmental conditions such as salinity,alkaline,shade,drought,high humidity,and frigid temperatures.Here,we produced and analyzed a high-quality genome sequence for R.rugosa to understand its ecology,floral characteristics and evolution.PacBio HiFi reads were initially used to construct the draft genome of R.rugosa,and then Hi-C sequencing was applied to assemble the contigs into 7 chromosomes.We obtained a 382.6Mb genome encoding 39,704 protein-coding genes.The genome of R.rugosa appears to be conserved with no additional whole-genome duplication after the gamma whole-genome triplication(WGT),which occurred~100 million years ago in the ancestor of core eudicots.Based on a comparative analysis of the high-quality genome assembly of R.rugosa and other high-quality Rosaceae genomes,we found a unique large inverted segment in the Chinese rose R.chinensis and a retroposition in strawberry caused by post-WGT events.We also found that floral development-and stress response signaling-related gene modules were retained after the WGT.Two MADS-box genes involved in floral development and the stress-related transcription factors DREB2A-INTERACTING PROTEIN 2(DRIP2)and PEPTIDE TRANSPORTER 3(PTR3)were found to be positively selected in evolution,which may have contributed to the unique ability of this plant to adapt to harsh environments.In summary,the high-quality genome sequence of R.rugosa provides a map for genetic studies and molecular breeding of this plant and enables comparative genomic studies of Rosa in the near future.
基金This work was supported by the National Natural Science Foundation of China(31972983,32072487)the Key Technology R&D Program of Zhejiang Province(2021C02006)the Central Public-interest Scientific Institution Basal Research Fund(CPSIBRF-CNRRI-202115).
文摘Invertebrate species are a natural reservoir of viral genetic diversity,and invertebrate pests are widely distributed in crop fields.However,information on viruses infecting invertebrate pests of crops is limited.In this report,we describe the deep metatranscriptomic sequencing of 88 invertebrate samples covering all major invertebrate pests in rice fields.We identified 296 new RNA viruses and 13 known RNA viruses.These viruses clustered within 31 families,with many highly divergent viruses constituting potentially new families and genera.Of the identified viruses,13 RNA viruses clustered within the Fiersviridae family of bacteriophages,and 48 RNA viruses clustered within families and genera of mycoviruses.We detected known rice viruses in novel invertebrate hosts at high abundances.Furthermore,some novel RNA viruses have genome structures closely matching to known plant viruses and clustered within genera of several plant virus species.Fortyfive potential insect pathogenic RNA viruses were detected in invertebrate species.Our analysis revealed that host taxonomy plays a major role and geographical location plays an important role in structuring viral diversity.Cross-species transmission of RNA viruses was detected between invertebrate hosts.Newly identified viral genomes showed extensive variation for invertebrate viral families or genera.Together,the large-scale metatranscriptomic analysis greatly expands our understanding of RNA viruses in rice invertebrate species,the results provide valuable information for developing efficient strategies to manage insect pests and virus-mediated crop diseases.
基金supported by the Agricultural Science and Technology Innovation Program of Jilin Province,“Precise identification and QTL location of cold resistance of new apple germplasm”(program number,CXGC2017JQ020)“Phylogenetic reconstruction technique and gene family reconstruction technique of Malus plants”(program number,C8223001602).
文摘Freezing tolerance is a significant trait in plants that grow in cold environments and survive through the winter.Apple(Malus domestica Borkh.)is a cold-tolerant fruit tree,and the cold tolerance of its bark is important for its survival at low temperatures.However,little is known about the gene activity related to its freezing tolerance.To better understand the gene expression and regulation properties of freezing tolerance in dormant apple trees,we analyzed the transcriptomic divergences in the bark from 1-year-old branches of two apple cultivars,“Golden Delicious”(G)and“Jinhong”(H),which have different levels of cold resistance,under chilling and freezing treatments.“H”can safely overwinter below−30℃in extremely low-temperature regions,whereas“G”experiences severe freezing damage and death in similar environments.Based on 28 bark transcriptomes(from the epidermis,phloem,and cambium)from 1-year-old branches under seven temperature treatments(from 4 to−29°C),we identified 4173 and 7734 differentially expressed genes(DEGs)in“G”and“H”,respectively,between the chilling and freezing treatments.A gene coexpression network was constructed according to this expression information using weighted gene correlation network analysis(WGCNA),and seven biologically meaningful coexpression modules were identified from the network.The expression profiles of the genes from these modules suggested the gene regulatory pathways that are responsible for the chilling and freezing stress responses of“G”and/or“H.”Module 7 was probably related to freezing acclimation and freezing damage in“H”at the lower temperatures.This module contained more interconnected hub transcription factors(TFs)and cold-responsive genes(CORs).Modules 6 and 7 contained C-repeat binding factor(CBF)TFs,and many CBF-dependent homologs were identified as hub genes.We also found that some hub TFs had higher intramodular connectivity(KME)and gene significance(GS)than CBFs.Specifically,most hub TFs in modules 6 and 7 were activated at the beginning of the early freezing stress phase and maintained upregulated expression during the whole freezing stress period in“G”and“H”.The upregulation of DEGs related to methionine and carbohydrate biosynthetic processes in“H”under more severe freezing stress supported the maintenance of homeostasis in the cellular membrane.This study improves our understanding of the transcriptional regulation patterns underlying freezing tolerance in the bark of apple branches.
基金the National Natural Science Foundation of China(No.31772337)the Lishui Research Fund(No.2020zdhz03)+1 种基金the China Postdoctoral Science Foundation(No.2017M612005)the National Key Research and Development Program of China(No.2018YFD1000401)。
文摘Starch is the predominant compound in bulb scales,and previous studies have shown that bulblet development is closely associated with starch enrichment.However,how starch synthesis affects bulbification at the molecular level is unclear.In this study,we demonstrate that Lilium brownii var.giganteum,a wild lily with a giant bulb in nature,and L.brownii,the native species,have different starch levels and characteristics according to cytological and ultra-structural observations.We cloned the complete sequence of three key gene-encoding enzymes(LbgAGPS,LbgGBSS,and LbgSSⅢ)during starch synthesis by rapid amplification of 5’and 3’complementary DNA(cDNA)ends(RACE)technology.Bioinformatics analysis revealed that the proteins deduced by these genes contain the canonical conserved domains.Constructed phylogenetic trees confirmed the evolutionary relationships with proteins from other species,including monocotyledons and dicotyledons.The transcript levels of various tissues and time course samples obtained during bulblet development uncovered relatively high expression levels in bulblets and gradual increase expression accompanying bulblet growth.Moreover,a set of single nucleotide polymorphisms(SNPs)was discovered in the AGPS genes of four lily genotypes,and a purifying selection fashion was predicted according to the non-synonymous/synonymous(Ka/Ks)values.Taken together,our results suggested that key starch-synthesizing genes might play important roles in bulblet development and lead to distinctive phenotypes in bulblet size.
基金supported by the Strategic Priority Research Program of Chinese Academy of Sciences(XDA24030504 and XDA24040305)the National Natural Science Foundation of China(32000144)the Key Research Program of the Chinese Academy of Sciences(ZDRW-ZS-2018-2)。
文摘Plants belonging to the genus Taraxacum are widespread all over the world,which contain rubber-producing and non-rubberproducing species.However,the genomic basis underlying natural rubber(NR)biosynthesis still needs more investigation.Here,we presented high-quality genome assemblies of rubber-producing T.kok-saghyz TK1151 and non-rubber-producing T.mongolicum TM5.Comparative analyses uncovered a large number of genetic variations,including inversions,translocations,presence/absence variations,as well as considerable protein divergences between the two species.Two gene duplication events were found in these two Taraxacum species,including one common ancestral whole-genome triplication and one subsequent round of gene amplification.In genomes of both TK1151 and TM5,we identified the genes encoding for each step in the NR biosynthesis pathway and found that the SRPP and CPT gene families have experienced a more obvious expansion in TK1151 compared to TM5.This study will have large-ranging implications for the mechanism of NR biosynthesis and genetic improvement of NR-producing crops.
