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1.
Nature ; 577(7790): 439-440, 2020 01.
Artículo en Inglés | MEDLINE | ID: mdl-31932750
2.
DNA Cell Biol ; 39(2): 273-288, 2020 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-31968175

RESUMEN

Cleistogenes songorica is a cultivated turfgrass species that employs a mixed breeding system. To determine the morphological differences and molecular mechanisms of the chasmogamous (CH) and cleistogamous (CL) flowers of this species, we evaluated seed traits and analyzed six transcription factor (TF) families related to floral development. The seed traits from the CH and CL flowers were significantly different. In total, 12 CsAP2, 13 CsSPL, 9 CsGRF, 21 CsMYB, 15 CsMADS, and 1 CsLFY differentially expressed genes were identified from the transcriptome of the C. songorica flowers, which was further supported by evolutionary relationships and conserved motifs. All collinear gene pairs had a Ka/Ks ratio <1. Analysis of the promoters and miRNAs of the TFs revealed that the members of the six TF families may coregulate the divergence of CH and CL flowers during evolution. Two CsAP2, 8 CsSPL, 6 CsGRF, 3 CsMYB (targeted by miR172s, miR156s, miR396a/b and miR159a/b, respectively), and 15 CsMADS genes as well as 1 CsLFY gene may be involved in the development of CH and CL flowers. This study is the first to analyze the differences between CH and CL flowers at the TF-family level, which will help in the understanding of dimorphic turfgrasses.


Asunto(s)
Flores/genética , Poaceae/genética , Factores de Transcripción/genética , Regulación de la Expresión Génica de las Plantas/genética , MicroARNs/genética , Fenotipo , Plantas/genética , ARN Mensajero/genética , Semillas/genética , Factores de Transcripción/metabolismo , Transcriptoma/genética
3.
J Agric Food Chem ; 68(3): 918-926, 2020 Jan 22.
Artículo en Inglés | MEDLINE | ID: mdl-31899636

RESUMEN

Theanine (thea) is the most abundant free amino acid in tea plant (Camellia sinensis) and one of the most important secondary metabolites conferring tea quality and health benefits. Great effort has recently been made to functionally dissect enzyme genes (e.g., GS, GDH, GOGAT) responsible for in vivo thea accumulation. However, the transcriptional regulation of its biosynthesis remains to be explored. Starting from publicly available (condition-independent) tea transcriptome data, we performed an exhaustive coexpression analysis between transcription factor (TF) genes and thea enzyme genes in tea plant. Our results showed that two typical plant-specialized (secondary) metabolites related TF families, such as MYB, bHLH, together with WD40 domain proteins, were prominently involved, suggesting a potential MYB-bHLH-WD40 (MBW) complex-mediated regulatory pattern in thea pathway. Aiming at the most involved MYB family, we screened seven MYB genes as thea candidate regulators through a stringent multistep selection (e.g., filtering with condition-specific nitrogen-treated transcriptome data). The control of MYB regulators in thea biosynthesis was further demonstrated using an integrated analysis of thea accumulation and MYB expression in several major tea tissues, including leave, bud, root, and stem. Our investigation aided tea researchers in having a comprehensive view of transcriptional regulatory landscape in thea biosynthesis, serving as the first platform for studying molecular regulation in thea pathway and a paradigm for understanding the characteristic components biosynthesis in nonmodel plants.


Asunto(s)
Camellia sinensis/genética , Camellia sinensis/metabolismo , Glutamatos/biosíntesis , Factores de Transcripción/metabolismo , Vías Biosintéticas , Regulación de la Expresión Génica de las Plantas , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Factores de Transcripción/genética , Transcriptoma
4.
Plant Mol Biol ; 102(3): 339-357, 2020 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-31894455

RESUMEN

KEY MESSAGE: NCP1, a NINJA family protein lacking EAR motif, acts as a negative regulator of ABA signaling by interacting with and inhibiting the activity of transcriptional activator ABP9. The phytohormone abscisic acid plays a pivotal role in regulating plant responses to a variety of abiotic stresses including drought and salinity. Maize ABP9 is an ABRE-binding bZIP transcription activator that enhances plant tolerance to multiple stresses by positively regulating ABA signaling, but the molecular mechanism by which ABP9 is regulated in mediating ABA responses remains unknown. Here, we report the identification of an ABP9-interacting protein, named ABP Nine Complex Protein 1 (NCP1) and its functional characterization. NCP1 belongs to the recently identified NINJA family proteins, but lacks the conserved EAR motif, which is a hallmark of this class of transcriptional repressors. In vitro and in vivo assays confirmed that NCP1 physically interacts with ABP9 and that they are co-localized in the nucleus. In addition, NCP1 and ABP9 are similarly induced with similar patterns by ABA treatment and osmotic stress. Interestingly, NCP1 over-expressing Arabidopsis plants exhibited a reduced sensitivity to ABA and decreased drought tolerance. Transient assay in maize protoplasts showed that NCP1 inhibits the activity of ABP9 in activating ABRE-mediated reporter gene expression, a notion further supported by genetic analysis of drought and ABA responses in the transgenic plants over-expressing both ABP9 and NCP1. These data together suggest that NCP1 is a novel negative regulator of ABA signaling via interacting with and inhibiting the activity of ABP9.


Asunto(s)
Sequías , Reguladores del Crecimiento de las Plantas/farmacología , Proteínas de Plantas/metabolismo , Transducción de Señal/efectos de los fármacos , Factores de Transcripción/metabolismo , Zea mays/metabolismo , Arabidopsis/genética , Arabidopsis/metabolismo , Proteínas de Arabidopsis , Regulación de la Expresión Génica de las Plantas/efectos de los fármacos , Genes de Plantas , Presión Osmótica , Reguladores del Crecimiento de las Plantas/genética , Proteínas de Plantas/genética , Plantas Modificadas Genéticamente/genética , Plantas Modificadas Genéticamente/metabolismo , Proteínas Represoras/metabolismo , Salinidad , Estrés Fisiológico , Factores de Transcripción/genética , Transcriptoma , Zea mays/genética
5.
Genes Dev ; 34(3-4): 166-178, 2020 02 01.
Artículo en Inglés | MEDLINE | ID: mdl-31919188

RESUMEN

Oocytes are indispensable for mammalian life. Thus, it is important to understand how mature oocytes are generated. As a critical stage of oocytes development, meiosis has been extensively studied, yet how chromatin remodeling contributes to this process is largely unknown. Here, we demonstrate that the ATP-dependent chromatin remodeling factor Snf2h (also known as Smarca5) plays a critical role in regulating meiotic cell cycle progression. Females with oocyte-specific depletion of Snf2h are infertile and oocytes lacking Snf2h fail to undergo meiotic resumption. Mechanistically, depletion of Snf2h results in dysregulation of meiosis-related genes, which causes failure of maturation-promoting factor (MPF) activation. ATAC-seq analysis in oocytes revealed that Snf2h regulates transcription of key meiotic genes, such as Prkar2b, by increasing its promoter chromatin accessibility. Thus, our studies not only demonstrate the importance of Snf2h in oocyte meiotic resumption, but also reveal the mechanism underlying how a chromatin remodeling factor can regulate oocyte meiosis.


Asunto(s)
Adenosina Trifosfatasas/genética , Adenosina Trifosfatasas/metabolismo , Ensamble y Desensamble de Cromatina/genética , Proteínas Cromosómicas no Histona/genética , Proteínas Cromosómicas no Histona/metabolismo , Factor Promotor de Maduración/genética , Meiosis/genética , Oogénesis/genética , Animales , Femenino , Regulación del Desarrollo de la Expresión Génica , Técnicas de Inactivación de Genes , Ratones , Oocitos/citología , Transcriptoma
6.
Medicine (Baltimore) ; 99(1): e18445, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31895772

RESUMEN

BACKGROUNDS: HER-2 positive breast cancer is a subtype of breast cancer with poor clinical outcome. The aim of this study was to identify differentially expressed genes (DEGs) for HER-2 positive breast cancer and elucidate the potential interactions among them. MATERIAL AND METHODS: Three gene expression profiles (GSE29431, GSE45827, and GSE65194) were derived from the Gene Expression Omnibus (GEO) database. GEO2R tool was applied to obtain DEGs between HER-2 positive breast cancer and normal breast tissues. Gene ontology (GO) annotation analysis and Kyoto Encyclopedia of Genes and Genome (KEGG) pathway enrichment analysis was performed by the Database for Annotation, Visualization and Integrated Discovery (David) online tool. Protein-protein interaction (PPI) network, hub gene identification and module analysis was conducted by Cytoscape software. Online Kaplan-Meier plotter survival analysis tool was also used to investigate the prognostic values of hub genes in HER-2 positive breast cancer patients. RESULTS: A total of 54 upregulated DEGs and 269 downregulated DEGs were identified. Among them, 10 hub genes including CCNB1, RAC1, TOP2A, KIF20A, RRM2, ASPM, NUSAP1, BIRC5, BUB1B, and CEP55 demonstrated by connectivity degree in the PPI network were screened out. In Kaplan-Meier plotter survival analysis, the overexpression of RAC1 and RRM2 were shown to be associated with an unfavorable prognosis in HER-2 positive breast cancer patients. CONCLUSIONS: This present study identified a number of potential target genes and pathways which might impact the oncogenesis and progression of HER-2 positive breast cancer. These findings could provide new insights into the detection of novel diagnostic and therapeutic biomarkers for this disease.


Asunto(s)
Neoplasias de la Mama/genética , Regulación Neoplásica de la Expresión Génica/genética , Ribonucleósido Difosfato Reductasa/genética , Proteína de Unión al GTP rac1/genética , Estudios de Casos y Controles , Biología Computacional , Regulación hacia Abajo , Femenino , Humanos , Receptor ErbB-2 , Transcriptoma/genética , Regulación hacia Arriba
7.
Medicine (Baltimore) ; 99(2): e18676, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31914060

RESUMEN

Adenoid cystic carcinoma (ACC) is one of the most frequent malignancies of salivary glands. The objective of this study was to identify key genes and potential mechanisms during ACC samples.The gene expression profiles of GSE88804 data set were downloaded from Gene Expression Omnibus. The GSE88804 data set contained 22 samples, including 15 ACC samples and 7 normal salivary gland tissues. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were constructed, and protein-protein interaction network of differentially expressed genes (DEGs) was performed by Cytoscape. The top 10 hub genes were analyzed based on Gene Expression Profiling Interactive Analysis. Then, DEGs between ACC samples and normal salivary gland samples were analyzed by gene set enrichment analysis. Furthermore, miRTarBase and Cytoscape were used for visualization of miRNA-mRNA regulatory network. KEGG pathway analysis was undertaken using DIANA-miRPath v3.0.In total, 382 DEGs were identified, including 119 upregulated genes and 263 downregulated genes. GO analysis showed that DEGs were mainly enriched in extracellular matrix organization, extracellular matrix, and calcium ion binding. KEGG pathway analysis showed that DEGs were mainly enriched in p53 signaling pathway and salivary secretion. Expression analysis and survival analysis showed that ANLN, CCNB2, CDK1, CENPF, DTL, KIF11, and TOP2A are all highly expressed, which all may be related to poor overall survival. Predicted miRNAs of 7 hub DEGs mainly enriched in proteoglycans in cancer and pathways in cancer.This study indicated that identified DEGs and hub genes might promote our understanding of molecular mechanisms, which might be used as molecular targets or diagnostic biomarkers for ACC.


Asunto(s)
Carcinoma Adenoide Quístico/genética , Perfilación de la Expresión Génica , Regulación Neoplásica de la Expresión Génica/fisiología , Neoplasias de las Glándulas Salivales/genética , Matriz Extracelular/metabolismo , Ontología de Genes , Redes Reguladoras de Genes , Humanos , MicroARNs/genética , Transcriptoma
8.
Insect Sci ; 27(2): 202-211, 2020 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-30203565

RESUMEN

Eusocial insects display a caste system in which different castes are morphologically and physiologically specialized for different tasks. Recent studies have revealed that epigenetic modifications, including DNA methylation and histone modification, mediate caste determination and differentiation, longevity, and polyethism in eusocial insects. Although there has been a growing interest in the relationship between epigenetic mechanisms and phenotypic plasticity in termites, there is little information about differential expression levels among castes and expression sites for these genes in termites. Here we show royal-tissue-specific expression of epigenetic modification genes in the termite Reticulitermes speratus. Using RNA-seq, we identified 74 genes, including three DNA methyltransferases, seven sirtuins, 48 Trithorax group proteins, and 16 Polycomb group proteins. Among these genes, 15 showed king-specific expression, and 52 showed age-dependent differential expression in kings and queens. Quantitative real-time PCR revealed that DNA methyltransferase 3 is expressed specifically in the king's testis and fat body, whereas some histone modification genes are remarkably expressed in the king's testis and queen's ovary. These findings imply that epigenetic modification plays important roles in the gamete production process in termite kings and queens.


Asunto(s)
Epigénesis Genética , Isópteros/genética , Animales , Cuerpo Adiposo/metabolismo , Femenino , Isópteros/metabolismo , Masculino , Ovario/metabolismo , Caracteres Sexuales , Testículo/metabolismo , Transcriptoma
9.
Int J Radiat Biol ; 96(1): 47-56, 2020 01.
Artículo en Inglés | MEDLINE | ID: mdl-30371121

RESUMEN

Purpose: Design and characterization of a radiation biodosimetry device are complicated by the fact that the requisite data are not available in the intended use population, namely humans exposed to a single, whole-body radiation dose. Instead, one must turn to model systems. We discuss our studies utilizing healthy, unexposed humans, human bone marrow transplant patients undergoing total body irradiation (TBI), non-human primates subjected to the same irradiation regimen received by the human TBI patients and NHPs given a single, whole-body dose of ionizing radiation.Materials and Methods: We use Bayesian linear mixed models to characterize the association between NHP and human expression patterns in radiation response genes when exposed to a common exposure regimen and across exposure regimens within the same species.Results: We show that population average differences in expression of our radiation response genes from one to another model system are comparable to typical differences between two randomly sampled members of a given model system and that these differences are smaller, on average, for linear combinations of the probe data and for the model-based combinations employed for dose prediction as part of a radiation biodosimetry device.Conclusions: Our analysis suggests that dose estimates based on our gene list will be accurate when applied to humans who have received a single, whole-body exposure to ionizing radiation.


Asunto(s)
Absorción de Radiación , Animales , Teorema de Bayes , Trasplante de Médula Ósea , Relación Dosis-Respuesta en la Radiación , Humanos , Macaca mulatta , Modelos Estadísticos , Exposición a la Radiación/efectos adversos , Especificidad de la Especie , Transcriptoma/efectos de la radiación
10.
Gut ; 69(2): 317-328, 2020 02.
Artículo en Inglés | MEDLINE | ID: mdl-31201285

RESUMEN

INTRODUCTION: Transcriptional analyses have identified several distinct molecular subtypes in pancreatic ductal adenocarcinoma (PDAC) that have prognostic and potential therapeutic significance. However, to date, an indepth, clinicomorphological correlation of these molecular subtypes has not been performed. We sought to identify specific morphological patterns to compare with known molecular subtypes, interrogate their biological significance, and furthermore reappraise the current grading system in PDAC. DESIGN: We first assessed 86 primary, chemotherapy-naive PDAC resection specimens with matched RNA-Seq data for specific, reproducible morphological patterns. Differential expression was applied to the gene expression data using the morphological features. We next compared the differentially expressed gene signatures with previously published molecular subtypes. Overall survival (OS) was correlated with the morphological and molecular subtypes. RESULTS: We identified four morphological patterns that segregated into two components ('gland forming' and 'non-gland forming') based on the presence/absence of well-formed glands. A morphological cut-off (≥40% 'non-gland forming') was established using RNA-Seq data, which identified two groups (A and B) with gene signatures that correlated with known molecular subtypes. There was a significant difference in OS between the groups. The morphological groups remained significantly prognostic within cancers that were moderately differentiated and classified as 'classical' using RNA-Seq. CONCLUSION: Our study has demonstrated that PDACs can be morphologically classified into distinct and biologically relevant categories which predict known molecular subtypes. These results provide the basis for an improved taxonomy of PDAC, which may lend itself to future treatment strategies and the development of deep learning models.


Asunto(s)
Carcinoma Ductal Pancreático/patología , Neoplasias Pancreáticas/patología , Adulto , Anciano , Carcinoma Ductal Pancreático/genética , Aprendizaje Profundo , Femenino , Regulación Neoplásica de la Expresión Génica , Humanos , Estimación de Kaplan-Meier , Masculino , Persona de Mediana Edad , Variaciones Dependientes del Observador , Neoplasias Pancreáticas/genética , Pronóstico , Reproducibilidad de los Resultados , Transcriptoma
11.
Cancer Sci ; 111(1): 253-265, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31785020

RESUMEN

FOLFOX (5-fluorouracil, leucovorin and oxaliplatin) is one of the main chemotherapy regimens for colorectal cancer (CRC), but only half of CRC patients respond to this regimen. Using gene expression profiles of 96 metastatic CRC patients treated with FOLFOX, we first selected gene pairs whose within-sample relative expression orderings (REO) were significantly associated with the response to FOLFOX using the exact binomial test. Then, from these gene pairs, we applied an optimization procedure to obtain a subset that achieved the largest F-score in predicting pathological response of CRC to FOLFOX. The REO-based qualitative transcriptional signature, consisting of five gene pairs, was developed in the training dataset consisting of 96 samples with an F-score of 0.90. In an independent test dataset consisting of 25 samples with the response information, an F-score of 0.82 was obtained. In three other independent survival datasets, the predicted responders showed significantly better progression-free survival than the predicted non-responders. In addition, the signature showed a better predictive performance than two published FOLFOX signatures across different datasets and is more suitable for CRC patients treated with FOLFOX than 5-fluorouracil-based signatures. In conclusion, the REO-based qualitative transcriptional signature can accurately identify metastatic CRC patients who may benefit from the FOLFOX regimen.


Asunto(s)
Protocolos de Quimioterapia Combinada Antineoplásica/uso terapéutico , Neoplasias Colorrectales/genética , Estudios de Evaluación como Asunto , Femenino , Fluorouracilo/administración & dosificación , Fluorouracilo/uso terapéutico , Humanos , Leucovorina/administración & dosificación , Leucovorina/uso terapéutico , Masculino , Persona de Mediana Edad , Compuestos Organoplatinos/administración & dosificación , Compuestos Organoplatinos/uso terapéutico , Oxaliplatino/administración & dosificación , Supervivencia sin Progresión , Transcripción Genética/efectos de los fármacos , Transcripción Genética/genética , Transcriptoma/efectos de los fármacos , Transcriptoma/genética
12.
J Cancer Res Clin Oncol ; 146(1): 87-96, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31758243

RESUMEN

PURPOSE: This study aimed to explore the potential competing endogenous RNA (ceRNA) network in forecasting HCC development in patients with cirrhosis through a comprehensive bioinformatic analysis. METHODS: Data mining from GEO and TCGA databases was employed to dig a spectrum of differentially expressed mRNA, lncRNA and miRNA profiles. Their expression was confirmed by RT-PCR in matched HCC cohorts (n = 6/group). The ceRNA network was constructed by co-expression analysis. Their reciprocal regulations and their roles in epithelial-to-mesenchymal transition (EMT) process were validated by gain- and loss-of-function experiments at the cellular level. Kaplan-Meier method was applied to reveal prognostic values. RESULTS: By intersecting differentially expressed genes (DEGs) in GEO and TCGA data sets and Pearson correlation analysis, 20 mRNAs, 24 miRNAs and 41 lncRNAs were identified. Of these, FOXD2-AS1, BLVRA and CYTH2 were markedly upregulated in HCC tissues and HCC cells with high metastatic potential (MHCC97H) compared with their adjacent normal/cirrhotic tissues and L02 and MHCC97L cells. However, dysregulated miR-139-5p exhibited the opposite expression pattern. Using miRanda algorithms, FOXD2-AS1, BLVRA and CYTH2 showed potential binding sites for miR-139-5p. FOXD2-AS1 knockdown induced a marked increase in miR-139-5p and EMT inhibition. The loss of miR-139-5p led to an increase in BLVRA and CYTH2 expression and EMT process. Conversely, miR-139-5p overexpression suppressed BLVRA and CYTH expression and EMT process. FOXD2-AS1, miR-139-5p, BLVRA and CYTH2 highly correlated with prognosis in patients with HCC. CONCLUSION: FOXD2-AS1/miR-139-5p/BLVRA or CYTH2 axis might be the underlying molecular mechanism that dissects HCC development caused by cirrhosis.


Asunto(s)
Carcinoma Hepatocelular/genética , Cirrosis Hepática/genética , Neoplasias Hepáticas/genética , MicroARNs/genética , ARN Largo no Codificante/genética , ARN Mensajero/genética , Carcinoma Hepatocelular/patología , Línea Celular , Línea Celular Tumoral , Análisis por Conglomerados , Biología Computacional , Minería de Datos , Bases de Datos Genéticas , Redes Reguladoras de Genes , Humanos , Cirrosis Hepática/patología , Neoplasias Hepáticas/patología , ARN Neoplásico , Transcriptoma
13.
Toxicol Lett ; 320: 95-102, 2020 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-31760062

RESUMEN

Exposure to organic solvent in industry, including n-hexane is correlated with central-peripheral axonopathy, which is mediated by its active metabolite, 2,5-hexanedione (HD). However, the underlying mechanism is still largely unknown. Recently identified microRNAs (miRNAs) may play important roles in toxicant exposure and in the process of toxicant-induced neuropathys. To examine the role of miRNAs in HD-induced toxicity, neuropathic animal model was successfully built. miRNA microarray analysis revealed 105 differentially expressed miRNAs after HD exposure. Bioinformatics analysis showed that "Axon" and "Neurotrophin Signaling Pathway" was the top significant GO term and pathway, respectively. 7 miRNAs both related to "Axon" and "Neurotrophin Signaling Pathway" were screened out and further confirmed by Real-Time PCR. Correspondingly, the deregulation expression levels of proteins of four target genes (GSK3ß, Map3k1, BDNF and MAP1B) were further confirmed via western blot, verifying the results of gene target analysis. Taken together, our results showed that the axon-related miRNAs to be associated with MAP1B or neurotrophin signal pathways changed in nerve tissues following HD exposure. These miRNAs may play important roles in HD-induced neurotoxicity.


Asunto(s)
Axones/efectos de los fármacos , Hexanonas/toxicidad , MicroARNs/metabolismo , Síndromes de Neurotoxicidad/etiología , Nervio Ciático/efectos de los fármacos , Solventes/toxicidad , Médula Espinal/efectos de los fármacos , Animales , Axones/metabolismo , Factor Neurotrófico Derivado del Encéfalo/genética , Factor Neurotrófico Derivado del Encéfalo/metabolismo , Bases de Datos Genéticas , Regulación de la Expresión Génica , Glucógeno Sintasa Quinasa 3 beta/genética , Glucógeno Sintasa Quinasa 3 beta/metabolismo , Quinasa 1 de Quinasa de Quinasa MAP/genética , Quinasa 1 de Quinasa de Quinasa MAP/metabolismo , Masculino , MicroARNs/genética , Proteínas Asociadas a Microtúbulos/genética , Proteínas Asociadas a Microtúbulos/metabolismo , Síndromes de Neurotoxicidad/genética , Síndromes de Neurotoxicidad/metabolismo , Ratas Sprague-Dawley , Nervio Ciático/metabolismo , Transducción de Señal , Médula Espinal/metabolismo , Transcriptoma
14.
Mol Genet Genomics ; 295(1): 233-249, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31673754

RESUMEN

In Chinese cabbage, hybrid seed production is performed using male sterility lines, an important approach to heterosis utilization. In this study, a stably inherited male sterile mutant msm was obtained from the 'FT'-doubled haploid line of Chinese cabbage using isolated microspore culture combined with 60Co γ-ray mutagenesis. The genetic backgrounds of 'FT' and msm were highly consistent; however, compared with wild-type 'FT', msm exhibited completely degenerated stamens and no pollen phenotype. Other characters showed no significant differences. Cytological observations revealed that stamen abortion in msm begins during the tetrad period and that tapetum cells were abnormally expanded and highly vacuolated, leading to microspore abortion. Genetic analysis indicated that the msm mutant phenotype is controlled by a single recessive nuclear gene. Comparative transcriptome analysis of 'FT' and msm flower buds using RNA-Seq technology revealed 1653 differentially expressed genes, among which, a large number associated with male sterility were detected, including 64 pollen development- and pollen tube growth-related genes, 94 pollen wall development-related genes, 11 phytohormone-related genes, and 16 transcription factor-related genes. An overwhelming majority of these genes were down-regulated in msm compared with 'FT'. Furthermore, KEGG pathway analysis indicated that a variety of carbohydrate metabolic and lipid metabolic pathways were significantly enriched, which may be related to pollen abortion. The expression patterns of 24 male sterility-related genes were analyzed using qRT-PCR. In addition, 24,476 single-nucleotide polymorphisms and 413,073 insertion-deletion events were specifically detected in msm. These results will facilitate elucidation of the regulatory mechanisms underlying male sterility in Chinese cabbage.


Asunto(s)
Brassica/genética , Genes de Plantas/genética , Infertilidad Vegetal/genética , Flores/genética , Perfilación de la Expresión Génica/métodos , Regulación de la Expresión Génica de las Plantas/genética , Genes Recesivos/genética , Reguladores del Crecimiento de las Plantas/genética , Proteínas de Plantas/genética , Polen/genética , Transcriptoma/genética , Secuenciación del Exoma Completo/métodos
15.
Fitoterapia ; 140: 104412, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31698060

RESUMEN

Aconitum carmichaelii has been used in traditional Chinese medicine for treating various diseases for several thousand years. Based on the biosynthetic pathway of some alkaloids such as C19-diterpenoid alkaloids and obvious differences in alkaloid content between leaves of two A. carmichaelii varieties has been reported, we performed leaves transcriptome analysis of two A. carmichaelii varieties. Besides we characterized the biosynthetic pathway of salsolinol. A total of 56 million raw reads (8.28 G) and 55 million clean reads (8.24 G) were obtained from two varieties (Z175 and R184) leaves transcriptome, respectively, and 176,793 unigenes were annotated. 281 and 843 unigenes are involved in the salsolinol biosynthetic pathway and the formation of C19-diterpenoid alkaloids respectively. And including 34 and 24 unigenes are the differentially expressed genes (DEGs) in the biosynthesis pathway for C19-diterpenoid alkaloids and salsolinol between Z175 and R184 respectively, which were target genes to explore differences in C19-diterpenoid alkaloid and salsolinol biosynthesis in Z175 and R184. Thus genes involved in alkaloid biosynthesis and accumulation differ between varieties leaves. The mechanisms underlying the differences and their relevance require further exploration. The results expand our knowledge of alkaloids biosynthesis in A. carmichaelii leaves, and provide a theoretical basis for analysis differences in alkaloids biosynthesis patterns in different varieties.


Asunto(s)
Aconitum/química , Vías Biosintéticas , Isoquinolinas/química , Transcriptoma , Alcaloides/biosíntesis , China , Diterpenos/química , Perfilación de la Expresión Génica , Fitoquímicos/aislamiento & purificación , Fitoquímicos/farmacología , Hojas de la Planta/química , Plantas Medicinales/química
16.
J Sci Food Agric ; 100(3): 1064-1071, 2020 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-31713870

RESUMEN

BACKGROUND: Glucosinolates (GSLs) are secondary metabolites, mainly existing in Brassica vegetables. Their breakdown products have health benefits and contribute to the distinctive taste of these vegetables. Because of their high value, there is a lot of interest in developing breeding strategies to increase the content of beneficial GSLs in Brassica species. GSLs are synthesized from certain amino acids and their biological roles depend largely on the structure of their side chains. Flavin-containing monooxygenase (FMOGS-OX ) genes are involved in the synthesis of these side chains. To better understand GSL biosynthesis, we sequenced the transcriptomes of turnip (Brassica rapa var. rapa) tubers at four developmental stages (S1-S4) and determined their GSL content. RESULTS: The total GSL content was high at the early stage (S1) of tuber development and increased up to S3, then decreased at S4. We detected 61 differentially expressed genes, including five FMOGS-OX genes, that were related for GSL biosynthesis among the four developmental stages. Most of these genes were highly expressed at stages S1 to S3, but their expression was much lower at S4. We estimated the effect of the five FMOGS-OX genes on GSL content by overexpressing them in turnip hairy roots and found that the amount of aliphatic GSLs increased significantly in the transgenic plants. CONCLUSION: The transcriptome data and characterization of genes involved in GSL biosynthesis, particularly the FMOGS-OX genes, will be valuable for improving the yield of beneficial GSLs in turnip and other Brassica crops. © 2019 Society of Chemical Industry.


Asunto(s)
Brassica rapa/enzimología , Brassica rapa/crecimiento & desarrollo , Glucosinolatos/biosíntesis , Oxigenasas de Función Mixta/metabolismo , Proteínas de Plantas/metabolismo , Vías Biosintéticas , Brassica rapa/genética , Brassica rapa/metabolismo , Dinitrocresoles/metabolismo , Regulación de la Expresión Génica de las Plantas , Oxigenasas de Función Mixta/genética , Proteínas de Plantas/genética , Raíces de Plantas/enzimología , Raíces de Plantas/genética , Raíces de Plantas/crecimiento & desarrollo , Raíces de Plantas/metabolismo , Plantas Modificadas Genéticamente/enzimología , Plantas Modificadas Genéticamente/genética , Plantas Modificadas Genéticamente/crecimiento & desarrollo , Plantas Modificadas Genéticamente/metabolismo , Transcriptoma
17.
Arch Insect Biochem Physiol ; 103(2): e21628, 2020 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-31599036

RESUMEN

The multifunctional insect cuticle serves as the exoskeleton, determines body shape, restricts water loss, provides attachment sites for muscles and internal organs and is a formidable barrier to invaders. It is morphologically divided into three layers, including envelope, epicuticle, and procuticle and is composed of chitin and cuticular proteins (CPs). Annotation of CPs and their cognate genes may help understand the structure and functions of insect cuticles. In this paper, we interrogated the genome of Pteromalus puparum, an endoparasitoid wasp that parasitizes Pieris rapae and Papilio xuthus pupae, and identified 82 genes encoding CPs belonging to six CP families, including 62 in the CPR family, 8 in CPAP3, 5 in CPF/CPFL, 2 low complexity proteins, 2 in TWDL, and 3 in Apidermin. We used six RNA-seq libraries to determine CP gene expression profiles through development and compared the cuticle hydrophobicity between the P. puparum and the ectoparasitoid Nasonia vitripennis based on GRAVY values of CPR sequences. In the Nasonia-Pteromalus comparison, we found in both N. vitripennis and P. puparum, the peak of their CPR hydrophobicity displayed at their pupal stage, whereas their adult stage showed the lowest level. Except at the adult stage, the CPR hydrophobicity in N. vitripennis is always higher than P. puparum. Finally, we identified three novel Apidermin genes, a family found solely in Hymenoptera and revealed a new sequence feature of this family. This new information contributes to a broader understanding of insect CPs generally.


Asunto(s)
Proteínas de Insectos/genética , Avispas/genética , Secuencia de Aminoácidos , Animales , Embrión no Mamífero/química , Embrión no Mamífero/metabolismo , Femenino , Perfilación de la Expresión Génica , Proteínas de Insectos/química , Proteínas de Insectos/metabolismo , Larva/genética , Larva/metabolismo , Masculino , Filogenia , Pupa/genética , Pupa/metabolismo , Transcriptoma , Avispas/crecimiento & desarrollo , Avispas/metabolismo
18.
Mol Genet Genomics ; 295(1): 107-120, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31506717

RESUMEN

The oriental gall wasp Dryocosmus kuriphilus represents a limiting pest for the European Chestnut (Castanea sativa, Fagaceae) as it creates severe yield losses. The European Chestnut is a deciduous tree, having major social, economic and environmental importance in Southern Europe, covering an area of 2.53 million hectares, including 75,000 ha devoted to fruit production. Cultivars show different susceptibility and very few are resistant to gall wasp. To deeply investigate the plant response and understand which factors can lead the plant to develop or not the gall, the study of transcriptome is basic (fundamental). To date, little transcriptomic information are available for C. sativa species. Hence, we present a de novo assembly of the chestnut transcriptome of the resistant Euro-Japanese hybrid 'Bouche de Bétizac' (BB) and the susceptible cultivar 'Madonna' (M), collecting RNA from buds at different stages of budburst. The two transcriptomes were assembled into 34,081 (BB) and 30,605 (M) unigenes, respectively. The former was used as a reference sequence for further characterization analyses, highlighting the presence of 1444 putative resistance gene analogs (RGAs) and about 1135 unigenes, as putative MiRNA targets. A global quantitative transcriptome profiling comparing the resistant and the susceptible cultivars, in the presence or not of the gall wasp, revealed some GO enrichments as "response to stimulus" (GO:0050896), and "developmental processes" (e.g., post-embryonic development, GO:0009791). Many up-regulated genes appeared to be transcription factors (e.g., RAV1, AP2/ERF, WRKY33) or protein regulators (e.g., RAPTOR1B) and storage proteins (e.g., LEA D29) involved in "post-embryonic development". Our analysis was able to provide a large amount of information, including 7k simple sequence repeat (SSR) and 335k single-nucleotide polymorphism (SNP)/INDEL markers, and generated the first reference unigene catalog for the European Chestnut. The transcriptome data for C. sativa will contribute to understand the genetic basis of the resistance to gall wasp and will provide useful information for next molecular genetic studies of this species and its relatives.


Asunto(s)
Fagaceae/genética , Transcriptoma/genética , Avispas/patogenicidad , Animales , Europa (Continente) , Fagaceae/parasitología , Perfilación de la Expresión Génica/métodos , Repeticiones de Microsatélite/genética , Anotación de Secuencia Molecular/métodos , Enfermedades de las Plantas/parasitología , Polimorfismo de Nucleótido Simple/genética , Factores de Transcripción/genética , Árboles/genética , Árboles/parasitología , Regulación hacia Arriba/genética
19.
Int J Phytoremediation ; 22(2): 224-225, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-31385520

RESUMEN

In response to Dr. Yang et al.'s comments on our article "Transcriptomic response of Arabidopsis thaliana exposed to hydroxylated polychlorinated biphenyls (OH-PCBs)", additional details were provided regarding the analysis of the gene expression level (One-Way Between-Subject ANOVA) and correction for false discovery rate (FDR) (Benjamini-Hochberg). The gene expression analysis was performed again using the new release of the Transcriptome Analysis Console™ (version 4.0.1, Life Technologies - not available at the time our initial study was conducted), which integrates the Limma differential expression portion of the Bioconductor package. Overall similar results were obtained regarding the number of genes differentially expressed and the enrichment of genes in different Gene Ontology (GO) categories. The transcriptomic profiles induced in response to the three OH-derivatives were shown, again, to be similar to those induced by inhibitors of the brassinosteroid synthesis (i.e., brassinazole, propiconazole, and uniconazole), potentially resulting in iron deficiency in exposed plants. The new (and improved) method used for the selection of differentially expressed genes did not change the conclusion of our initial study, which suggested that the higher phytotoxicity of OH-derivatives, as compared to the parent compound 2,5-dichlorobiphenyl (2,5-DCB), may be explained by the inhibition of the brassinosteroid synthesis pathway.


Asunto(s)
Arabidopsis , Contaminantes Ambientales , Bifenilos Policlorados , Biodegradación Ambiental , Hidroxilación , Transcriptoma
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