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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: https://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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Brazilian coffee genome project: an EST-based genomic resource Braz. J. Plant Physiol.
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
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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 analysis of Tibetan medicinal plant Dysphania schraderiana Genet. Mol. Biol.
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
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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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Deep sequencing analysis of toad Rhinella schneideri skin glands and partial biochemical characterization of its cutaneous secretion J. Venom. Anim. Toxins incl. Trop. Dis.
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
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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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Gene expression in the salivary gland of Rhipicephalus (Boophilus) microplus fed on tick-susceptible and tick-resistant hosts. Repositório Alice
GIACHETTO, P. F.; CUNHA, R. C.; NHANI JUNIOR, A.; GARCIA, M. V.; FERRO, J. A.; ANDREOTTI, R..
The success of cattle tick fixation largely depends on the secretion of substances that alter the immune response of the host. The majority of these substances are expressed by the parasite salivary gland and secreted in tick saliva. It is known that hosts can mount immune responses against ticks and bovine European breeds, and bovine industrial crossbreeds are more susceptible to infestations than are Bos indicus cattle. To identify candidates for the development of novel control strategies for the cattle tick Rhipicephalus (Boophilus) microplus, a salivary gland transcriptome analysis of engorged females fed on susceptible or resistant hosts was performed. Using RNA-Seq, transcriptomes were de novo assembled and produced a total of 235,451 contigs with...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Bioinformática; Expressão gênica; RNA-Seq; Cattle tick; Host-parasite interaction; Gado de Corte; Carrapato; Sialome; Transcriptome; Cattle; Bioinformatics; Rhipicephalus microplus.
Ano: 2020 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1124241
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Gene Expression in the Salivary Gland of Rhipicephalus (Boophilus) microplus Fed on Tick-Susceptible and Tick-Resistant Hosts. Repositório Alice
GIACHETTO, P. F.; CUNHA, R. C.; NHANI JUNIOR, A.; GARCIA, M. V.; FERRO, J. A.; ANDREOTTI, R..
The success of cattle tick fixation largely depends on the secretion of substances that alter the immune response of the host. The majority of these substances are expressed by the parasite salivary gland and secreted in tick saliva. It is known that hosts can mount immune responses against ticks and bovine European breeds, and bovine industrial crossbreeds are more susceptible to infestations than are Bos indicus cattle. To identify candidates for the development of novel control strategies for the cattle tick Rhipicephalus (Boophilus) microplus, a salivary gland transcriptome analysis of engorged females fed on susceptible or resistant hosts was performed. Using RNA-Seq, transcriptomes were de novo assembled and produced a total of 235,451 contigs with...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: RNA-Seq; Cattle tick; Host-parasite interaction; Sialome; Transcriptome; Cattle.
Ano: 2020 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1119455
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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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