Consulta: subjectFacets:"Transcriptome"
Registros recuperados: 43
Data/hora: 06/06/2024 16:59:04

In silico analysis of Eucalyptus thioredoxins
Provedor de dados: 74
Autores: Barbosa,Aulus Estevão; Marinho,Paulo.
The Eucalyptus Genome Sequencing Project (FORESTs), an initiative from the Brazilian ONSA consortium (Organization for Nucleotide Sequencing and Analysis), has achieved the sequencing of 123.889 EST clones from 18 different cDNA libraries. We have investigated the FORESTs data set to identify EST clusters potentially encoding thioredoxins (TRX). Two types of thioredoxin families described in plants, chloroplastic (TRXm/f/x/y) and cytosolic (TRXh), have been found in the transcriptome. Putative typical TRXs have been identified in fifteen clusters, four m-type, seven h-type, two f-type, one cluster for each x/y-types and one putative homologue of the TDX gene from Arabidopsis thaliana. One cluster presents an atypical active site WCMPS, different from the...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Eucalyptus; Transcriptome; Thioredoxin.
Ano: 2005
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572005000400008

Identification of citrus expressed sequence tags (ESTs) encoding pleiotropic drug resistance (PDR)-like proteins
Provedor de dados: 74
Autores: Amaral,Alexandre Morais do; Saito,Daniel; Formighieri,Eduardo Fernandes; Rabello,Edenilson; Souza,Adriane N. de; Silva-Stenico,Maria Estela; Tsai,Siu Mui.
Pleiotropic drug resistance (PDR) proteins, a subfamily of the ATP-binding cassette (ABC) transporters, have been recently shown to play a role in plant defense against biotic and abiotic stresses. However, nothing is known about their expression in citrus. To investigate the occurrence of PDR homologues in citrus species, we have surveyed EST sequences from different tissues and conditions of the Citrus Expressed Sequence Tags (CitEST) database, through sequence similarity search analyses and inspections for characteristic PDR domains. Multiple sequence alignments, prediction of transmembrane topology and phylogenetic analysis of PDR-like proteins were additionally performed. This study allowed the identification of nine putative proteins showing...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: ABC transporters; CitEST; Expressed sequence tag; Transcriptome; Stress.
Ano: 2007
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572007000500014

In silico evaluation of the Eucalyptus transcriptome
Provedor de dados: 74
Autores: Vicentini,Renato; Sassaki,Flávio T.; Gimenes,Marcos A.; Maia,Ivan G.; Menossi,Marcelo.
The expressed sequence tags (ESTs) produced in the Forests project provide an invaluable opportunity to assess the Eucalyptus transcriptome. Besides providing information on the different proteins produced by this plant, it is possible to infer gene expression profiles because non-normalized cDNA libraries were used. The EST frequency from any gene is correlated to the transcript levels in the tissues from which the cDNA libraries were constructed. The goal of this work was to identify Eucalyptus genes that showed either differential expression pattern or were ubiquitously expressed in the tissues sampled in the Forests project. Six robust statistical tests and very restrictive rules were applied to gain confidence in the in silico data aiming to avoid...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Transcriptome; Eucalyptus; Tissue-specific; Statistics; Differential expression.
Ano: 2005
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572005000400002

Insights into the Melipona scutellaris (Hymenoptera, Apidae, Meliponini) fat body transcriptome
Provedor de dados: 74
Autores: Sousa,Cristina Soares de; Serrão,José Eduardo; Bonetti,Ana Maria; Amaral,Isabel Marques Rodrigues; Kerr,Warwick Estevam; Maranhão,Andréa Queiroz; Ueira-Vieira,Carlos.
The insect fat body is a multifunctional organ analogous to the vertebrate liver. The fat body is involved in the metabolism of juvenile hormone, regulation of environmental stress, production of immunity regulator-like proteins in cells and protein storage. However, very little is known about the molecular mechanisms involved in fat body physiology in stingless bees. In this study, we analyzed the transcriptome of the fat body from the stingless bee Melipona scutellaris. In silico analysis of a set of cDNA library sequences yielded 1728 expressed sequence tags (ESTs) and 997 high-quality sequences that were assembled into 29 contigs and 117 singlets. The BLAST X tool showed that 86% of the ESTs shared similarity with Apis mellifera (honeybee) genes. The...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Fat body; Gene expression; Melipona; Stingless bees; Transcriptome.
Ano: 2013
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572013000200022

De novo transcriptome analysis of Tibetan medicinal plant Dysphania schraderiana
Provedor de dados: 74
Autores: Fu,Suhong; Lei,Ming; Zhang,Yongqun; Deng,Zhaomin; Shi,Jing; Hao,Doudou.
Abstract Dysphania schraderiana is widely distributed in Lhasa (Tibet, China) and used as a traditional medicine. However, the lack of genetic information hinders the understanding of its physiological processes, such as the biosynthesis of secondary metabolites. Herein, we used Illumina Hiseq4000 platform to sequence the transcriptome of flower and leaf tissues from D. schraderiana for the first time. Totally, 40,142 unigenes were assembled from approximately 5.2 million clean reads. All unigenes underwent gene prediction and were subsequently annotated in a NR (NCBI non-redundant protein) database, COG (Clusters of Orthologous Groups of proteins) database, and KEGG (Kyoto Encyclopedia of Genes and Genomes) database. Among the 40,142 unigenes, 2,579 genes...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Dysphania schraderiana; De novo assembly; Transcriptome; Annotation; Terpenoid biosynthesis.
Ano: 2019
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572019000300480

Subtractive libraries for prospecting differentially expressed genes in the soybean under water deficit
Provedor de dados: 74
Autores: Rodrigues,Fabiana Aparecida; Marcolino-Gomes,Juliana; Carvalho,Josirlei de Fátima Corrêa; Nascimento,Leandro Costa do; Neumaier,Norman; Farias,José Renato Bouças; Carazzolle,Marcelo Falsarella; Marcelino,Francismar Corrêa; Nepomuceno,Alexandre Lima.
Soybean has a wide range of applications in the industry and, due to its crop potential, its improvement is widely desirable. During drought conditions, soybean crops suffer significant losses in productivity. Therefore, understanding the responses of the soybean under this stress is an effective way of targeting crop improvement techniques. In this study, we employed the Suppressive Subtractive Hybridization (SSH) technique to investigate differentially expressed genes under water deficit conditions. Embrapa 48 and BR 16 soybean lines, known as drought-tolerant and -sensitive, respectively, were grown hydroponically and subjected to different short-term periods of stress by withholding the nutrient solution. Using this approach, we have identified genes...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Gene expression; Drought; Transcriptome.
Ano: 2012
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572012000200011

Transcriptome analysis of resistant soybean roots infected by Meloidogyne javanica
Provedor de dados: 74
Autores: Sá,Maria Eugênia Lisei de; Lopes,Marcus José Conceição; Campos,Magnólia de Araújo; Paiva,Luciano Vilela; Amorim,Regina Maria Santos de; Beneventi,Magda Aparecida; Firmino,Alexandre Augusto Pereira; Sá,Maria Fátima Grossi de.
Soybean is an important crop for Brazilian agribusiness. However, many factors can limit its production, especially root-knot nematode infection. Studies on the mechanisms employed by the resistant soybean genotypes to prevent infection by these nematodes are of great interest for breeders. For these reasons, the aim of this work is to characterize the transcriptome of soybean line PI 595099-Meloidogyne javanica interaction through expression analysis. Two cDNA libraries were obtained using a pool of RNA from PI 595099 uninfected and M. javanica (J2) infected roots, collected at 6, 12, 24, 48, 96, 144 and 192 h after inoculation. Around 800 ESTs (Expressed Sequence Tags) were sequenced and clustered into 195 clusters. In silico subtraction analysis...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Gene expression; Root knot nematode; Transcriptome.
Ano: 2012
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572012000200008

Sequencing and de novo assembly of the Asian gypsy moth transcriptome using the Illumina platform
Provedor de dados: 74
Autores: Xiaojun,Fan; Chun,Yang; Jianhong,Liu; Chang,Zhang; Yao,Li.
Abstract The Asian gypsy moth (Lymantria dispar) is a serious pest of forest and shade trees in many Asian and some European countries. However, there have been few studies of L. dispar genetic information and comprehensive genetic analyses of this species are needed in order to understand its genetic and metabolic sensitivities, such as the molting mechanism during larval development. In this study, high-throughput sequencing technology was used to sequence the transcriptome of the Asian subspecies of the gyspy moth, after which a comprehensive analysis of chitin metabolism was undertaken. We generated 37,750,380 high-quality reads and assembled them into contigs. A total of 37,098 unigenes were identified, of which 15,901 were annotated in the NCBI...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Asian gypsy moth; Chitin metabolism; Transcriptome; Unigenes.
Ano: 2017
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572017000100160

Transcriptome analyses of Ditylenchus destructor in responses to cold and desiccation stress
Provedor de dados: 74
Autores: Ma,Juan; Gao,Bo; Wang,Rongyan; Li,Xiuhua; Chen,Shulong.
Abstract The objective of this study was to identify molecular responses in Ditylenchus destructor to cold and desiccation by means of transcriptomes analyses. A total of 102,517 unigenes were obtained, with an average length of 1,076 bp, in which 58,453 (57%) had a functional annotation. A total of 1154 simple sequence repeats (SSRs) distributed over 1078 unigenes were detected. Gene expression profiles in response to cold and desiccation stress and the expression of specific stress-related genes were compared. Gene ontology analysis and pathway-based analysis were used to further investigate the functions of the differentially expressed genes. The reliability of the sequencing data was verified through quantitative real-time PCR analysis of 19...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Potato rot nematode; Transcriptome; Tolerance; Differentially expressed genes.
Ano: 2020
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572020000100202

The role of noncoding RNAs in the response of oil palm plants to abiotic stresses.
Provedor de dados: 14
Autores: SALGADO, F. F.; GRYNBERG, P.; SOUZA JUNIOR, M. T.
The discovery of noncoding RNAs (ncRNAs) is changed our understanding of genome, transcriptome, and interactions with proteome in a cell. Since the discovery of the first microRNA (miRNA) called lin-4 on Caenorhabditis elegans in 1993, our understanding of gene expression has deepened. Further miRNA discoveries have led to the investigation of new ncRNA families and their function, biogenesis, and interactions with other types of molecules. Recent developments in bioinformatics, public databases, sequencing technologies, and biochemical techniques have increased our understanding of the biogenesis, function, and interactions of ncRNAs. This book provides an overview of current ncRNA research dealing with human diseases and cancer and plant miRNAs.
Tipo: Parte de livro
Palavras-chave: Óleo Vegetal; Oil palm products; Abiotic stress; Salt stress; Transcriptome; Oilseed crops.
Ano: 2022
URL: http://www.infoteca.cnptia.embrapa.br/infoteca/handle/doc/1148820

De novo assembly, characterization and functional annotation of Senegalese sole (Solea senegalensis) and common sole (Solea solea) transcriptomes: integration in a database and design of a microarray
Provedor de dados: 5
Autores: Benzekri, Hicham; Armesto, Paula; Cousin, Xavier; Rovira, Mireia; Crespo, Diego; Alejandro Merlo, Manuel; Mazurais, David; Bautista, Rocio; Guerrero-fernandez, Dario; Fernandez-pozo, Noe; Ponce, Marian; Infante, Carlos; Zambonino, Jose Luis; Nidelet, Sabine; Gut, Marta; Rebordinos, Laureana; Planas, Josep V.; Begout, Marie-laure; Gonzalo Claros, M.; Manchado, Manuel.
Background Senegalese sole (Solea senegalensis) and common sole (S. solea) are two economically and evolutionary important flatfish species both in fisheries and aquaculture. Although some genomic resources and tools were recently described in these species, further sequencing efforts are required to establish a complete transcriptome, and to identify new molecular markers. Moreover, the comparative analysis of transcriptomes will be useful to understand flatfish evolution. Results A comprehensive characterization of the transcriptome for each species was carried out using a large set of Illumina data (more than 1,800 millions reads for each sole species) and 454 reads (more than 5 millions reads only in S. senegalensis), providing coverages ranging from...
Tipo: Text
Palavras-chave: Soles; Transcriptome; Microarray; Orthology; Molecular markers; SoleaDB.
Ano: 2014
URL: http://archimer.ifremer.fr/doc/00238/34918/33626.pdf

Transcriptomic response to parasite infection in Nile tilapia (Oreochromis niloticus) depends on rearing density
Provedor de dados: 5
Autores: Ellison, Amy R.; Uren Webster, Tamsyn M.; Rey, Olivier; Garcia De Leaniz, Carlos; Consuegra, Sofia; Orozco-terwengel, Pablo; Cable, Jo.
Background: Captive animal populations, be it for food production or conservation programmes, are often maintained at densities far beyond those in natural environments, which can have profound effects on behaviour, immune and stress levels, and ultimately welfare. How such alterations impact transcriptional responses to pathogen infection is a 'different kettle of fish' and remains poorly understood. Here, we assessed survival and gene expression profiles of infected fish reared at two different densities to elucidate potential functional genomic mechanisms for density-related differences in disease susceptibility. Results: Utilising a whole-transcriptome sequencing (RNAseq) approach, we demonstrate that rearing density in tilapia (Oreochromis niloticus)...
Tipo: Text
Palavras-chave: Stocking density; Stress; Saprolegnia; Aquaculture; Transcriptome; Tilapia; Circadian rhythm; Disease risk.
Ano: 2018
URL: https://archimer.ifremer.fr/doc/00462/57353/78952.pdf

Identification of Hypoxia-Regulated Genes in the Liver of Common Sole (Solea solea ) Fed Different Dietary Lipid Contents
Provedor de dados: 5
Autores: Mazurais, David; Ferraresso, Serena; Gatta, Pier Paolo; Desbruyeres, Elisabeth; Severe, Armelle; Corporeau, Charlotte; Claireaux, Guy; Bargelloni, Luca; Zambonino, Jose-luis.
Coastal systems could be affected by hypoxic events brought about by global change. These areas are essential nursery habitats for several fish species including the common sole (Solea solea L.). Tolerance of fish to hypoxia depends on species and also on their physiological condition and nutritional status. Indeed, high dietary lipid content has been recently shown to negatively impact the resistance of sole to a severe hypoxic challenge. In order to study the molecular mechanisms involved in the early response to hypoxic stress, the present work examined the hepatic transcriptome in common sole fed diets with low and high lipid content, exposed to severe hypoxia. The activity of AMP-activated protein kinase (AMPK) was also investigated through the...
Tipo: Text
Palavras-chave: Fish; Hypoxia; Nutrition; Liver; Transcriptome; AMPK.
Ano: 2014
URL: http://archimer.ifremer.fr/doc/00169/28062/26474.pdf

Gonad transcriptome analysis of pearl oyster Pinctada margaritifera: identification of potential sex differentiation and sex determining genes
Provedor de dados: 5
Autores: Teaniniuraitemoana, Vaihiti; Huvet, Arnaud; Levy, Peva; Klopp, Christophe; Lhuillier, Emeline; Gaertner-mazouni, Nabila; Gueguen, Yannick; Le Moullac, Gilles.
Background  Black pearl farming is based on culture of the blacklip pearl oyster Pinctada margaritifera (Mollusca, lophotrochozoa), a protandrous hermaphrodite species. At first maturation, all individuals are males. The female sex appears progressively from two years old, which represents a limitation for broodstock conditioning for aquaculture production. In marine mollusks displaying hermaphroditic features, data on sexual determinism and differentiation, including the molecular sex determining cascade, are scarce. To increase genomic resources and identify the molecular mechanisms whereby gene expression may act in the sexual dimorphism of P. margaritifera, we performed gonad transcriptome analysis.  Results  The gonad transcriptome of P. margaritifera...
Tipo: Text
Palavras-chave: Pinctada margaritifera; Gametogenesis; Transcriptome; Differential expression; Sex determinism.
Ano: 2014
URL: http://archimer.ifremer.fr/doc/00201/31194/29593.pdf

Relation between Biofilm and Virulence in Vibrio tapetis: A Transcriptomic Study
Provedor de dados: 5
Autores: Rodrigues, Sophie; Paillard, Christine; Van Dillen, Sabine; Tahrioui, Ali; Berjeaud, Jean-marc; Dufour, Alain; Bazire, Alexis.
Marine pathogenic bacteria are able to form biofilms on many surfaces, such as mollusc shells, and they can wait for the appropriate opportunity to induce their virulence. Vibrio tapetis can develop such biofilms on the inner surface of shells of the Ruditapes philippinarum clam, leading to the formation of a brown conchiolin deposit in the form of a ring, hence the name of the disease: Brown Ring Disease. The virulence of V. tapetis is presumed to be related to its capacity to form biofilms, but the link has never been clearly established at the physiological or genetic level. In the present study, we used RNA-seq analysis to identify biofilm- and virulence-related genes displaying altered expression in biofilms compared to the planktonic condition. A...
Tipo: Text
Palavras-chave: Biofilm; Virulence; Vibrio tapetis; Transcriptome; Quorum sensing; Type VI secretion system; Brown ring disease.
Ano: 2018
URL: https://archimer.ifremer.fr/doc/00470/58140/60611.pdf

Impact moléculaire et physiologique de la guêpe parasitoïde Cotesia congregata et de son polydnavirus sur l'insecte hôte Manduca sexta
Provedor de dados: 5
Autores: Chevignon, Germain.
Cotesia congregata est une guêpe parasitoïde qui se développe à l’intérieur de la larve du Lépidoptère, Manduca sexta. Ce parasitoïde a développé une stratégie de virulence qui utilise un symbionte viral de la famille des Polydnavirus nommé Cotesia congregata bracovirus. Mon travail de thèse a permis de caractériser le dialogue moléculaire au cours de l’interaction par des approches de transcriptomique à haut débit et de physiologie. Ces travaux ont permis d’établir la première carte fonctionnelle du génome viral et de visualiser l’ensemble des gènes de M. sexta régulés au cours du parasitisme. La régulation des gènes de l’immunité a révélé que le parasitisme n’empêche pas l’induction de peptides antimicrobiens, mais entraine la sous-expression de gènes...
Tipo: Text
Palavras-chave: Polydnavirus; Parsitoid wasp; Transcriptome; 454; Cell death. Cotesia congregata; Manduca sexta; Polydnavirus; Guêpe parasitoïde; Transcriptome; 454; Mort cellulaire; Cotesia congregata; Manduca sexta.
Ano: 2014
URL: https://archimer.ifremer.fr/doc/00634/74649/74597.pdf

Natural resistance to Fasciola hepatica (Trematoda) in Pseudosuccinea columella snails: A review from literature and insights from comparative “omic” analyses
Provedor de dados: 5
Autores: Alba, Annia; Tetreau, Guillaume; Chaparro, Cristian; Sánchez, Jorge; Vázquez, Antonio A.; Gourbal, Benjamin.
The snail Pseudosuccinea columella is one of the main vectors of the medically-important trematode Fasciola hepatica. In Cuba, the existence of natural P. columella populations that are either susceptible or resistant to F. hepatica infection offers a unique snail-parasite for study of parasite-host compatibility and immune function in gastropods. Here, we review all previous literature on this system and present new “omic” data that provide a molecular baseline of both P. columella phenotypes from naïve snails. Comparison of whole snail transcriptomes (RNAseq) and the proteomes of the albumen gland (2D-electrophoresis, MS) revealed that resistant and susceptible strains differed mainly in an enrichment of particular biological processes/functions and a...
Tipo: Text
Palavras-chave: Transcriptome; Albumen gland; Allocation of resources; Response to stress; Immune defense; Cost of resistance.
Ano: 2019
URL: https://archimer.ifremer.fr/doc/00509/62039/66180.pdf

Assessing the effects of genotype-by-environment interaction on epigenetic, transcriptomic, and phenotypic response in a Pacific salmon
Provedor de dados: 5
Autores: Christensen, Kris A; Le Luyer, Jeremy; Chan, Michelle T T; Rondeau, Eric B; Koop, Ben F; Bernatchez, Louis; Devlin, Robert H.
Genotype-by-environment (GxE) interactions are non-parallel reaction norms among individuals with different genotypes in response to different environmental conditions. GxE interactions are an extension of phenotypic plasticity and consequently studying such interactions improves our ability to predict effects of different environments on phenotype as well as the fitness of genetically distinct organisms and their capacity to interact with ecosystems. Growth hormone transgenic coho salmon grow much faster than non-transgenics when raised in tank environments, but show little difference in growth when reared in nature-like streams. We used this model system to evaluate potential mechanisms underlying this growth rate GxE interaction, performing RNA-seq to...
Tipo: Text
Palavras-chave: Epigenetics; Transcriptome; GxE; Transgenic; Growth hormone; Salmonid.
Ano: 2021
URL: https://archimer.ifremer.fr/doc/00677/78890/81188.pdf

Unravelling the genes forming the wing pattern supergene in the polymorphic butterfly Heliconius numata
Provedor de dados: 5
Autores: Saenko, Suzanne, V; Chouteau, Mathieu; Piron-prunier, Florence; Blugeon, Corinne; Joron, Mathieu; Llaurens, Violaine.
Background Unravelling the genetic basis of polymorphic characters is central to our understanding of the origins and diversification of living organisms. Recently, supergenes have been implicated in a wide range of complex polymorphisms, from adaptive colouration in butterflies and fish to reproductive strategies in birds and plants. The concept of a supergene is now a hot topic in biology, and identification of its functional elements is needed to shed light on the evolution of highly divergent adaptive traits. Here, we apply different gene expression analyses to study the supergene P that controls polymorphism of mimetic wing colour patterns in the neotropical butterfly Heliconius numata. Results We performed de novo transcriptome assembly and...
Tipo: Text
Palavras-chave: Supergene; Wing pattern; Lepidoptera; Heliconius butterflies; Transcriptome; RNA sequencing; Gene expression.
Ano: 2019
URL: https://archimer.ifremer.fr/doc/00659/77123/78514.pdf

Deciphering the Infectious Process of Colletotrichum lupini in Lupin through Transcriptomic and Proteomic Analysis
Provedor de dados: 5
Autores: Dubrulle, Guillaume; Picot, Adeline; Madec, Stephanie; Corre, Erwan; Pawtowski, Audrey; Baroncelli, Riccardo; Zivy, Michel; Balliau, Thierry; Le Floch, Gaétan; Pensec, Flora.
The fungal phytopathogen Colletotrichum lupini is responsible for lupin anthracnose, resulting in significant yield losses worldwide. The molecular mechanisms underlying this infectious process are yet to be elucidated. This study proposes to evaluate C. lupini gene expression and protein synthesis during lupin infection, using, respectively, an RNAseq-based transcriptomic approach and a mass spectrometry-based proteomic approach. Patterns of differentially-expressed genes in planta were evaluated from 24 to 84 hours post-inoculation, and compared to in vitro cultures. A total of 897 differentially-expressed genes were identified from C. lupini during interaction with white lupin, of which 520 genes were predicted to have a putative function, including...
Tipo: Text
Palavras-chave: Anthracnose disease; Transcriptome; Proteome; Pathogenicity factors.
Ano: 2020
URL: https://archimer.ifremer.fr/doc/00656/76795/77961.pdf

In Silico Analysis of Pacific Oyster (Crassostrea gigas) Transcriptome over Developmental Stages Reveals Candidate Genes for Larval Settlement
Provedor de dados: 5
Autores: Foulon, Valentin; Boudry, Pierre; Artigaud, Sebastien; Guérard, Fabienne; Hellio, Claire.
Following their planktonic phase, the larvae of benthic marine organisms must locate a suitable habitat to settle and metamorphose. For oysters, larval adhesion occurs at the pediveliger stage with the secretion of a proteinaceous bioadhesive produced by the foot, a specialized and ephemeral organ. Oyster bioadhesive is highly resistant to proteomic extraction and is only produced in very low quantities, which explains why it has been very little examined in larvae to date. In silico analysis of nucleic acid databases could help to identify genes of interest implicated in settlement. In this work, the publicly available transcriptome of Pacific oyster Crassostrea gigas over its developmental stages was mined to select genes highly expressed at the...
Tipo: Text
Palavras-chave: Crassostrea gigas; Pacific oyster; Pediveliger larvae; Bioadhesive; Transcriptome.
Ano: 2019
URL: https://archimer.ifremer.fr/doc/00475/58677/61172.pdf

Déterminisme nutritionnel et génétique de la teneur en lipides musculaires chez la truite arc-en-ciel (Oncorhynchus mykiss) [Texte imprimé]  : étude par analyse de l'expression de gènes candidats, du protéome et du transcriptome du foie et du muscle
Provedor de dados: 5
Autores: Kolditz, Catherine-inès.
The objective of the study was to identify genes and proteins that are involved in the control of muscle fat deposition in rainbow trout. We analyzed the combined effects exerted by genetic selection and dietary treatment, which are the two main factors that can be used to manage body fat content. Two lines of rainbow trout, obtained after 3 generations of divergent selection for high or low muscle fat content, were fed diets containing either 10% or 23% lipids (% dry matter), for six months. We analyzed the activity and gene expression of key enzymes involved in energy utilization, and performed a more global approach through transcriptome (nylon microarray) and proteome (twodimensional electrophoresis) analysis. We analyzed the liver, which is the centre...
Tipo: Text
Palavras-chave: Proteomics; Transcriptomics; Selective breeding; Dietary energy; Rainbow trout; Protéome; Transcriptome; Sélection génétique; Apport énergétique alimentaire; Truite arc en ciel.
Ano: 2008
URL: http://archimer.ifremer.fr/doc/2008/these-6794.pdf

Additive transcriptomic variation associated with reproductive traits suggest local adaptation in a recently settled population of the Pacific oyster, Crassostrea gigas
Provedor de dados: 5
Autores: Sussarellu, Rossana; Huvet, Arnaud; Lapegue, Sylvie; Quillen, Virgile; Lelong, Christophe; Cornette, Florence; Jensen, Lasse Fast; Bierne, Nicolas; Boudry, Pierre.
Background Originating from Northeast Asia, the Pacific oyster Crassostrea gigas has been introduced into a large number of countries for aquaculture purpose. Following introduction, the Pacific oyster has turned into an invasive species in an increasing number of coastal areas, notably recently in Northern Europe.  Methods To explore potential adaptation of reproductive traits in populations with different histories, we set up a common garden experiment based on the comparison of progenies from two populations of Pacific oyster sampled in France and Denmark and their hybrids. Sex ratio, condition index and microarray gene expression in gonads, were analyzed in each progeny (n = 60).  Results A female-biased sex-ratio and a higher condition index were...
Tipo: Text
Palavras-chave: Crassostrea gigas; Adaptation; Invasiveness; Fertility; Sex-ratio; Transcriptome; Microarray.
Ano: 2015
URL: https://archimer.ifremer.fr/doc/00287/39829/38343.pdf

The red coral (Corallium rubrum) transcriptome: a new resource for population genetics and local adaptation studies
Provedor de dados: 5
Autores: Pratlong, M.; Haguenauer, A.; Chabrol, O.; Klopp, C.; Pontarotti, P.; Aurelle, D.
The question of species survival and evolution in heterogeneous environments has long been a subject for study. Indeed, it is often difficult to identify the molecular basis of adaptation to contrasted environments, and nongenetic effects increase the difficulty to disentangle fixed effects, such as genetic adaptation, from variable effects, such as individual phenotypic plasticity, in adaptation. Nevertheless, this question is also of great importance for understanding the evolution of species in a context of climate change. The red coral (Corallium rubrum) lives in the Mediterranean Sea, where at depths ranging from 5 to 600m, it meets very contrasted thermal conditions. The shallowest populations of this species suffered from mortality events linked...
Tipo: Text
Palavras-chave: Cnidarians; Gene expression; Local adaptation; Octocoral polymorphism; Transcriptome.
Ano: 2015
URL: https://archimer.ifremer.fr/doc/00371/48257/48661.pdf

Transcriptome based SNP discovery and validation for parentage assignment in hatchery progeny of the European abalone Haliotis tuberculata
Provedor de dados: 5
Autores: Harney, Ewan; Lachambre, Sebastien; Roussel, Sabine; Huchette, Sylvain; Enez, Florian; Morvezen, Romain; Haffray, Pierrick; Boudry, Pierre.
Selective breeding strategies require pedigree information over generations, but many species produced in aquaculture are too small to be physically tagged at early stages. Consequently, maintaining a sufficient number of separate families is often needed but costly and logistically difficult. Alternatively, parentage assignment can be obtained using DNA markers. We developed a panel of single nucleotide polymorphism (SNP) markers for the European abalone Haliotis tuberculata using an existing transcriptomic resource. An initial set of 2,176,887 SNPs was filtered to select 500 for high throughput genotyping. Of these, 298 SNPs were amplified in at least 90% of our H. tuberculata samples, consisting of a mixed family cohort (945 offspring) generated by...
Tipo: Text
Palavras-chave: Abalone; Parentage assignment; Pedigree; Selective breeding; Transcriptome; SNP.
Ano: 2018
URL: https://archimer.ifremer.fr/doc/00429/54061/55396.pdf

Gill transcriptomic analysis in fast- and slow-growing individuals of Mytilus galloprovincialis
Provedor de dados: 5
Autores: Prieto, Daniel; Markaide, Pablo; Urrutxurtu, Iñaki; Navarro, Enrique; Artigaud, Sebastien; Fleury, Elodie; Ibarrola, Irrintzi; Urrutia, Miren Bego.
The molecular basis underlying the mechanisms at the origin of growth variation in bivalves is still poorly understood, although several genes have been described as upregulated in fast-growing individuals. In the present study, we reared mussel spat of the species Mytilus galloprovincialis under diets below the pseudofaeces threshold (BP) and above the pseudofaeces threshold (AP). After 3 months, F and S mussels from each condition were selected to obtain 4 experimental groups: FBP, SBP, FAP and SAP. We hypothesized that the nurturing conditions during the growing period would modify the molecular basis of their growth rate differences. To decipher the molecular mechanisms underlying the growth variation, the gill transcriptomes for the four mussel groups...
Tipo: Text
Palavras-chave: Fast-growing; Mussel; Gill; Transcriptome.
Ano: 2019
URL: https://archimer.ifremer.fr/doc/00503/61490/65293.pdf

Differential gene expression after total replacement of dietary fish meal and fish oil by plant products in rainbow trout (Oncorhynchus mykiss) liver
Provedor de dados: 5
Autores: Panserat, S.; Hortopan, G. A.; Plagnes-juan, E.; Kolditz, C.; Lansard, M.; Skiba-cassy, S.; Esquerre, D.; Geurden, I.; Medale, Francoise; Kaushik, Sadasivam; Corraze, Genevieve.
Our objective was to analyse the hepatic transcriptomes of juvenile rainbow trout fed with a plant-based diet. We focused our analysis on the total replacement of fish meal (FM) and fish oil (FO) by a 100% plant-based diet (0% FM, 0% FO). We analysed the postprandial hepatic transcriptomes of rainbow trout fed the two diets 8 h after feeding. Six total hepatic RNAs from each dietary group were hybridised against a trout cDNA microarray (9K). After treatment of the data respecting the standard MIAME (Minimum Information About a Microarray Experiment) protocol, we found that 176 hepatic genes were differentially expressed between fish fed the two diets: 96 and 80 were over-expressed and under-expressed, respectively, in trout fed the plant-based diet. A...
Tipo: Text
Palavras-chave: Rainbow trout; Transcriptome; Metabolism; Liver; Vegetable products; Marine ingredients.
Ano: 2009
URL: http://archimer.ifremer.fr/doc/2009/publication-6684.pdf

Venom Diversity and Evolution in the Most Divergent Cone Snail Genus Profundiconus
Provedor de dados: 5
Autores: Fassio, Giulia; Modica, Maria Vittoria; Mary, Lou; Zaharias, Paul; Fedosov, Alexander E.; Gorson, Juliette; Kantor, Yuri I.; Holford, Mandё; Puillandre, Nicolas.
Profundiconus is the most divergent cone snail genus and its unique phylogenetic position, sister to the rest of the family Conidae, makes it a key taxon for examining venom evolution and diversity. Venom gland and foot transcriptomes of Profundiconus cf. vaubani and Profundiconus neocaledonicus were de novo assembled, annotated, and analyzed for differential expression. One hundred and thirty-seven venom components were identified from P. cf. vaubani and 82 from P. neocaledonicus, with only four shared by both species. The majority of the transcript diversity was composed of putative peptides, including conotoxins, profunditoxins, turripeptides, insulin, and prohormone-4. However, there were also a significant percentage of other putative venom components...
Tipo: Text
Palavras-chave: Conidae; Conotoxins; Turripeptides; Transcriptome; Venom gland.
Ano: 2019
URL: https://archimer.ifremer.fr/doc/00589/70155/68142.pdf

Caractérisation et diversité des mécanismes du syndrome de mortalité affectant les juvéniles de Crassostrea gigas
Provedor de dados: 5
Autores: Lucasson, Aude.
nfectious diseases are very often explored using reductionist approaches, despite repeated evidence showing them to be strongly influenced by numerous interacting host and environmental factors. Many diseases with complex etiology therefore remain misunderstood. In this thesis, by developing a holistic approach to tackle the complexity of the interaction, (i) we deciphered the complex intra-host interactions underlying the Pacific oyster mortality syndrome affecting juveniles of Crassostrea gigas, the main oyster species exploited worldwide and (ii) we validated this mechanism in different infectious environments and oyster genotypes. Using ecologically realistic experimental infections combined with thorough molecular (metabarcoding, transcriptomics,...
Tipo: Text
Palavras-chave: Maladie multifactorielle; Pathosystème; Huîtres; Transcriptome; Structure du microbiote; Séquençage haut débit; Microbiota structure; Ngs; Multifactorial diseases; Pathosystem; Oysters.
Ano: 2018
URL: https://archimer.ifremer.fr/doc/00498/60998/64415.pdf

GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas
Provedor de dados: 5
Autores: Riviere, Guillaume; Klopp, Christophe; Ibouniyamine, Nabihoudine; Huvet, Arnaud; Boudry, Pierre; Favrel, Pascal.
Background: The Pacific oyster, Crassostrea gigas, is one of the most important aquaculture shellfish resources worldwide. Important efforts have been undertaken towards a better knowledge of its genome and transcriptome, which makes now C. gigas becoming a model organism among lophotrochozoans, the under-described sister clade of ecdysozoans within protostomes. These massive sequencing efforts offer the opportunity to assemble gene expression data and make such resource accessible and exploitable for the scientific community. Therefore, we undertook this assembly into an up-to-date publicly available transcriptome database: the GigaTON (Gigas TranscriptOme pipeliNe) database. Description: We assembled 2204 million sequences obtained from 114 publicly...
Tipo: Text
Palavras-chave: Oyster; Transcriptome; Development; Stress; Tissues; NGS.
Ano: 2015
URL: https://archimer.ifremer.fr/doc/00302/41321/40520.pdf

Etude des interactions hôte/virus chez l’huître creuse Crassostrea gigas et son virus Ostreid herpesvirus 1
Provedor de dados: 5
Autores: Segarra, Amelie.
Ostreid herpesvirus type 1 (OsHV-1) can be considered one of the major infectious agents in Pacific oysters, Crassostrea gigas, in France and all around the world. Differences in terms of mortality among infected animals were reported suggesting a genetic basis of the susceptibility to the OsHV-1 infection. In this context, the main objective of this thesis was to understand the interactions between Pacific oysters and OsHV-1, in particular, the molecular basis of the viral cycle. Results showed that the virus is able to replicate in the host regardless of its stage of development or its susceptibility. However, multiplication kinetics is faster in the most susceptible individuals compared to less susceptible ones. After an active replication phase, it...
Tipo: Text
Palavras-chave: Bivalves; Huître creuse; Crassostrea gigas; Mortalités; OsHV-1; Gènes viruax; Interaction hôte-virus; Transcriptome; Sensibilité; PCR en temps réel; Bivalve; Pacific oyster; Crassostrea ggias; Mortality; OsHV-1; Viral gene; Interaction host-virus; Transcriptome; Susceptibility; Real-time PCR.
Ano: 2014
URL: http://archimer.ifremer.fr/doc/00252/36297/34826.pdf

Different secretory repertoires control the biomineralization processes of prism and nacre deposition of the pearl oyster shell
Provedor de dados: 5
Autores: Marie, Benjamin; Joubert, Caroline; Tayale, Alexandre; Zanella-cleon, Isabelle; Belliard, Corinne; Piquemal, David; Cochennec-laureau, Nathalie; Marin, Frederic; Gueguen, Yannick; Montagnani, Caroline.
Mollusca evolutionary success can be attributed partly to their efficiency to sustain and protect their soft body with an external biomineralized structure, the shell. Current knowledge of the protein set responsible for the formation of the shell microstructural polymorphism and unique properties remains largely patchy. In Pinctada margaritifera and Pinctada maxima, we identified 80 shell matrix proteins, among which 66 are entirely unique. This is the only description of the whole "biomineralization toolkit" of the matrices that, at least in part, is thought to regulate the formation of the prismatic and nacreous shell layers in the pearl oysters. We unambiguously demonstrate that prisms and nacre are assembled from very different protein repertoires....
Tipo: Text
Palavras-chave: Mantle; Mollusk shell matrix proteins; Proteome; Transcriptome; Evolution.
Ano: 2012
URL: http://archimer.ifremer.fr/doc/00118/22959/20922.pdf

Deep sequencing analysis of toad Rhinella schneideri skin glands and partial biochemical characterization of its cutaneous secretion
Provedor de dados: 80
Autores: Shibao,Priscila Yumi Tanaka; Cologna,Camila Takeno; Morandi-Filho,Romualdo; Wiezel,Gisele Adriano; Fujimura,Patricia Tiemi; Ueira-Vieira,Carlos; Arantes,Eliane Candiani.
Abstract  Background: Animal poisons and venoms are sources of biomolecules naturally selected. Rhinella schneideri toads are widespread in the whole Brazilian territory and they have poison glands and mucous gland. Recently, protein from toads’ secretion has gaining attention. Frog skin is widely known to present great number of host defense peptides and we hypothesize toads present them as well. In this study, we used a RNA-seq analysis from R. schneideri skin and biochemical tests with the gland secretion to unravel its protein molecules.  Methods: Total RNA from the toad skin was extracted using TRizol reagent, sequenced in duplicate using Illumina Hiseq2500 in paired end analysis. The raw reads were trimmed and de novo assembled using Trinity. The...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: RNA-seq; Rhinella schneideri; Toad secretion; Transcriptome; Illumina; Cutaneous secretion; Skin secretion; Toad protein.
Ano: 2018
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1678-91992018000100326

Non-coding RNAs in schistosomes: an unexplored world
Provedor de dados: 42
Autores: Oliveira,Katia C; Carvalho,Mariana L. P; Maracaja-Coutinho,Vinicius; Kitajima,João P; Verjovski-Almeida,Sergio.
Non-coding RNAs (ncRNAs) were recently given much higher attention due to technical advances in sequencing which expanded the characterization of transcriptomes in different organisms. ncRNAs have different lengths (22 nt to &gt;1, 000 nt) and mechanisms of action that essentially comprise a sophisticated gene expression regulation network. Recent publication of schistosome genomes and transcriptomes has increased the description and characterization of a large number of parasite genes. Here we review the number of predicted genes and the coverage of genomic bases in face of the public ESTs dataset available, including a critical appraisal of the evidence and characterization of ncRNAs in schistosomes. We show expression data for ncRNAs in Schistosoma...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Schistosoma mansoni; Non-coding RNAs; Gene expression profile; Genome; Transcriptome.
Ano: 2011
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0001-37652011000200026

De novo transcriptome assembly, functional annotation and differential gene expression analysis of juvenile and adult E. fetida, a model oligochaete used in ecotoxicological studies
Provedor de dados: 48
Autores: Thunders,Michelle; Cavanagh,Jo; Li,Yinsheng.
Abstract  Background  Earthworms are sensitive to toxic chemicals present in the soil and so are useful indicator organisms for soil health. Eisenia fetida are commonly used in ecotoxicological studies; therefore the assembly of a baseline transcriptome is important for subsequent analyses exploring the impact of toxin exposure on genome wide gene expression.  Results  This paper reports on the de novo transcriptome assembly of E. fetida using Trinity, a freely available software tool. Trinotate was used to carry out functional annotation of the Trinity generated transcriptome file and the transdecoder generated peptide sequence file along with BLASTX, BLASTP and HMMER searches and were loaded into a Sqlite3 database. To identify differentially expressed...
Tipo: Journal article
Palavras-chave: Earthworm; Trinity; Transcriptome; E. fetida; Ecotoxicology; RNA; Sequence; Gene expression.
Ano: 2017
URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602017000100401

The antioxidative defense system is involved in the premature senescence in transgenic tobacco (Nicotiana tabacum NC89)
Provedor de dados: 48
Autores: Liu,Yu; Wang,Lu; Liu,Heng; Zhao,Rongrong; Liu,Bin; Fu,Quanjuan; Zhang,Yuanhu.
BACKGROUND: &amp;#945;-Farnesene is a volatile sesquiterpene synthesized by the plant mevalonate (MVA) pathway through the action of &amp;#945;-farnesene synthase. The &amp;#945;-farnesene synthase 1 (MdAFS1) gene was isolated from apple peel (var. white winterpearmain), and transformed into tobacco (Nicotiana tabacum NC89). The transgenic plants had faster stem elongation during vegetative growth and earlier flowering than wild type (WT). Our studies focused on the transgenic tobacco phenotype. RESULTS: The levels of chlorophyll and soluble protein decreased and a lower seed biomass and reduced net photosynthetic rate (Pn) in transgenic plants. Reactive oxygen species (ROS) such as hydrogen peroxide (H2O2) and superoxide radicals (O2._) had higher levels...
Tipo: Journal article
Palavras-chave: Tobacco; Senescence; Transcriptome; Reactive oxygen species (ROS).
Ano: 2016
URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602016000100030

Production of DNA microarray and expression analysis of genes from Xylella fastidiosa in different culture media
Provedor de dados: 52
Autores: Travensolo,Regiane de Fátima; Costa,Maria Vitória Cecchette Gottardi; Carareto-Alves,Lucia Maria; Carrilho,Emanuel; Lemos,Eliana Gertrudes de Macedo.
DNA Microarray was developed to monitor the expression of many genes from Xylella fastidiosa, allowing the side by-side comparison of two situations in a single experiment. The experiments were performed using X. fastidiosa cells grown in two culture media: BCYE and XDM2. The primers were synthesized, spotted onto glass slides and the array was hybridized against fluorescently labeled cDNAs. The emitted signals were quantified, normalized and the data were statistically analyzed to verify the differentially expressed genes. According to the data, 104 genes were differentially expressed in XDM2 and 30 genes in BCYE media. The present study showed that DNA microarray technique efficiently differentiate the expressed genes under different conditions.
Tipo: Info:eu-repo/semantics/article
Palavras-chave: DNA Microarray; Xylella fastidiosa; Expression; Transcriptome.
Ano: 2009
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-89132009000300006

Transcriptomic differential lncRNA expression is involved in neuropathic pain in rat dorsal root ganglion after spared sciatic nerve injury
Provedor de dados: 56
Autores: Mao,P.; Li,C.R.; Zhang,S.Z.; Zhang,Y.; Liu,B.T.; Fan,B.F.
Dorsal root ganglia (DRG) neurons regenerate spontaneously after traumatic or surgical injury. Long noncoding RNAs (lncRNAs) are involved in various biological regulation processes. Conditions of lncRNAs in DRG neuron injury deserve to be further investigated. Transcriptomic analysis was performed by high-throughput Illumina HiSeq2500 sequencing to profile the differential genes in L4–L6 DRGs following rat sciatic nerve tying. A total of 1,228 genes were up-regulated and 1,415 down-regulated. By comparing to rat lncRNA database, 86 known and 26 novel lncRNA genes were found to be differential. The 86 known lncRNA genes modulated 866 target genes subject to gene ontology (GO) and KEGG enrichment analysis. The genes involved in the neurotransmitter status of...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Spared nerve injury; Neuropathic pain; Long noncoding RNA; Transcriptome; Hypm gene.
Ano: 2018
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2018001000601

High pressure-sensitive gene expression in Lactobacillus sanfranciscensis
Provedor de dados: 56
Autores: Vogel,R.F.; Pavlovic,M.; Hörmann,S.; Ehrmann,M.A.
Lactobacillus sanfranciscensis is a Gram-positive lactic acid bacterium used in food biotechnology. It is necessary to investigate many aspects of a model organism to elucidate mechanisms of stress response, to facilitate preparation, application and performance in food fermentation, to understand mechanisms of inactivation, and to identify novel tools for high pressure biotechnology. To investigate the mechanisms of the complex bacterial response to high pressure we have analyzed changes in the proteome and transcriptome by 2-D electrophoresis, and by microarrays and real time PCR, respectively. More than 16 proteins were found to be differentially expressed upon high pressure stress and were compared to those sensitive to other stresses. Except for one...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: High pressure; Lactobacillus sanfranciscensis; Proteome; Transcriptome; Stress response.
Ano: 2005
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2005000800013

Whole transcriptome organisation in the dehydrated supraoptic nucleus
Provedor de dados: 56
Autores: Hindmarch,C.C.T.; Franses,P.; Goodwin,B.; Murphy,D.
The supraoptic nucleus (SON) is part of the central osmotic circuitry that synthesises the hormone vasopressin (Avp) and transports it to terminals in the posterior lobe of the pituitary. Following osmotic stress such as dehydration, this tissue undergoes morphological, electrical and transcriptional changes to facilitate the appropriate regulation and release of Avp into the circulation where it conserves water at the level of the kidney. Here, the organisation of the whole transcriptome following dehydration is modelled to fit Zipf's law, a natural power law that holds true for all natural languages, that states if the frequency of word usage is plotted against its rank, then the log linear regression of this is -1. We have applied this model to our...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Transcriptome; Supraoptic nucleus; Dehydration; Zipf; Microarray; Vasopressin.
Ano: 2013
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2013001201000

Brazilian coffee genome project: an EST-based genomic resource
Provedor de dados: 61
Autores: Vieira,Luiz Gonzaga Esteves; Andrade,Alan Carvalho; Colombo,Carlos Augusto; Moraes,Ana Heloneida de Araújo; Metha,Ângela; Oliveira,Angélica Carvalho de; Labate,Carlos Alberto; Marino,Celso Luis; Monteiro-Vitorello,Claúdia de Barros; Monte,Damares de Castro; Giglioti,Éder; Kimura,Edna Teruko; Romano,Eduardo; Kuramae,Eiko Eurya; Lemos,Eliana Gertrudes Macedo; Almeida,Elionor Rita Pereira de; Jorge,Érika C.; Albuquerque,Érika V. S.; Silva,Felipe Rodrigues da; Vinecky,Felipe; Sawazaki,Haiko Enok; Dorry,Hamza Fahmi A.; Carrer,Helaine; Abreu,Ilka Nacif; Batista,João A. N.; Teixeira,João Batista; Kitajima,João Paulo; Xavier,Karem Guimarães; Lima,Liziane Maria de; Camargo,Luis Eduardo Aranha de; Pereira,Luiz Filipe Protasio; Coutinho,Luiz Lehmann; Lemos,Manoel Victor Franco; Romano,Marcelo Ribeiro; Machado,Marcos Antonio; Costa,Marcos Mota do Carmo; Sá,Maria Fátima Grossi de; Goldman,Maria Helena S.; Ferro,Maria Inês T.; Tinoco,Maria Laine Penha; Oliveira,Mariana C.; Van Sluys,Marie-Anne; Shimizu,Milton Massao; Maluf,Mirian Perez; Eira,Mirian Therezinha Souza da; Guerreiro Filho,Oliveiro; Arruda,Paulo; Mazzafera,Paulo; Mariani,Pilar Drummond Sampaio Correa; Oliveira,Regina L.B.C. de; Harakava,Ricardo; Balbao,Silvia Filippi; Tsai,Siu Mui; Mauro,Sonia Marli Zingaretti di; Santos,Suzana Neiva; Siqueira,Walter José; Costa,Gustavo Gilson Lacerda; Formighieri,Eduardo Fernandes; Carazzolle,Marcelo Falsarella; Pereira,Gonçalo Amarante Guimarães.
Coffee is one of the most valuable agricultural commodities and ranks second on international trade exchanges. The genus Coffea belongs to the Rubiaceae family which includes other important plants. The genus contains about 100 species but commercial production is based only on two species, Coffea arabica and Coffea canephora that represent about 70 % and 30 % of the total coffee market, respectively. The Brazilian Coffee Genome Project was designed with the objective of making modern genomics resources available to the coffee scientific community, working on different aspects of the coffee production chain. We have single-pass sequenced a total of 214,964 randomly picked clones from 37 cDNA libraries of C. arabica, C. canephora and C. racemosa,...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Coffea; CDNA; EST; Transcriptome.
Ano: 2006
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1677-04202006000100008

Transcriptome analysis for the restrained stem development of the wheat mutant dms
Provedor de dados: 65
Autores: He,Ruishi; Zhu,Xinxin; Li,Qiaoyun; Jiang,Yumei; Yu,Dongyan; Sun,Yulong; Liang,Xiaolong; Ni,Yongjing; Niu,Jishan.
ABSTRACT: Wheat (Triticum aestivum L.) stem development significantly affects grain yield. The dwarf plants (D) of wheat mutant dms was less than 30cm. Here, we were to explore the molecular basis for the restrained stem development of the dwarf plants. The results were reached by compare the young spikes and stems transcriptomes of the tall (T) and D plants of mutant dms. We identified 663 genes highly expressed in stem tips. We identified 997 differentially expressed genes (DEGs) in stem tips between T and D, 403 DEGs were significantly related with stem development. Most biological processes in stem tips on dwarf plants were significantly suppressed, such as phytohormone signaling etc. The sequencing analysis results were confirmed by quantitatively...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Wheat (Triticum aestivum L.); Dms mutant; Transcriptome; Stem development.
Ano: 2017
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0103-84782017001200401

Transcriptomic analysis of differential gene expression reveals an increase in COX2 levels during in vitro canine herpesvirus infection
Provedor de dados: 65
Autores: Kurissio,Jacqueline Kazue; Araújo Júnior,João Pessoa.
ABSTRACT: Canine herpesvirus (CaHV-1) affects canids worldwide, causing death in neonates and immunosuppressed hosts. Acute infection by CaHV-1 can cause reproductive, respiratory, and neurological problems in adult animals. Viral pathogenesis and host genes expressions during of CaHV-1infection are not clearly understood. In the present study, the transcriptome of canine kidney cell Mardin-Darby (MDCK) infected in vitro with canine herpesvirus was explored. For this, RNA sequencing (RNA-seq) of the samples in different moments during infection was carried out. Subsequently, the transcriptomic analysis genes related to cell activities and process involved to viral cycle infection were evaluated until 32h post-inoculation (pi). Among evaluated genes, was...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Transcriptome; Herpesvirus; CaHV-1; PTGS2; COX2; Canine pathogen.
Ano: 2018
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0103-84782018001000451