RESUMO
Monkeypox virus (MPXV) is a cross-kingdom pathogen infecting both humans and wildlife, which poses a significant health risk to the public. Although MPXV attracts broad attention, there is a lack of adequate studies to elucidate pathogenic mechanisms associated with viral infections. In this study, a high-throughput RNA sequencing (RNA-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach was used to explore the transcriptional and metabolic responses of MPXV A23 protein to HEK293T cells. The protein-protein interactions and signaling pathways were conducted by GO and KEGG analyses. The localization of A23 protein in HEK293T cells was detected by immunofluorescence. A total of 648 differentially expressed genes (DEGs) were identified in cells by RNA-Seq, including 314 upregulated genes and 334 downregulated genes. Additionally, liquid chromatography-tandem mass spectrometry (LC-MS/MS) detected 115 cellular proteins that interact with the A23 proteins. Transcriptomic sequencing analysis revealed that transfection of MPXV A23 protein modulated genes primarily associated with cellular apoptosis and DNA damage repair. Proteomic analysis indicated that this protein primarily interacted with host ribosomal proteins and histones. Following the identification of the nuclear localization sequence RKKR within the A23 protein, a truncated mutant A23ΔRKKR was constructed to investigate the subcellular localization of A23 protein. The wild-type A23 protein exhibits a significantly higher nuclear-to-cytoplasmic ratio, exceeding 1.5, in contrast to the mutant A23ΔRKKR, which has a ratio of approximately 1. Immunofluorescence assays showed that the A23 protein was mainly localized in the nucleus. The integration of transcriptomics and proteomics analysis provides a comprehensive understanding of the interaction between MPXV A23 protein and the host. Our findings highlight the potential role of this enzyme in suppressing host antiviral immune responses and modulating host gene expression.
Assuntos
Monkeypox virus , Proteômica , Transcriptoma , Proteínas Virais , Humanos , Células HEK293 , Proteômica/métodos , Proteínas Virais/metabolismo , Proteínas Virais/genética , Monkeypox virus/genética , Monkeypox virus/metabolismo , Espectrometria de Massas em Tandem , Perfilação da Expressão Gênica , Cromatografia Líquida , Proteoma/metabolismoRESUMO
Accumulated evidence demonstrates that Japanese encephalitis virus (JEV) infection triggers endoplasmic reticulum (ER) stress and neuron apoptosis. ER stress sensor protein kinase R-like endoplasmic reticulum kinase (PERK) has been reported to induce apoptosis under acute or prolonged ER stress. However, the precise role of PERK in JEV-induced apoptosis and encephalitis remains unknown. Here, we report that JEV infection activates the PERK-ATF4-CHOP apoptosis pathway both in vitro and in vivo PERK activation also promotes the formation of stress granule, which in turn represses JEV-induced apoptosis. However, PERK inhibitor reduces apoptosis, indicating that JEV-activated PERK predominantly induces apoptosis via the PERK-ATF4-CHOP apoptosis pathway. Among JEV proteins that have been reported to induce ER stress, only JEV NS4B can induce PERK activation. PERK has been reported to form an active molecule by dimerization. The coimmunoprecipitation assay shows that NS4B interacts with PERK. Moreover, glycerol gradient centrifugation shows that NS4B induces PERK dimerization. Both the LIG-FHA and the LIG-WD40 domains within NS4B are required to induce PERK dimerization, suggesting that JEV NS4B pulls two PERK molecules together by simultaneously interacting with them via different motifs. PERK deactivation reduces brain cell damage and encephalitis during JEV infection. Furthermore, expression of JEV NS4B is sufficient to induce encephalitis via PERK in mice, indicating that JEV activates PERK primarily via its NS4B to cause encephalitis. Taken together, our findings provide a novel insight into JEV-caused encephalitis.IMPORTANCE Japanese encephalitis virus (JEV) infection triggers endoplasmic reticulum (ER) stress and neuron apoptosis. ER stress sensor protein kinase R-like endoplasmic reticulum kinase (PERK) has been reported to induce apoptosis under acute or prolonged ER stress. However, whether the PERK pathway of ER stress response plays important roles in JEV-induced apoptosis and encephalitis remains unknown. Here, we found that JEV infection activates ER stress sensor PERK in neuronal cells and mouse brains. PERK activation induces apoptosis via the PERK-ATF4-CHOP apoptosis pathway upon JEV infection. Among the JEV proteins prM, E, NS1, NS2A, NS2B, and NS4B, only NS4B activates PERK. Moreover, activated PERK participates in apoptosis and encephalitis induced by JEV and NS4B. These findings provide a novel therapeutic approach for JEV-caused encephalitis.
Assuntos
Vírus da Encefalite Japonesa (Espécie)/patogenicidade , Encefalite Japonesa/metabolismo , Neurônios/citologia , Proteínas não Estruturais Virais/metabolismo , eIF-2 Quinase/metabolismo , Fator 4 Ativador da Transcrição/metabolismo , Adenina/análogos & derivados , Adenina/farmacologia , Adenina/uso terapêutico , Animais , Apoptose , Sítios de Ligação , Linhagem Celular , Modelos Animais de Doenças , Vírus da Encefalite Japonesa (Espécie)/metabolismo , Encefalite Japonesa/virologia , Estresse do Retículo Endoplasmático , Fator de Iniciação 2 em Eucariotos/metabolismo , Indóis/farmacologia , Indóis/uso terapêutico , Camundongos , Neurônios/metabolismo , Neurônios/virologia , Multimerização Proteica , Transdução de Sinais , Fator de Transcrição CHOP/metabolismo , Proteínas não Estruturais Virais/química , Proteínas não Estruturais Virais/genética , eIF-2 Quinase/químicaRESUMO
Crop domestications are long-term selection experiments that have greatly advanced human civilization. The domestication of cultivated rice (Oryza sativa L.) ranks as one of the most important developments in history. However, its origins and domestication processes are controversial and have long been debated. Here we generate genome sequences from 446 geographically diverse accessions of the wild rice species Oryza rufipogon, the immediate ancestral progenitor of cultivated rice, and from 1,083 cultivated indica and japonica varieties to construct a comprehensive map of rice genome variation. In the search for signatures of selection, we identify 55 selective sweeps that have occurred during domestication. In-depth analyses of the domestication sweeps and genome-wide patterns reveal that Oryza sativa japonica rice was first domesticated from a specific population of O. rufipogon around the middle area of the Pearl River in southern China, and that Oryza sativa indica rice was subsequently developed from crosses between japonica rice and local wild rice as the initial cultivars spread into South East and South Asia. The domestication-associated traits are analysed through high-resolution genetic mapping. This study provides an important resource for rice breeding and an effective genomics approach for crop domestication research.
Assuntos
Agricultura/história , Produtos Agrícolas/genética , Evolução Molecular , Variação Genética/genética , Genoma de Planta/genética , Mapeamento Geográfico , Oryza/genética , Cruzamento/história , Produtos Agrícolas/classificação , Produtos Agrícolas/crescimento & desenvolvimento , Genômica , História Antiga , Oryza/classificação , Oryza/crescimento & desenvolvimento , Filogenia , Polimorfismo de Nucleotídeo Único/genética , Seleção GenéticaRESUMO
The role of endoplasmic reticulum (ER) stress in Japanese encephalitis is largely unknown. In this study, we found that Japanese encephalitis virus (JEV) strain SA14-14-2 regulates the expression of glucose-regulated protein 78 (GRP78), transcription factor 4 (ATF4) and C/EBP homologous protein (CHOP), and splicing of X-box-binding protein 1 (XBP1) mRNA in BHK-21 cells. SA14-14-2-induced cytopathic effect and decrease in viability were also observed. Moreover, the inositol-requiring enzyme 1 (IRE1) inhibitor 3,5-dibromosalicylaldehyde and JNK inhibitor SP600125 increased cell viability and reduced cell apoptosis but did not alter virus replication in SA14-14-2-infected BHK-21 cells. These results, for the first time, demonstrate that JEV induces apoptosis by the IRE1/JNK pathway of ER stress response.
Assuntos
Apoptose , Vírus da Encefalite Japonesa (Espécie)/crescimento & desenvolvimento , Fibroblastos/virologia , Interações Hospedeiro-Patógeno , MAP Quinase Quinase 4/metabolismo , Proteínas Serina-Treonina Quinases/metabolismo , Transdução de Sinais , Animais , Linhagem Celular , Sobrevivência Celular , Cricetinae , Efeito Citopatogênico Viral , Retículo Endoplasmático/fisiologia , Fibroblastos/fisiologia , Estresse FisiológicoRESUMO
Oxidative stress induces the activation of signal transducer and activator of transcription 3 (STAT3), which plays an important role in hepatocellular carcinoma (HCC). We have previously reported that hepatitis C virus (HCV) and its protein NS4B induce the production of reactive oxygen species (ROS) via the endoplasmic reticulum overload response (EOR) in human hepatocytes. Here, we found that NS4B and HCV induce STAT3 activation and stimulate the expression of cancer-related STAT3 target genes, including VEGF, c-myc, MMP-9 and Mcl-1, by EOR in human hepatocytes. Moreover, the cancer-related STAT3 pathway activated by NS4B and HCV via EOR were found to promote human hepatocyte viability. Taken together, these findings revealed that HCV NS4B might contribute to HCC by activating the EOR-mediated cancer-related STAT3 pathway, and this could provide novel insights into HCV-induced HCC.
Assuntos
Carcinoma Hepatocelular/metabolismo , Estresse do Retículo Endoplasmático , Hepacivirus/metabolismo , Neoplasias Hepáticas/metabolismo , Neoplasias Hepáticas/fisiopatologia , Fator de Transcrição STAT3/metabolismo , Proteínas não Estruturais Virais/metabolismo , Carcinoma Hepatocelular/genética , Carcinoma Hepatocelular/virologia , Retículo Endoplasmático/metabolismo , Hepacivirus/genética , Hepatócitos/metabolismo , Hepatócitos/virologia , Interações Hospedeiro-Patógeno , Humanos , Neoplasias Hepáticas/genética , Neoplasias Hepáticas/virologia , Metaloproteinase 9 da Matriz/genética , Metaloproteinase 9 da Matriz/metabolismo , Estresse Oxidativo , Espécies Reativas de Oxigênio/metabolismo , Fator de Transcrição STAT3/genética , Transdução de Sinais , Fator A de Crescimento do Endotélio Vascular/genética , Fator A de Crescimento do Endotélio Vascular/metabolismo , Proteínas não Estruturais Virais/genéticaRESUMO
Herein, an adenosine triphosphate (ATP)-induced enzyme-catalyzed cascade reaction system based on metal-organic framework/alkaline phosphatase (MOF/ALP) nanocomposites was designed to establish a surface-enhanced Raman spectroscopy (SERS) biosensor for use in rapid, sensitive ATP detection. Numerous ALP molecules were first encapsulated using ZIF-90 to temporarily deactivate the enzyme activity, similar to a lock. Au nanostars (AuNSs), as SERS-enhancing substrates, were combined with o-phenylenediamine (OPD) to form AuNSs@OPD, which could significantly improve the Raman signal of OPD. When the target ATP interacted with the MOF/ALP nanocomposites, ATP could act as a key to open the MOF structure, releasing ALP, which should further catalyze the conversion of OPD to oxOPD with the aid of ascorbic acid 2-phosphate. Therefore, with the increasing concentrations of ATP, more ALP was released to catalyze the conversion of OPD, resulting in the reduced intensity of the Raman peak at 1262 cm-1, corresponding to the level of OPD. Based on this principle, the ATP-induced enzyme-catalyzed cascade reaction SERS biosensor enabled the ultrasensitive detection of ATP, with a low detection limit of 0.075 pM. Consequently, this study provides a novel strategy for use in the ultrasensitive, rapid detection of ATP, which displays considerable potential for application in the fields of biomedicine and disease diagnosis.
Assuntos
Nanopartículas Metálicas , Estruturas Metalorgânicas , Fenilenodiaminas , Estruturas Metalorgânicas/química , Fosfatase Alcalina/química , Trifosfato de Adenosina/química , Análise Espectral Raman/métodos , Imunoensaio , Catálise , Ouro/química , Nanopartículas Metálicas/químicaRESUMO
The functional complexity of the rice transcriptome is not yet fully elucidated, despite many studies having reported the use of DNA microarrays. Next-generation DNA sequencing technologies provide a powerful approach for mapping and quantifying the transcriptome, termed RNA sequencing (RNA-seq). In this study, we applied RNA-seq to globally sample transcripts of the cultivated rice Oryza sativa indica and japonica subspecies for resolving the whole-genome transcription profiles. We identified 15,708 novel transcriptional active regions (nTARs), of which 51.7% have no homolog to public protein data and >63% are putative single-exon transcripts, which are highly different from protein-coding genes (<20%). We found that approximately 48% of rice genes show alternative splicing patterns, a percentage considerably higher than previous estimations. On the basis of the available rice gene models, 83.1% (46,472 genes) of the current rice gene models were validated by RNA-seq, and 6228 genes were identified to be extended at the 5' and/or 3' ends by at least 50 bp. Comparative transcriptome analysis demonstrated that 3464 genes exhibited differential expression patterns. The ratio of SNPs with nonsynonymous/synonymous mutations was nearly 1:1.06. In total, we interrogated and compared transcriptomes of the two rice subspecies to reveal the overall transcriptional landscape at maximal resolution.
Assuntos
Perfilação da Expressão Gênica , Oryza/genética , Análise de Sequência de RNA , Processamento Alternativo , Sequência de Bases , Genes de Plantas , Genoma de Planta , Anotação de Sequência Molecular , Análise de Sequência com Séries de Oligonucleotídeos , Polimorfismo de Nucleotídeo ÚnicoRESUMO
Hepatitis C virus (HCV) is an important human pathogen infecting more than 170 million people worldwide with approximately three million new cases each year. HCV depends heavily on interactions between viral proteins and host factors for its survival and propagation. Among HCV viral proteins, the HCV non-structural protein 4B (NS4B) has been shown to mediate virus-host interactions that are essential for HCV replication and pathogenesis and emerged as the target for anti-HCV therapy. Here, we reviewed recent knowledge about the NS4B interaction networks with host factors and its possible regulatory mechanisms, which will both advance our understanding of the role of NS4B in HCV life cycle and illuminate potential viral and host therapeutic targets.
Assuntos
Antivirais/farmacologia , Hepacivirus/efeitos dos fármacos , Hepacivirus/patogenicidade , Interações Hospedeiro-Patógeno , Mapeamento de Interação de Proteínas , Proteínas não Estruturais Virais/metabolismo , Replicação Viral/efeitos dos fármacos , Hepacivirus/fisiologia , HumanosRESUMO
BACKGROUND: Cis-natural antisense transcripts (cis-NATs) are RNAs transcribed from the antisense strand of a gene locus, and are complementary to the RNA transcribed from the sense strand. Common techniques including microarray approach and analysis of transcriptome databases are the major ways to globally identify cis-NATs in various eukaryotic organisms. Genome-wide in silico analysis has identified a large number of cis-NATs that may generate endogenous short interfering RNAs (nat-siRNAs), which participate in important biogenesis mechanisms for transcriptional and post-transcriptional regulation in rice. However, the transcriptomes are yet to be deeply sequenced to comprehensively investigate cis-NATs. RESULTS: We applied high-throughput strand-specific complementary DNA sequencing technology (ssRNA-seq) to deeply sequence mRNA for assessing sense and antisense transcripts that were derived under salt, drought and cold stresses, and normal conditions, in the model plant rice (Oryza sativa). Combined with RAP-DB genome annotation (the Rice Annotation Project Database build-5 data set), 76,013 transcripts corresponding to 45,844 unique gene loci were assembled, in which 4873 gene loci were newly identified. Of 3819 putative rice cis-NATs, 2292 were detected as expressed and giving rise to small RNAs from their overlapping regions through integrated analysis of ssRNA-seq data and small RNA data. Among them, 503 cis-NATs seemed to be associated with specific conditions. The deep sequence data from isolated epidermal cells of rice seedlings further showed that 54.0% of cis-NATs were expressed simultaneously in a population of homogenous cells. Nearly 9.7% of rice transcripts were involved in one-to-one or many-to-many cis-NATs formation. Furthermore, only 17.4-34.7% of 223 many-to-many cis-NAT groups were all expressed and generated nat-siRNAs, indicating that only some cis-NAT groups may be involved in complex regulatory networks. CONCLUSIONS: Our study profiles an abundance of cis-NATs and nat-siRNAs in rice. These data are valuable for gaining insight into the complex function of the rice transcriptome.
Assuntos
Oryza/genética , RNA Interferente Pequeno/genética , Transcriptoma/genética , Sequência de Bases , Northern Blotting , Primers do DNA/genética , Perfilação da Expressão Gênica , Biblioteca Gênica , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Microdissecção e Captura a Laser , Dados de Sequência Molecular , Oryza/metabolismo , Folhas de Planta/genética , Reação em Cadeia da Polimerase Via Transcriptase ReversaRESUMO
Hepatitis C virus (HCV) infection remains a serious public health burden around the world. So far there is no effective vaccine against this virus. Neutralizing antibody (NAb) responses to the epitopes within HCV E1 and E2 proteins are related to the resolution of hepatitis C infection. E. coli heat-labile enterotoxin B subunit (LTB) has been described as potent immunity adjuvants. In this study, we constructed recombinant pET vectors: pET-R9-Bp (B cell polyepitopes) expressing 7 epitopes from HCV E1 and E2 proteins including R9 (E2384-411aa)-Bp (E1313-327aa-E2396-424aa-E2436-447aa-E2523-540aa-E2610-627aa-E2631-648aa) and pET-LTB-R9-Bp expressing LTB adjuvant in combination with R9-Bp. Recombinant proteins R9-Bp and LTB-R9-Bp were expressed successfully in E. coli and purified by the Ni-NTA column. Both R9-Bp and LTB-R9-Bp in BALB/c mice induced robust humoral immune response in the context of intraperitoneal or intramuscular immunization but not oral immunization. Intraperitoneal administration of LTB-R9-Bp induced a higher antibody titer (peak titer: 1:341000) than that of R9-Bp (peak titer: 1:85000) after the second boost (P = 0.0036 or 0.0002). However, comparable antibody peak titers were elicited for both R9-Bp and LTB-R9-Bp in intramuscular immunization albeit with significant difference (P = 0.0032) a week after the second boost. In addition, both R9-Bp and LTB-R9-Bp induced the secretion of cytokines including IFN-γ and IL-4 at similar levels. anti-sera induced by both R9-Bp and LTB-R9-Bp recognized native HCV E1 and E2 proteins. Moreover, these HCV-specific antisera inhibited significantly the entry of HCV (P < 0.0001). Taken together, these findings showed that E. coli-based both R9-Bp and LTB-R9-Bp could become promising HCV vaccines.
Assuntos
Hepacivirus , Hepatite C , Adjuvantes Imunológicos , Animais , Anticorpos Neutralizantes , Enterotoxinas , Epitopos , Escherichia coli/genética , Hepacivirus/genética , Hepatite C/prevenção & controle , Soros Imunes , Interleucina-4 , Camundongos , Camundongos Endogâmicos BALB C , Proteínas Recombinantes , Vacinas ViraisRESUMO
The mammalian epididymis not only plays a fundamental role in the maturation of spermatozoa, but also provides protection against various stressors. The foremost among these is the threat posed by oxidative stress, which arises from an imbalance in reactive oxygen species and can elicit damage to cellular lipids, proteins, and nucleic acids. In mice, the risk of oxidative damage to spermatozoa is mitigated through the expression and secretion of glutathione peroxidase 5 (GPX5) as a major luminal scavenger in the proximal caput epididymidal segment. Accordingly, the loss of GPX5-mediated protection leads to impaired DNA integrity in the spermatozoa of aged Gpx5-/- mice. To explore the underlying mechanism, we have conducted transcriptomic analysis of caput epididymidal epithelial cells from aged (13 months old) Gpx5-/- mice. This analysis revealed the dysregulation of several thousand epididymal mRNA transcripts, including the downregulation of a subgroup of piRNA pathway genes, in aged Gpx5-/- mice. In agreement with these findings, we also observed the loss of piRNAs, which potentially bind to the P-element-induced wimpy testis (PIWI)-like proteins PIWIL1 and PIWIL2. The absence of these piRNAs was correlated with the elevated mRNA levels of their putative gene targets in the caput epididymidis of Gpx5-/- mice. Importantly, the oxidative stress response genes tend to have more targeting piRNAs, and many of them were among the top increased genes upon the loss of GPX5. Taken together, our findings suggest the existence of a previously uncharacterized somatic piRNA pathway in the mammalian epididymis and its possible involvement in the aging and oxidative stress-mediated responses.
Assuntos
Epididimo/metabolismo , Glutationa Peroxidase/fisiologia , RNA Interferente Pequeno/metabolismo , Envelhecimento/metabolismo , Animais , Regulação para Baixo , Epididimo/enzimologia , Perfilação da Expressão Gênica , Técnicas de Inativação de Genes , Glutationa Peroxidase/metabolismo , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Knockout , Reação em Cadeia da Polimerase Via Transcriptase ReversaRESUMO
Japanese encephalitis virus (JEV) infection induces brain tissue disease characterized by neuron death. however, little is known about the underlying mechanism. Using RNA sequencing, we profiled global mRNA expression changes in response to in vitro and in vivo JEV infection. Integration analysis of in vitro and in vivo mRNA transcriptome revealed that JEV infection regulated apoptosis-related Foxo signaling pathway. Foxo expression was reduced by JEV infection in vitro and in vivo. Knockdown of Foxo promoted apoptosis, while its overexpression reduced apoptosis in JEV-infected Neuro-2a cells. JEV infection in Neuro-2a cells decreased the expression of Foxo downstream genes including pro-apoptotic protein Bim, anti-apoptotic protein Bcl-6 and p21. Overexpression of anti-apoptotic proteins Bcl-6 and p21 repressed JEV-induced apoptosis. These findings suggest that Foxo primarily exerts an anti-apoptotic function via Bcl-6 and p21 in JEV-infected Neuro-2a cells. A STAT3 binding site was identified in the promoter region of Foxo by TFBIND software and confirmed by ChIP and reporter assays. JEV infection reduced STAT3 expression as well as its binding at the Foxo promoter compared to mock infection in Neuro-2a cells. Moreover, STAT3 knockdown reduced Foxo promoter activity and Foxo expression. Therefore, JEV reduced Foxo expression, at least in part, by downregulating STAT3. Taken together, we found that JEV induced cell apoptosis by inhibiting STAT3-Foxo-Bcl-6/p21 pathway, which provides a novel insight into JEV-caused encephalitis.
Assuntos
Apoptose , Vírus da Encefalite Japonesa (Espécie)/fisiologia , Fatores de Transcrição Forkhead/genética , Animais , Encéfalo/virologia , Linhagem Celular , Regulação para Baixo , Vírus da Encefalite Japonesa (Espécie)/patogenicidade , Encefalite Japonesa/virologia , Fatores de Transcrição Forkhead/deficiência , Perfilação da Expressão Gênica , Camundongos , Proteínas Proto-Oncogênicas c-bcl-6/genética , RNA Mensageiro , Fator de Transcrição STAT3/genética , Análise de Sequência de RNA , Transdução de Sinais , Quinases Ativadas por p21/genéticaRESUMO
Hepatitis C virus (HCV) replication is associated with endoplasmic reticulum (ER) and its infection triggers ER stress. In response to ER stress, ER overload response (EOR) can be activated, which involves the release of Ca2+ from ER, production of reactive oxygen species (ROS) and activation of nuclear factor κB (NF-κB). We have previously reported that HCV NS4B expression activates NF-κB via EOR-Ca2+-ROS pathway. Here, we showed that NS4B expression and HCV infection activated cancer-related NF-κB signaling pathway and induced the expression of cancer-related NF-κB target genes via EOR-Ca2+-ROS pathway. Moreover, we found that HCV-activated EOR-Ca2+-ROS pathway had profound effects on host cell viability and HCV replication. HCV infection induced human hepatocyte death by EOR-Ca2+-ROS pathway, whereas activation of EOR-Ca2+-ROS-NF-κB pathway increased the cell viability. Meanwhile, EOR-Ca2+-ROS-NF-κB pathway inhibited acute HCV replication, which could alleviate the detrimental effect of HCV on cell viability and enhance chronic HCV infection. Together, our findings provide new insights into the functions of EOR-Ca2+-ROS-NF-κB pathway in natural HCV replication and pathogenesis.
Assuntos
Retículo Endoplasmático/metabolismo , Hepacivirus/fisiologia , Hepatócitos/metabolismo , Hepatócitos/virologia , Proteínas não Estruturais Virais/metabolismo , Replicação Viral , Cálcio/metabolismo , Linhagem Celular , Sobrevivência Celular/genética , Transformação Celular Viral , Fluxo Gênico , Humanos , NF-kappa B/metabolismo , Espécies Reativas de Oxigênio/metabolismo , Transdução de Sinais , Proteínas não Estruturais Virais/genéticaRESUMO
Foxtail millet (Setaria italica) is an important grain crop that is grown in arid regions. Here we sequenced 916 diverse foxtail millet varieties, identified 2.58 million SNPs and used 0.8 million common SNPs to construct a haplotype map of the foxtail millet genome. We classified the foxtail millet varieties into two divergent groups that are strongly correlated with early and late flowering times. We phenotyped the 916 varieties under five different environments and identified 512 loci associated with 47 agronomic traits by genome-wide association studies. We performed a de novo assembly of deeply sequenced genomes of a Setaria viridis accession (the wild progenitor of S. italica) and an S. italica variety and identified complex interspecies and intraspecies variants. We also identified 36 selective sweeps that seem to have occurred during modern breeding. This study provides fundamental resources for genetics research and genetic improvement in foxtail millet.
Assuntos
Variação Genética , Genoma de Planta , Estudo de Associação Genômica Ampla , Haplótipos , Característica Quantitativa Herdável , Setaria (Planta)/genética , China , Biologia Computacional , Genética Populacional , Genômica , Mutação INDEL , Desequilíbrio de Ligação , Anotação de Sequência Molecular , Fenótipo , Filogenia , Filogeografia , Polimorfismo de Nucleotídeo ÚnicoRESUMO
Bamboo represents the only major lineage of grasses that is native to forests and is one of the most important non-timber forest products in the world. However, no species in the Bambusoideae subfamily has been sequenced. Here, we report a high-quality draft genome sequence of moso bamboo (P. heterocycla var. pubescens). The 2.05-Gb assembly covers 95% of the genomic region. Gene prediction modeling identified 31,987 genes, most of which are supported by cDNA and deep RNA sequencing data. Analyses of clustered gene families and gene collinearity show that bamboo underwent whole-genome duplication 7-12 million years ago. Identification of gene families that are key in cell wall biosynthesis suggests that the whole-genome duplication event generated more gene duplicates involved in bamboo shoot development. RNA sequencing analysis of bamboo flowering tissues suggests a potential connection between drought-responsive and flowering genes.
Assuntos
Bambusa/genética , Parede Celular/metabolismo , Secas , Flores/genética , Genes de Plantas , Genoma de Planta , Árvores/genética , Bambusa/crescimento & desenvolvimento , Parede Celular/genética , DNA de Plantas/genética , Regulação da Expressão Gênica de Plantas , Família Multigênica , RNA de Plantas/genéticaAssuntos
Epididimo/metabolismo , Inflamação/genética , RNA Ribossômico 28S/genética , Pequeno RNA não Traduzido/genética , Espermatozoides/metabolismo , Animais , Conjuntos de Dados como Assunto , Modelos Animais de Doenças , Epididimite/genética , Epididimite/patologia , Regulação da Expressão Gênica , Humanos , Inflamação/imunologia , Inflamação/patologia , Mucosa Intestinal/metabolismo , Mucosa Intestinal/patologia , Lipopolissacarídeos/imunologia , Masculino , Camundongos , Prostatite/genética , Prostatite/patologia , Contagem de Espermatozoides , Baço/metabolismo , Baço/patologiaRESUMO
A high-density haplotype map recently enabled a genome-wide association study (GWAS) in a population of indica subspecies of Chinese rice landraces. Here we extend this methodology to a larger and more diverse sample of 950 worldwide rice varieties, including the Oryza sativa indica and Oryza sativa japonica subspecies, to perform an additional GWAS. We identified a total of 32 new loci associated with flowering time and with ten grain-related traits, indicating that the larger sample increased the power to detect trait-associated variants using GWAS. To characterize various alleles and complex genetic variation, we developed an analytical framework for haplotype-based de novo assembly of the low-coverage sequencing data in rice. We identified candidate genes for 18 associated loci through detailed annotation. This study shows that the integrated approach of sequence-based GWAS and functional genome annotation has the potential to match complex traits to their causal polymorphisms in rice.
Assuntos
Estudo de Associação Genômica Ampla , Oryza/genética , Grão Comestível/genética , Flores/genética , Perfilação da Expressão Gênica , Genes de Plantas , Genética Populacional , Haplótipos , Polimorfismo Genético , Análise de Sequência de DNARESUMO
Uncovering the genetic basis of agronomic traits in crop landraces that have adapted to various agro-climatic conditions is important to world food security. Here we have identified â¼ 3.6 million SNPs by sequencing 517 rice landraces and constructed a high-density haplotype map of the rice genome using a novel data-imputation method. We performed genome-wide association studies (GWAS) for 14 agronomic traits in the population of Oryza sativa indica subspecies. The loci identified through GWAS explained â¼ 36% of the phenotypic variance, on average. The peak signals at six loci were tied closely to previously identified genes. This study provides a fundamental resource for rice genetics research and breeding, and demonstrates that an approach integrating second-generation genome sequencing and GWAS can be used as a powerful complementary strategy to classical biparental cross-mapping for dissecting complex traits in rice.