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

PROTASIO, A. V.; TSAI, I. J.; BABBAGE, A.; NICHOL, S.; HUNT, M.; ASLETT, M. A.; SILVA, N. de; VELARDE, G. S.; ANDERSON, T. J. C.; CLARK, R. C.; DAVIDSON, C.; DILLON, G. P.; HOLROYD, N. E.; LOVERDE, P. T.; LLOYD, C.; MCQUILLAN, J.; OLIVEIRA, G.; OTTO, T. D.; PARKER-MANUEL, S. J.; QUAIL, M. A.; WILSON, R. A.; ZERLOTINI, A.; DUNNE, D. W.; BERRIMAN, M..

Schistosomiasis is one of the most prevalent parasitic diseases, affecting millions of people in developing countries. Amongst the human-infective species, Schistosoma mansoni is also the most commonly used in the laboratory and here we present the systematic improvement of its draft genome. We used Sanger capillary and deep-coverage Illumina sequencing from clonal worms to upgrade the highly fragmented draft 380 Mb genome to one with only 885 scaffolds and more than 81% of the bases organised into chromosomes. We have also used transcriptome sequencing (RNA-seq) from four time points in the parasite?s life cycle to refine gene predictions and profile their expression. More than 45% of predicted genes have been extensively modified and the total number has...

Allele specific expression analysis in bovine muscle tissue.

Palavras-chave: Schistosoma.

Ano: 2012

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/940202

SOUZA, M. M.; MOKRY, F. C.; TIZIOTO, P. C.; OLIVEIRA, P. S. N.; SOMAVILLA, A.; CESAR, A. S. M.; MORÉ, D.; MOURÃO, G.; DINIZ, W. J. S.; MUDADU, M. A.; NICIURA, S. C. M.; COUTINHO, L. L.; ZERLOTINI, A.; REGITANO, L. C..

Imprinted genes have been target of many studies, mainly in human and mouse, and lately in bovines due to the interest of understanding the epigenetic mechanisms underlying important meat quality phenotypes and the possibility of applying it in animal breeding programs in the future. Genomic DNA from 146 steers was genotyped using the Illumina BovineHD BeadChip in order to identify heterozygous individuals with known allele origin.

Chromatin structural changes around satellite repeats on the female sex chromosome in Schistosoma mansoni and their possible role in sex chromosome emergence.

Palavras-chave: Bioinformática; Expressão gênica; Genoma; Bioinformatics; Genome; Gene expression.

Ano: 2015

URL: http://www.alice.cnptia.embrapa.br/handle/doc/1035029

LEPESANT, J. M. J.; COSSEAU, C.; BOISSIER, J.; FREITAG, M.; PORTELA, J.; CLIMENT, D.; PERRIN, C.; ZERLOTINI, A.; GRUNAU, C..

Background: In the leuphotrochozoan parasitic platyhelminth Schistosoma mansoni, male individuals are homogametic (ZZ) whereas females are heterogametic (ZW). To elucidate the mechanisms that led to the emergence of sex chromosomes, we compared the genomic sequence and the chromatin structure of male and female individuals. As for many eukaryotes, the lower estimate for the repeat content is 40%, with an unknown proportion of domesticated repeats. We used massive sequencing to de novo assemble all repeats, and identify unambiguously Z-specific, W-specific and pseudoautosomal regions of the S. mansoni sex chromosomes. Results: We show that 70 to 90% of S. mansoni W and Z are pseudoautosomal. No female-specific gene could be identified. Instead, the...

Counting RNAseq reads: which way is better?

Palavras-chave: Schistosoma.

Ano: 2012

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/940197

SILVA, F. R. da; NODA, R. W.; ZERLOTINI, A.; LOBO, F. P.; CARNEIRO, N. P..

In this work we show the variation of results we?ve found while working with ~1 billion Illumina reads from drought tolerant Sorghum bicolor genotype in the presence and absence of the stress and compared results found for key genes already characterized.

De novo assembly of a Nelore (Bos indicus) bull genome based on short read sequences.

Palavras-chave: Bioinformática; Sequência de RNA; Sorgo; Bioinformatics; Sorghum.

Ano: 2013

URL: http://www.alice.cnptia.embrapa.br/handle/doc/981626

CINTRA, L. C.; ZERLOTINI, A.; LOBO, F. P.; SILVA, F. R. da; GIACHETTO, P. F.; KUSER-FALCÃO, P. R. K.; SILVA, L. O. C. da; EGITO, A. A. do; SIQUEIRA, F.; SILVA, N. M. A. da; PAIVA, S. R.; YAMAGISHI, M. E. B.; CAETANO, A. R..

Zebu cattle breeds (Bos indicus) are widely used for milk and beef production in the tropics and show natural adaptations to biotic and abiotic stresses especially found in these regions. Advanced genomic tools will be essential to help unveil and explore the underlying genetic variations that distinguish taurine and indicine cattle and, at the same time, will facilitate the work of breeders striding towards incorporating genomic tools into breeding programs aiming to improve productivity and beef and milk quality.

Efficient gap-closure of eukaryotic genome sequence assemblies by third-generation sequencing.

Palavras-chave: Bioinformática; Gado de corte; Zebu; Cattle; Bioinformatics.

Ano: 2014

URL: http://www.alice.cnptia.embrapa.br/handle/doc/1006398

CRUZ, I. R. da C.; GERALDO, J. A.; LEITE, L. R.; ZERLOTINI, A.; ARAÚJO, F.; SILVA, M. V. G. B.; COIMBRA, R. S.; CARVALHO, M. R. S.; OLIVEIRA, G..

Recently, we produced the first draft assemblies of Guzerá and Gir genomes. Two Zebu (Bos indicus) breeds adapted to tropical climate and under genetic evaluation to milk purposes in Brazil.

Embrapa Bioinformatic Multi-user laboratory.

Palavras-chave: Sequenciamento de genoma de zebu; Plataforma SOLiD; Genome; Zebu; Sequence analysis.

Ano: 2012

URL: http://www.alice.cnptia.embrapa.br/handle/doc/946528

CINTRA, L. C.; ZERLOTINI, A.; SILVA, F. R. da; LOBO, F. P.; YAMAGISHI, M. E. B.; KUSER-FALCÃO, P. R. K.; GIACHETTO, P. F..

Recently Brazilian Agricultural Research Corporation (Embrapa) implemented the Embrapa Bioinformatic Multi-user Laboratory(LMB) that provides a central point of convergency for related bioinformatics issues in the organization, a high performance computing (HPC) infrastructure to be used by employees and partners on solution of computational intensive problems in bioinformatics, and principally, provides specialized collaborators to realize training, assist the elaboration of projects with bioinformatics components and in specific cases contribute to execute them. The importance of LMB is best understood when one takes into account the way Embrapa research centers are geographically located. The research centers are distributed among the several regions of...

Embrapa Bioinformatics Multi-Users Laboratory - LMB.

Palavras-chave: Bioinformática; Bioinformatics.

Ano: 2013

URL: http://www.alice.cnptia.embrapa.br/handle/doc/974773

KUSER-FALCÃO, P. R.; YAMAGISHI, M. E. B.; GIACHETTO, P. F.; SILVA, F. R.; LOBO, F. P.; CINTRA, L. C.; ZERLOTINI, A.; HIGA, R.; VIEIRA, F..

The Bioinformatics Multi-Users Laboratory of Embrapa provides an array of shared research resources and infra-structure to the Embrapa community and research collaborators The primary mission of the LMB is to address the increasing need of Embrapa investigators for support and solutions in Bioinformatics in a collaborative environment. To fulfill this mission, the LMB collaborates on research projects that require expertise in genome assembly, meta-genomics analysis to unravel candidate genes, molecular markers, differential gene expression, and structural bioinformatics, and assists in the implementation of computational solutions .

Evidence for reductive genome evolution and lateral acquisition of virulence functions in two Corynebacterium pseudotuberculosis strains.

Palavras-chave: Pesquisa e desenvolvimento; Bioinformática; Research and development; Bioinformatics.

Ano: 2012

URL: http://www.alice.cnptia.embrapa.br/handle/doc/946438

RUIZ, J. C.; D'AFONSECA, V.; SILVA, A.; ALI, A.; PINTO, A. C.; SANTOS, A. R.; ROCHA, A. A. M. C.; LOPES, D. O.; DORELLA, F. A.; PACHECO, L. G. C.; COSTA, M. P.; TURK, M. Z.; SEYFFERT, N.; MORAES, P. M. R. O.; SOARES, S. C.; ALMEIDA, S. S.; CASTRO, T. L. P.; ABREU, V. A. C.; TROST, E.; BAUMBACH, J.; TAUCH, A.; SCHNEIDER, M. P. C.; McCULLOCH, J.; CERDEIRA, L. T.; RAMOS, R. T. J.; ZERLOTINI, A.; DOMINITINI, A.; RESENDE, D. M.; COSER, E. M.; OLIVEIRA, L. M.; PEDROSA, A. L.; VIEIRA, C. U.; GUIMARÃES, C. T.; BARTHOLOMEU, D. C.; OLIVEIRA, D. M.; SANTOS, F. R.; RABELO, É. M.; LOBO, F. P.; FRANCO, G. R.; COSTA, A. F.; CASTRO, I. M.; DIAS, S. R. C.; FERRO, J. A.; ORTEGA, J. M.; PAIVA, L. V.; GOULART, L. R.; ALMEIDA, J. F.; FERRO, M. I. T.; CARNEIRO, N. P.; FALCÃO, P. R. K.; GRYNBERG, P.; TEIXEIRA, S. M. R.; BROMMONSCHENKEL, S.; OLIVEIRA, S. C.; MEYER, R.; MOORE, R. J.; MIYOSHI, A.; OLIVEIRA, G. C.; AZEVEDO, V..

Background: Corynebacterium pseudotuberculosis, a Gram-positive, facultative intracellular pathogen, is the etiologic agent of the disease known as caseous lymphadenitis (CL). CL mainly affects small ruminants, such as goats and sheep; it also causes infections in humans, though rarely. This species is distributed worldwide, but it has the most serious economic impact in Oceania, Africa and South America. Although C. pseudotuberculosis causes major health and productivity problems for livestock, little is known about the molecular basis of its pathogenicity. Methodology and Findings: We characterized two C. pseudotuberculosis genomes (Cp1002, isolated from goats; and CpC231, isolated from sheep). Analysis of the predicted genomes showed high similarity in...

Evidence for reductive genome evolution and lateral acquisition of virulence functions in two Corynebacterium pseudotuberculosis strains.

Palavras-chave: Genoma de C pseudotuberculosis; Análise de genoma; Ilhas de patogenicidade; Corynebacterium Pseudotuberculosis; Caseous lymphadenitis; Pathogenicity.

Ano: 2011

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/914696

RUIZ, J. C.; D'AFONSECA, V.; SILVA, A.; ALI, A.; PINTO, A. C.; SANTOS, A. R.; ROCHA, A. A. M. C.; LOPES, D. O.; DORELLA, F. A.; PACHECO, L. G. C.; COSTA, M. P.; TURK, M. Z.; SEYFFERT, N.; MORAES, P. M. R. O.; SOARES, S. C.; ALMEIDA, S. S.; CASTRO, T. L. P.; ABREU, V. A. C.; TROST, E.; BAUMBACH, J.; TAUCH, A.; SCHNEIDER, M. P. C.; McCULLOCH, J.; CERDEIRA, L. T.; RAMOS, R. T. J.; ZERLOTINI, A.; DOMINITINI, A.; RESENDE, D. M.; COSER, E. M.; OLIVEIRA, L. M.; PEDROSA, A. L.; VIEIRA, C. U.; GUIMARAES, C. T.; BARTHOLOMEU, D. C.; OLIVEIRA, D. M.; SANTOS, F. R.; RABELO, E. M.; LOBO, F. P.; FRANCO, G. R.; COSTA, A. F.; CASTRO, I. M.; DIAS, S. R. C.; FERRO, J. A.; ORTEGA, J. M.; PAIVA, L. V.; ALMEIDA, J. F.; GOULART, L. R.; FERRO, M. I. T.; CARNEIRO, N. P.; FALCÃO, P. R. K.; GRYNBERG, P.; TEIXEIRA, S. M. R.; BROMMONSCHENKEL, S.; OLIVEIRA, S. C.; MEYER, R.; MOORE, R. J.; MIYOSHI, A.; OLIVEIRA, G. C.; AZEVEDO, V..

Genética da resistência de planta adulta à ferrugem da folha em trigo - cultivar Toropi.

Palavras-chave: Patógeno; Genética; Genome.

Ano: 2011

URL: http://www.alice.cnptia.embrapa.br/handle/doc/906799

CASASSOLA, A.; BRAMMER, S. P.; CHAVES, M. S.; NHANI JUNIOR, A.; MARTINELLI, J. A.; KUSER-FALCAO, P. R.; ZERLOTINI, A.; GRANDO, M. F.; STEFANATO, F.; BOYD, L..

2015

Genome sequencing and de novo assembly of the South American tiger catfish (Pseudoplatystoma Punctifer) using 10X sequencing data.

Palavras-chave: Ferrugem da folha; RNA-Seq; Expressão diferencial.

Ano: 2015

URL: http://www.alice.cnptia.embrapa.br/handle/doc/1018075

ZERLOTINI, A.; LOBO, F. P.; CINTRA, L. C.; YAMAGISHI, M. E. B.; VARELA, E. S.; PAIVA, S. R.; IANELLA, P.; CAETANO, A. R..

bitstream/item/208152/1/Genome-Sequencing-PAG.pdf

Genome sequencing and de novo assembly of the South American tiger catfish (Pseudoplatystoma Punctifer) using 10X sequencing data.

Palavras-chave: Pseudoplatystoma Punctifer; Aquacultura; Bioinformática; Aquaculture; Genome assembly; Bioinformatics.

Ano: 2019

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1118157

ZERLOTINI, A.; LOBO, F. P.; CINTRA, L. C.; YAMAGISHI, M. E. B.; VARELA, E. S.; PAIVA, S. R.; IANELLA, P.; CAETANO, A. R..

bitstream/item/206503/1/genome-sequencing-and-de-novo-assembly-of-the-southe-american.pdf

GO enrichment of microarray data from maize root under drough.

Palavras-chave: Pseudoplatystoma Punctifer; Aquaculture.

Ano: 2019

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1116379

NODA, R. W.; LAAT, D. M. de; GUIMARÃES, C. T.; SOUZA, T. C. de; DIAS, L. L. C.; LOBO, F. P.; MAGALHÃES, J. V. de; COIMBRA, R. S.; MAGALHÃES, P. C.; ZERLOTINI, A.; FRANCO, G. M.; CARNEIRO, N. P..

In this study microarray data from roots of a drought tolerant inbred maize line (Embrapa?s breeding program) under two water regimes was analyzed. The analysis revealed that 746 genes were differentially expressed, of which 455 were up- and 291 were down-regulated.

Monoallelic expression of NNAT gene in Nelore steers skeletal muscle.

Palavras-chave: Genômica; Milho; Microarray technology; Corn; Genomics.

Ano: 2013

URL: http://www.alice.cnptia.embrapa.br/handle/doc/981622

New single sucleotide polymorphisms in Guzerá breed revealed by whole-genome re-sequencing.

SOUZA, M. M.; ZERLOTINI, A.; TIZIOTO, P. C.; OLIVEIRA, P. S. N.; SOMAVILLA, A. L.; MOKRY, F. B.; CESAR, A. S. M.; DINIZ, W. J. S.; MUDADU, M. A.; NICIURA, S. C. M.; COUTINHO, L. L.; REGITANO, L. C. A..

ABSTRACT: The NNAT gene plays a role on adipogenesis, brain development and insulin secretion. NNAT is described as paternal imprinted in bovine fetal tissue, but it is still underexplored in adult tissues. In order to improve the understanding of NNAT expression, muscle from Nellore was used to assess its allelic expression. Genomic DNA from 38 steers was genotyped for identification of heterozygous individuals with known allele origin. Total mRNA from muscle was extracted and sequenced by HiScanSQ, and afterwards the reads of each allele were counted for each animal. A total of 8 reciprocal heterozygous had more than 10 reads for the chosen SNP. All animals showed monoallelic expression, being 5 with paternal allele expressed, while 7 had the G allele...

Tipo: Artigo em anais de congresso (ALICE)

Palavras-chave: Neuronatin; Zebu; Genomic imprinting.

Ano: 2014

URL: http://www.alice.cnptia.embrapa.br/handle/doc/1006155

CRUZ, I. R.; GERALDO, J. A.; OLIVEIRA, F. S. de; LEITE, L. R.; ARAÚJO, F.; ZERLOTINI, A.; LOPES, B. C.; ARBEX, W. A.; MACHADO, M. A.; PEIXOTO, M. G. C. D.; VERNEQUE, R. da S.; MARTINS, M. F.; SILVA, M. V. G. B.; COIMBAR, R. S.; CARVALHO, M. R. S.; OLIVEIRA, G..

The objective of our work was to sequence and assemble the Guzerá genome in order to identify race-specific variations that might be used in breeding programs.

Novel polymorphisms in genes associated with milk and meat production and disease resistance in the Guzerá breed identified by whole-genome sequencing.

Palavras-chave: Polimorfismo de nucleotídeo único; Criação de animais; Análise de sequência de genomas; Single nucleotide polymorphism; Animal breeding; Sequence analysis; Genomics.

Ano: 2013

URL: http://www.alice.cnptia.embrapa.br/handle/doc/973157

ROSSE, I. C.; ASSIS, J. G.; OLIVEIRA, F. S.; LEITE, L. R.; ARAUJO, F.; ZERLOTINI, A.; LOPES, B. C.; ARBEX, W. A.; MACHADO, M. A.; PEIXOTO, M. G. C. D.; VERNEQUE, R. S.; GUIMARÃES, M. F. M.; SILVA, M. V. G. B.; COIMBRA, R. S.; OLIVEIRA, G.; CARVALHO, M. R. S..

In this context, the objective of this work was to sequence and assemble the genome of one Guzerá bull in order to identify breed-specific variations that might be included in the genotyping arrays and be useful in breeding programs.

POTION: a massive parallel program for identification of homologous genes under positive selection on genomic scale datasets.

Palavras-chave: Polimorfismo de nucleotídeo único; Gado de corte; Single nucleotide polymorphism; Cattle.

Ano: 2014

URL: http://www.alice.cnptia.embrapa.br/handle/doc/1006143

HONGO, J.; CASTRO, G.; SILVA, F.; CINTRA, L.; ZERLOTINI, A.; LOBO, F..

The search for positive selection is also highly parallelizable, since each group of homologous can be analyzed independently. Here we describe POTION (POsitive selecTION), a massively parallel software to automatically detect positive selection on genomic scale data, ideal for analysis of large datasets in cluster infrastructures