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Registros recuperados: 31
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Additive transcriptomic variation associated with reproductive traits suggest local adaptation in a recently settled population of the Pacific oyster, Crassostrea gigas ArchiMer
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: http://archimer.ifremer.fr/doc/00287/39829/38343.pdf
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Análise do transcriptoma de arroz (Oryza sativa) cultivado sob déficit hídrico. Repositório Alice
SILVEIRA, R. D. D.; VIANELLO, R. P.; LANNA, A. C.; BRONDANI, C.; CARNEIRO, N. P..
2013
Tipo: Artigo em anais de congresso (ALICE) Palavras-chave: Gene; Genética vegetal; Plant genetics; Plant-water relations; Transcriptome.
Ano: 2013 URL: http://www.alice.cnptia.embrapa.br/handle/doc/974343
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Analysis of the leaf transcriptome of Musa acuminata during interaction with Mycosphaerella musicola: gene assembly, annotation and marker development. Repositório Alice
PASSOS, M. A. N.; CRUZ, V. O. de; EMEDIATO, F. L.; TEIXEIRA, C. C. de; AZEVEDO, V. C. R.; BRASILEIRO, A. C. M.; AMORIM, E. P.; FERREIRA, C. F.; MARTINS, N. F.; TOGAWA, R. C.; PAPPAS JÚNIOR, G. J.; SILVA JUNIOR, O. B. da; MILLER, R. T N. G..
Background: Although banana (Musa sp.) is an important edible crop, contributing towards poverty alleviation and food security, limited transcriptome datasets are available for use in accelerated molecular-based breeding in this genus. 454 GS-FLX Titanium technology was employed to determine the sequence of gene transcripts in genotypes of Musa acuminata ssp. burmannicoides Calcutta 4 and M. acuminata subgroup Cavendish cv. Grande Naine, contrasting in resistance to the fungal pathogen Mycosphaerella musicola, causal organism of Sigatoka leaf spot disease. To enrich for transcripts under biotic stress responses, full length-enriched cDNA libraries were prepared from whole plant leaf materials, both uninfected and artificially challenged with pathogen...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Banana; Fungo; Musa Acuminata; Mycosphaerella Musicola; Transcriptome; Microsatellite repeats.
Ano: 2013 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/964212
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Analysis of the transcriptome in Aspergillus tamarii during enzymatic degradation of sugarcane bagasse. Repositório Alice
MIDORIKAWA, G. E. O.; CORREA, C. L.; NORONHA, E. F.; FERREIRA FILHO, E. X.; TOGAWA, R. C.; COSTA, M. M. do C.; SILVA JUNIOR, O. B. da; GRYNBERG, P.; MILLER, R. N. G..
bitstream/item/183671/1/Midorikawa-et-al-2018-Frontiers-in-Bioengineering-and-Biotechnology.pdf
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Carbohydrate-active enzymes; XlnR; Sugar transporters; ClrA; Aspergillus tamarii; Transcriptome; Lignocellulose; Bioethanol.
Ano: 2018 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1096563
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Caractérisation et diversité des mécanismes du syndrome de mortalité affectant les juvéniles de Crassostrea gigas ArchiMer
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
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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 ArchiMer
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
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De novo transcriptome assembly, functional annotation and differential gene expression analysis of juvenile and adult E. fetida, a model oligochaete used in ecotoxicological studies Biol. Res.
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
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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 ArchiMer
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
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Different secretory repertoires control the biomineralization processes of prism and nacre deposition of the pearl oyster shell ArchiMer
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
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Differential gene expression after total replacement of dietary fish meal and fish oil by plant products in rainbow trout (Oncorhynchus mykiss) liver ArchiMer
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
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Distinct transcriptional networks control environment sensing and development in wild and cultivated grapevine genotypes. Repositório Alice
BOSCO, D. D.; FERNANDO, J. A.; MAZZAFERA, P.; MAIA, J. D. G.; RITSCHEL, P. S.; QUECINI, V..
2015
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Genetic diversity; Light; Temperature; Transcriptome; Vitis.
Ano: 2015 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1036605
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Etude des interactions hôte/virus chez l’huître creuse Crassostrea gigas et son virus Ostreid herpesvirus 1 ArchiMer
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
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Gene expression analysis in Musa acuminata during compatible interactions with Meloidogyne incognita. Repositório Alice
CASTAÑEDA, N. E. N.; ALVES, G. S. C.; ALMEIDA, R. M.; AMORIM, E. P.; FERREIRA, C. F.; TOGAWA, R. C.; COSTA, M. M. do C.; GRYNBERG, P.; SANTOS, J. R. P.; CARES, J. E.; MILLER, R. N. G..
Background and Aims: Endoparasitic root-knot nematodes (RKNs) ( Meloidogyne spp.) cause considerable losses in banana ( Musa spp.), with Meloidogyne incognita a predominant species in Cavendish sub-group bananas. This study investigates the root transcriptome in Musa acuminata genotypes 4297-06 (AA) and Cavendish Grande Naine (CAV; AAA) during early compatible interactions with M. incognita . Methods: Roots were analysed by brightfield light microscopy over a 35 d period to examine nematode penetration and morphological cell transformation. RNA samples were extracted 3, 7 and 10 days after inoculation (DAI) with nematode J2 juveniles, and cDNA libraries were sequenced using lllumina HiSeq technology. Sequences were mapped to the M. acuminata ssp....
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Musa acuminata; Meloidogyne incognita; Root-knot nematode; Biotic stress; Transcriptome; Monocotyledons.
Ano: 2017 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1076414
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Gene expression analysis in Musa acuminata during compatible interactions with Meloidogyne incognita. Repositório Alice
CASTAÑEDA, N. E. N.; ALVES, G. S. C.; ALMEIDA, R. M.; AMORIM, E. P.; FERREIRA, C. F.; TOGAWA, R. C.; COSTA, M. M. do C.; GRYNBERG, P.; SANTOS, J. R. P.; CARES, J. E.; MILLER, R. N. G..
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Musa acuminata; Meloidogyne incognita; Root-knot nematode; Biotic stress; Transcriptome; Monocotyledons.
Ano: 2017 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1074046
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Genome sequencing of thermofilic fungus Humicola grisea var. thermoidea and effect of pH in sugarcane biomass transformation. Repositório Alice
STEINDORFF, A. S.; FORMIGHIERI, E. F.; FARIA, F. P. de.; POÇAS-FONSECA, M. J.; ALMEIDA, J. R. M. de.
Tipo: Artigo em anais de congresso (ALICE) Palavras-chave: Humicola grisea; Transcriptome; Genome sequencing; Sugarcane bagasse pH.
Ano: 2017 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1075990
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GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas ArchiMer
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: http://archimer.ifremer.fr/doc/00302/41321/40520.pdf
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Gonad transcriptome analysis of pearl oyster Pinctada margaritifera: identification of potential sex differentiation and sex determining genes ArchiMer
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
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High throughput transcriptome analysis of coffee reveals prehaustorial resistance in response to Hemileia vastatrix infection. Repositório Alice
FLORES, J. C.; MOFATTO, L. S.; FREITAS-LOPES, R. do L.; FERREIRA, S. S.; ZAMBOLIM, E. M.; CARAZZOLLE, M. F.; ZAMBOLIM, L.; CAIXETA, E. T..
Coffee rust disease, caused by the fungus Hemileia vastatrix, is one of the major diseases in coffee throughout the world. The use of resistant cultivars is considered to be the most effective control strategy for this disease. To identify candidate genes related to different mechanism defense in coffee, we present a time-course comparative gene expression profile of Caturra (susceptible) and Híbrido de Timor (HdT, resistant) in response to H. vastatrix race XXXIII infection. The main objectives were to obtain a global overview of transcriptome in both interaction, compatible and incompatible, and, specially, analyze up-regulated HdT specific genes with inducible resistant and defense signaling pathways. Using both Coffea canephora as a reference genome...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Coffee rust; Biotrophic interaction; Transcriptome; Disease resistance.
Ano: 2017 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1082688
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Identification and expression profile of odorant-binding proteins in Halyomorpha halys (Hemiptera: Pentatomidae). Repositório Alice
PAULA, D. P.; TOGAWA, R. C.; COSTA, M. M. C.; GRYNBERG, P.; MARTINS, N. F.; ANDOW, D. A..
2016
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Brown marmorated stink bug; Chemoreception; RNA-Seq; Semiochemicals; Transcriptome.
Ano: 2016 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1055555
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Identification of Hypoxia-Regulated Genes in the Liver of Common Sole (Solea solea ) Fed Different Dietary Lipid Contents ArchiMer
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
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