SABIIA - Sistema Aberto e Integrado de Informação em Agricultura (Sabiia)

Piórkowska,Katarzyna; Żukowski,Kacper; Ropka-Molik,Katarzyna; Tyra,Mirosław; Gurgul,Artur.

Abstract Pork is the most popular meat in the world. Unfortunately, the selection pressure focused on high meat content led to a reduction in pork quality. The present study used RNA-seq technology to identify metabolic process genes related to pork quality traits and fat deposition. Differentially expressed genes (DEGs) were identified between pigs of Pulawska and Polish Landrace breeds for two the most important muscles (semimembranosus and longissimus dorsi). A total of 71 significant DEGs were reported: 15 for longissimus dorsi and 56 for semimembranosus muscles. The genes overexpressed in Pulawska pigs were involved in lipid metabolism (APOD, LXRA, LIPE, AP2B1, ENSSSCG00000028753 and OAS2) and proteolysis (CST6, CTSD, ISG15 and UCHL1). In Polish...

An integrated analysis of mRNA and sRNA transcriptional profiles in Coffea arabica L. roots: insights on nitrogen starvation responses.

Palavras-chave: RNA-seq; Firmness; Fat content; Polish pigs.

Ano: 2018

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572018000100125

BASiNET - Biological Sequences NETwork: a case study on coding and non-coding RNAs identification.

SANTOS, T. B. dos; SOARES, J. D. M.; LIMA, J. E.; SILVA, J. C.; IVAMOTO, S. T.; BABA, V. Y.; SOUZA, S. G. H.; LORENZETTI, A. P. R.; PASCHOAL, A. R.; MEDA, A. R.; NISHIYAMA JÚNIOR, M. Y.; OLIVEIRA, U. C. de; MOKOCHINSKI, J. B.; GUYOT, R.; JUNQUEIRA-DE-AZEVEDO, I. L. M.; FIGUEIR, A. V. O.; MAZZAFERA, P.; R. JÚNIO, O.; VIEIRA, L. G. E.; PEREIRA, L. F. P.; DOMINGUES, D. S..

Coffea arabica L. is an important agricultural commodity, accounting for 60% of traded coffee worldwide. Nitrogen (N) is a macronutrient that is usually limiting to plant yield; however, molecular mechanisms of plant acclimation to N limitation remain largely unknown in tropical woody crops. In this study, we investigated the transcriptome of coffee roots under N starvation, analyzing poly-A+ libraries and small RNAs. We also evaluated the concentration of selected amino acids and N-source preferences in roots. Ammonium was preferentially taken up over nitrate, and asparagine and glutamate were the most abundant amino acids observed in coffee roots.We obtained 34,654 assembled contigs by mRNA sequencing, and validated the transcriptional profile of 12...

Tipo: Artigo em periódico indexado (ALICE)

Palavras-chave: Nitrogen transport; Differential gene expression; RNA-seq; MicroRNA.

Ano: 2019

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1108713

Deep sequencing analysis of toad Rhinella schneideri skin glands and partial biochemical characterization of its cutaneous secretion

ITO, E. A.; KATAHIRA, I.; VICENTE, F. F. da R.; PEREIRA, L. F. P.; LOPES, F. M..

With the emergence of Next Generation Sequencing (NGS) technologies, a large volume of sequence data in particular de novo sequencing was rapidly produced at relatively low costs. In this context, computational tools are increasingly important to assist in the identification of relevant information to understand the functioning of organisms. This work introduces BASiNET, an alignment-free tool for classifying biological sequences based on the feature extraction from complex network measurements. The method initially transform the sequences and represents them as complex networks. Then it extracts topological measures and constructs a feature vector that is used to classify the sequences. The method was evaluated in the classification of coding and...

Tipo: Artigo em periódico indexado (ALICE)

Palavras-chave: RNA-seq; Neurodegenerative diseases; Cardiovascular diseases; Epigenetics; Nucleotides.

Ano: 2018

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1108754

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...

Etude des facteurs de transcription impliqués dans l’accumulation lipidique en condition de stress azoté chez la microalgue haptophyte Isochrysis affinis galbana

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

ArchiMer

Thiriet-rupert, Stanislas.

In every organism, evolution and acclimation to environmental changes are orchestrated by numerous molecular players. Among them, transcription factors (TFs) play a crucial role by regulating gene expression. Therefore, identify TFs involved in the production of high value products is a significant step in a biotechnological context. The laboratory has at its disposal a mutant strain of the haptophyte microalga Tisochrysis lutea producing twice more storage lipids than the wild type strain when exposed to nitrogen deprivation. Given the key role of TFs in phenotype establishment, this PhD aim at identify the TFs involved in that of the mutant phenotype of T. lutea. A TFs identification and classification pipeline was elaborated and applied to T. lutea’s...

Tipo: Text

Palavras-chave: Bioinformatique; Biologie moléculaire; Évolution; Facteur de transcription; Micro-algue; Réseau de gènes; RNA-seq; Bioinformatic; Evolution; Gene network; Molecular biology; Microalgae; RNAseq; Transcription factor.

Ano: 2017

URL: http://archimer.ifremer.fr/doc/00371/48233/48368.pdf

Expressão diferencial de genes associados à degradação enzimática e destoxificação da torta de pinhão-manso em Pleurotus pulmonarius.

Genes diferencialmente expressos no músculo Longissimus dorsi de novilhos nelore divergentes para eficiência bruta.

GOMES, T. G..

A biodestoxificação da torta de pinhão-manso oferece vantagens sobre outros métodos de destoxificação em termos de eficiência, custo e potencial para desenvolvimento de produtos secundários. No entanto, apesar de todas essas vantagens ainda não foi elucidado o mecanismo envolvido (genes, proteínas e vias metabólicas) nesse processo de biodegradação dos EFs por micro-organismo. No cenário de biodestoxificação, o macro-basidiomiceto Pleurotus pulmonarius EF-88 degrada com eficiência esse composto e ainda produzir cogumelos comercialmente viáveis. O presente estudo foi conduzido com a finalidade de identificar genes e mecanismos celulares envolvidos no processo de destoxificação dantorta de pinhão-manso. E para isso, ferramentas transcritômicas (RNA-seq) e...

Tipo: Tese/dissertação (ALICE)

Palavras-chave: Basidiomiceto; Éster de forbol; RNA-seq; Metaloprotease; Hidrofobina.

Ano: 2019

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1120440

SILVA, J. V. da; TIZIOTO, P. C.; OLIVEIRA, P. S. N. de; AFONSO, J.; DINIZ, W. J. da S.; LIMA, A. O. de; SOUZA, M. M. de; ROCHA, M. I. P.; BUSS, C. E.; COUTINHO, L. L.; REGITANO, L. C. de A..

2016

Genes expressos conservados em genótipos de arroz tolerante e suscetível à seca.

Palavras-chave: RNA-seq; Bos indicus; Eficiência alimentar.

Ano: 2016

URL: http://www.alice.cnptia.embrapa.br/handle/doc/1054252

GOMES, M.; SILVEIRA, R.; LANNA, A. C.; VIANELLO, R. P.; MENDONÇA, J. A.; BRONDANI, C..

O objetivo desse trabalho foi identificar genes diferencialmente expressos (GDEs) envolvidos na tolerância à seca de duas cultivares de arroz de terras altas da subespécie Japônica, a Douradão, tolerante, e Primavera, suscetível.

Identificação e caracterização de microssatélites de Coffea arabica a partir de dados de sequenciamento de RNA e de BACS.

Palavras-chave: Transcriptoma; Rotas metabólicas; RNA-seq; Arroz; Oryza sativa; Melhoramento genético vegetal; Resistência a seca.

Ano: 2017

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1078895

Identification of LincRNA from Dermatophagoides farinae (Acari: Pyroglyphidae) for Potential Allergen-Related Targets

SILVA, B. S. R. da; CAÇÃO, S. B.; IVAMOTO, S. T.; SILVA, J. C.; DOMINGUES, D. S.; PEREIRA, L. F. P..

O café é uma das principais commodities agrícolas mundiais, sendo consumido regularmente por 40% de toda população. As espécies, Coffea arabica L. e Coffea canephora P. são as de maior importância respondendo por 65% e 35% da produção mundial, respectivamente. Em C. arabica , o desenvolvimento de novas cultivares é demorado, podendo levar mais de 20 anos para finalização dos trabalhos. Além disso, estreita base genética de C. arabica dificulta a obtenção de cultivares resistentes a várias pragas e doenças, assim como uma maior tolerância a estresses abióticos. A utilização de marcadores moleculares para análise da diversidade e seleção de genótipos representa uma importante ferramenta para auxiliar o melhoramento e tentar diminuir esses problemas. Neste...

Tipo: Artigo em anais de congresso (ALICE)

Palavras-chave: Marcador SSR; Análise in silico; RNA-seq; Cromossomo artificial de bactéria.

Ano: 2013

URL: http://www.alice.cnptia.embrapa.br/handle/doc/975072

Zhou,Ying; Wu,Meili; Zhu,Hanting; Shao,Junjie; Liu,Chang; Cui,Yubao.

Abstract Long noncoding RNAs (lncRNAs), especially their important subclass of long intergenic noncoding RNAs (lincRNAs), have been identified in some insects. They play important roles in the regulation of biological processes, such as immune response or cell differentiation and as possible evolutionary precursors for protein coding genes. House dust mites (HDMs) are recognized as allergenic mites because allergens are found in their feces and bodies. Dermatophagoides farinae is one of the most important pyroglyphid mites because of its abundance in the household. To determine if lincRNAs can regulate allergen presentation in HDMs, we analyzed RNA-seq data for HDMs. We identified 11 lincRNAs that are related to mRNAs coding for allergens in HDMs. Using...

Identification of potential target genes of USP22 via ChIP-seq and RNA-seq analysis in HeLa cells

Palavras-chave: House dust mites (HDMs); Dermatophagoides farinae; Long noncoding RNAs (lncRNAs); Allergen; RNA-seq.

Ano: 2020

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572020000100804

Gong,Zhen; Liu,Jianyun; Xie,Xin; Xu,Xiaoyuan; Wu,Ping; Li,Huimin; Wang,Yaqin; Li,Weidong; Xiong,Jianjun.

Abstract The ubiquitin-specific protease 22 (USP22) is an oncogene and its expression is upregulated in many types of cancer. In the nucleus, USP22 functions as one subunit of the SAGA to regulate gene transcription. However, the genome-wide USP22 binding sites and its direct target genes are yet clear. In this study, we characterized the potential genomic binding sites of UPS22 and GCN5 by ChIP-seq using specific antibodies in HeLa cells. There were 408 overlapping putative target genes bound by both USP22 and GCN5. Motif analysis showed that the sequences bound by USP22 and GCN5 shared two common motifs. Gene ontology (GO) and pathway analysis indicated that the genes targeted by USP22 and GCN5 were involved in different physiological processes and...

Network analysis of ABA-dependent and ABA-independent drought responsive genes in Arabidopsis thaliana

Palavras-chave: USP22; Target genes; ChIP-seq; Knockdown; RNA-seq.

Ano: 2018

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572018000300488

Liu,Shiwei; Lv,Zongyou; Liu,Yihui; Li,Ling; Zhang,Lida.

Abstract Drought is one of the most severe abiotic factors restricting plant growth and yield. Numerous genes functioning in drought response are regulated by abscisic acid (ABA) dependent and independent pathways, but knowledge of interplay between the two pathways is still limited. Here, we integrated transcriptome sequencing and network analyses to explore interplays between ABA-dependent and ABA-independent pathways responding to drought stress in Arabidopsis thaliana. We identified 211 ABA-dependent differentially expressed genes (DEGs) and 1,118 ABA-independent DEGs under drought stress. Functional analysis showed that ABA-dependent DEGs were significantly enriched in expected biological processes in response to water deprivation and ABA stimulus,...

Optimized Exon-Exon Junction Library and its Application on Rodents' Brain Transcriptome Analysis

Palavras-chave: Drought stress; Abscisic acid; RNA-seq; Gene expression; Protein-protein interaction network; Arabidopsis thaliana.

Ano: 2018

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572018000400624

BABT

Dou,Tong-Hai; Gao,Yuan; Chen,Cheng-Wen; Xu,Min-Jie; Fu,Mao-Bin; Zhang,Liang; Zhou,Yan.

ABSTRACT Background: Alternative splicing (AS), which plays an important role in gene expression and functional regulation, has been analyzed on genome-scale by various bioinformatic approaches based on RNA-seq data. Compared with the huge number of studies on mouse, the AS researches approaching the rat, whose genome is intermedia between mouse and human, were still limited. To enrich the knowledge on AS events in rodents' brain, we perfomed a comprehensive analysis on four transcriptome libraries (mouse cerebrum, mouse cerebellum, rat cerebrum, and rat cerebellum), recruiting high-throughput sequencing technology. An optimized exon-exon junction library approach was introduced to adapt the longer RNA-seq reads and to improve mapping efficiency....

RNA-seq analysis of Eucalyptus genotypes that differ in carbon allocation.

Palavras-chave: RNA-seq; Exon-exon junction; Alternative splicing; Cerebrum; Cerebellum.

Ano: 2017

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-89132017000100400

GERHARDT, I. R.; GIACHETTO, P. F.; YAMAGISHI, M. E. B.; LOBO, F. P.; PENCHEL, R. M.; MISSIAGGIA, A. A.; ZERLOTINI, A.; SILVA, F. R. da.

2012

RNA-Seq Analysis of Eucalyptus Genotypes that Differ in Carbon Allocation.

Palavras-chave: Eucalyptus; Alocação de carbono; RNA-seq.

Ano: 2012

URL: http://www.alice.cnptia.embrapa.br/handle/doc/943662

GERHARDT, I. R.; GIACHETTO, P. F.; YAMAGISHI, M. E. B.; LOBO, F. P.; PENCHEL, R. M.; MISSIAGGIA, A. A.; ZERTOLINI, A.; SILVA, F. R. da.

2012

RNA-seq analysis of the Rhizobium tropici CIAT 899 Transcripitome shows similarites in the activation patterns of symbiotic genes in the presence of apigenin and salt.

Palavras-chave: Eucalyptus; Alocação de carbono; RNA-seq.

Ano: 2012

URL: http://www.alice.cnptia.embrapa.br/handle/doc/943656

PÉREZ-MONTAÑO, F.; CERRO, P. del; JIMÉNEZ-GUERRERO, I.; LÓPEZ-BAENA, F. J.; CUBO, M. T.; HUNGRIA, M.; MEGÍAS, M.; OLLERO, F. J..

Rhizobium tropici strain CIAT 899 establishes effective symbioses with several legume species, including Phaseolus vulgaris and Leucaena leucocephala. This bacterium synthesizes a large variety of nodulation factors in response to nod-gene inducing flavonoids and, surprisingly, also under salt stress conditions. The aim of this study was to identify differentially expressed genes in the presence of both inducer molecules, and analyze the promoter regions located upstream of these genes. Results obtained by RNA-seq analyses of CIAT 899 induced with apigenin, a nod gene-inducing flavonoid for this strain, or salt allowed the identification of 19 and 790 differentially expressed genes, respectively. Fifteen of these genes were up-regulated in both conditions...

Tracing key genes associated with the Pinctada margaritifera albino phenotype from juvenile to cultured pearl harvest stages using multiple whole transcriptome sequencing

Palavras-chave: RNA-seq; Nod factors; Lipochitooligosaccharides; Nodulação; Rhizobium; Rhizobium tropici; Nodutlation; Apigenin; Salt stress.

Ano: 2016

URL: http://www.alice.cnptia.embrapa.br/handle/doc/1041600

ArchiMer

Auffret, Pauline; Le Luyer, Jeremy; Sham Koua, Manaarii; Quillien, Virgile; Ky, Chin-long.

Background Albino mutations are commonly observed in the animal kingdom, including in bivalves. In the black-lipped pearl oyster Pinctada margaritifera, albino specimens are characterized by total or partial absence of colouration resulting in typical white shell phenotype expression. The relationship of shell colour with resulting cultured pearl colour is of great economic interest in P. margaritifera, on which a pearl industry is based. Hence, the albino phenotype provides a useful way to examine the molecular mechanisms underlying pigmentation. Results Whole transcriptome RNA-sequencing analysis comparing albino and black wild-type phenotypes at three stages over the culture cycle of P. margaritifera revealed a total of 1606, 798 and 187 differentially...

Tipo: Text

Palavras-chave: Pinctada margaritifera; Albinism; Pigmentation; RNA-seq; Notch signaling pathway; Tyrosinase; Biomineralization.

Ano: 2020

URL: https://archimer.ifremer.fr/doc/00652/76420/77477.pdf

Transcriptoma do cafeeiro (Coffea arabica L.) na interação com Hemileia vastatrix Berk. & BR.

FLOREZ, J. C.; CAIXETA, E. T.; FREITAS, R. do L.; MOFATO, L. S.; FALSARELLA CARAZZOLE, M.; ZAMBOLIM, L..

Os estudos de transcriptoma revelam a expressão de determinados genes na célula em uma condição biológica específica. Em um patossistema, entender a expressão gênica é essencial para a identificação dos genes relacionados com os mecanismos de defesa e resistência da planta, que são ativados pela presença do patógeno, bem como dos genes de patogenicidade do microrganismo. Para estudar o transcriptoma de um organismo, o método que tem sido utilizado é o sequenciamento de nova geração de mRNA, denominado RNA-seq. Esta abordagem permite monitorar a expressão de genes dos dois organismos em diferentes etapas ao longo do processo infeccioso. Desta forma, o objetivo deste trabalho foi estudar o transcriptoma do cafeeiro durante a interação com Hemileia vastatrix,...

Transcriptoma para seca revela novos genes para o germoplasma do feijão comum mesoamericano.

Palavras-chave: Ferrugem do cafeeiro; Sequenciamento de nova geração; RNA-seq; Ferrugem; Café; Variedade resistente.

Ano: 2015

URL: http://www.alice.cnptia.embrapa.br/handle/doc/1041487

PEREIRA, W. J.; ABREU, F. R. M.; MELO, A. T. de O.; COELHO, A. S. G.; RODRIGUES, F. A.; MAMIDI, S.; ALENCAR, S. A. de; LANNA, A. C.; VALDISSER, P. A. M. R.; BRONDANI, C.; NASCIMENTO JUNIOR, I. R. do; BORBA, T. C. de O.; VIANELLO, R. P..

Este estudo foi realizado com o objetivo de promover uma ampla caracterização de genes do feijoeiro comum relacionados à seca.