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

Reis,Marcelo S.; Takita,Marco A.; Palmieri,Darío A.; Machado,Marcos A..

In this work we describe all the computational environments, pipelines, and web services developed for the CitEST transcriptome project, on which all the annotation researchers relied. We also present a complete list of CitEST libraries and, for each of them, the general features after the in silico processing, showing some quantitative information.

Combined functional genomics and genetic approach in oyster to identify summer mortality-resistant markers

Palavras-chave: Transcriptomics; Comparative genomics; Clustering; Trimming; Digital northern.

Ano: 2007

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572007000500031

Huvet, Arnaud; Lapegue, Sylvie.

The oyster Crassostrea gigas has global distribution and for the past several years the highest annual production of any freshwater or marine organism. Economic importance of oysters motivates a great deal of biological research, which provides the most immediate scientific rationales for sequencing ESTs and developing genomic tools.

Tipo: Text

Palavras-chave: Environmental genomics; Comparative genomics; Functional genomics; Markers; Summer mortalities; Genetic; Oysters; Crassostrea gigas.

Ano: 2008

URL: http://archimer.ifremer.fr/doc/2008/publication-4006.PDF

Computational analysis suggests that virulence of Chromobacterium violaceum might be linked to biofilm formation and poly-NAG biosynthesis

Becker,Sidnei; Soares,Cíntia; Porto,Luismar Marques.

Groups of genes that produce exopolysaccharide with a N-acetyl-D-glucosamine monomer are in the genome of several pathogenic bacteria. Chromobacterium violaceum, an opportunistic pathogen, has the operon hmsHFR-CV2940, whose proteins can synthesize such polysaccharide. In this work, multiple alignments among proteins from bacteria that synthesize such polysaccharide were used to verify the existence of amino acids that might be critical for pathogen activity. Three-dimensional models were generated for spatial visualization of these amino acid residues. The analysis carried out showed that the protein HmsR preserves the amino acids D135, D228, Q264 and R267, considered critical for the formation of biofilms and, furthermore, that these amino acids are...

Contribution of Genome Analysis to Understanding of the Biology of, and Diseases Caused by, African Trypanosomes

Palavras-chave: Biofilms; Exopolysaccharide; Chromobacterium violaceum pathogenicity; Comparative genomics.

Ano: 2009

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572009000300031

OAK

Majiwa, P. A. O.; Djikeng, A.; Donelson, J. E.; Agufa, C..

Palavras-chave: ESTs; Comparative genomics; Trypanosoma.

Ano: 1998

URL: http://ir.obihiro.ac.jp/dspace/handle/10322/301

Cultivation-Assisted Genome of Candidatus Fukatsuia symbiotica; the Enigmatic "X-Type" Symbiont of Aphids

Patel, Vilas; Chevignon, Germain; Manzano-marin, Alejandro; Brandt, Jayce W.; Strand, Michael R.; Russell, Jacob A.; Oliver, Kerry M..

Heritable symbionts are common in terrestrial arthropods and often provide beneficial services to hosts. Unlike obligate, nutritional symbionts that largely persist under strict host control within specialized host cells, heritable facultative symbionts exhibit large variation in within-host lifestyles and services rendered with many retaining the capacity to transition among roles. One enigmatic symbiont, Candidatus Fukatsuia symbiotica, frequently infects aphids with reported roles ranging from pathogen, defensive symbiont, mutualism exploiter, and nutritional co-obligate symbiont. Here, we used an in vitro culture-assisted protocol to sequence the genome of a facultative strain of Fukatsuia from pea aphids (Acyrthosiphon pisum). Phylogenetic and genomic...

Tipo: Text

Palavras-chave: Heritable symbiont; Bacteria; Comparative genomics; Insect; Evolutionary transition.

Ano: 2019

URL: https://archimer.ifremer.fr/doc/00635/74663/74594.pdf

Culture-Facilitated Comparative Genomics of the Facultative Symbiont Hamiltonella defensa

Chevignon, Germain; Boyd, Bret M.; Brandt, Jayce W.; Oliver, Kerry M.; Strand, Michael R..

Many insects host facultative, bacterial symbionts that confer conditional fitness benefits to their hosts. Hamiltonella defensa is a common facultative symbiont of aphids that provides protection against parasitoid wasps. Protection levels vary among strains of H. defensa that are also differentially infected by bacteriophages named APSEs. However, little is known about trait variation among strains because only one isolate has been fully sequenced. Generating complete genomes for facultative symbionts is hindered by relatively large genome sizes but low abundances in hosts like aphids that are very small. Here, we took advantage of methods for culturing H. defensa outside of aphids to generate complete genomes and transcriptome data for four strains of...

Tipo: Text

Palavras-chave: Insect; Aphid; Bacteria; Comparative genomics; Parasitoid; Defense.

Ano: 2018

URL: https://archimer.ifremer.fr/doc/00635/74665/74590.pdf

Differential metabolism of Mycoplasma species as revealed by their genomes

Arraes,Fabricio B.M.; Carvalho,Maria José A. de; Maranhão,Andrea Q.; Brígido,Marcelo M.; Pedrosa,Fábio O.; Felipe,Maria Sueli S..

The annotation and comparative analyses of the genomes of Mycoplasma synoviae and Mycoplasma hyopneumonie, as well as of other Mollicutes (a group of bacteria devoid of a rigid cell wall), has set the grounds for a global understanding of their metabolism and infection mechanisms. According to the annotation data, M. synoviae and M. hyopneumoniae are able to perform glycolytic metabolism, but do not possess the enzymatic machinery for citrate and glyoxylate cycles, gluconeogenesis and the pentose phosphate pathway. Both can synthesize ATP by lactic fermentation, but only M. synoviae can convert acetaldehyde to acetate. Also, our genome analysis revealed that M. synoviae and M. hyopneumoniae are not expected to synthesize polysaccharides, but they can take...

Genome-Wide Assessment of Putative Superoxide Dismutases in Unicellular and Filamentous Cyanobacteria

Palavras-chave: Mollicutes; Mycoplasma; Metabolism; Comparative genomics.

Ano: 2007

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572007000200004

BABT

Prajapati,Rajesh; Yadav,Shivam; Mitra,Sonali; Rai,Priya; Mishra,Rajeev; Atri,Neelam.

Abstract Cyanobacteria are photoautotrophic prokaryotes capable to grow in diverse ecological habitats, originated 2.5-3.5 billion years ago and were first to produce oxygen. Since then superoxide dismutases (SOD) acquired great significance due to their ability to catalyze detoxification of byproducts of oxygenic photosynthesis i.e. superoxide radicals. In the present study, we extracted information regarding SODs from species of sequenced cyanobacteria and investigated their diversity, conservation, domain structure, and evolution. 144 putative SOD homologs were identified. Unlike other protein families (ex. serine-threonine kinases) SODs are present in all cyanobacterial species reflecting their significant role in survival. However, their distribution...

Homo sapiens, Homo neanderthalensis and the Denisova specimen: new insights on their evolutionary histories using whole-genome comparisons

Palavras-chave: Superoxide dismutases; Cyanobacteria; Comparative genomics; Phylogeny.

Ano: 2019

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-89132019000100422

Paixão-Côrtes,Vanessa Rodrigues; Viscardi,Lucas Henrique; Salzano,Francisco Mauro; Hünemeier,Tábita; Bortolini,Maria Cátira.

After a brief review of the most recent findings in the study of human evolution, an extensive comparison of the complete genomes of our nearest relative, the chimpanzee (Pan troglodytes), of extant Homo sapiens, archaic Homo neanderthalensis and the Denisova specimen were made. The focus was on non-synonymous mutations, which consequently had an impact on protein levels and these changes were classified according to degree of effect. A total of 10,447 non-synonymous substitutions were found in which the derived allele is fixed or nearly fixed in humans as compared to chimpanzee. Their most frequent location was on chromosome 21. Their presence was then searched in the two archaic genomes. Mutations in 381 genes would imply radical amino acid changes, with...

In search of essentiality: Mollicute-specific genes shared by twelve genomes

Palavras-chave: Human evolution; Comparative genomics; Positive selection; Neanderthal; Denisova.

Ano: 2012

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572012000600003

Souza,Rangel Celso; Almeida,Darcy Fontoura de; Zaha,Arnaldo; Morais,David Anderson de Lima; Vasconcelos,Ana Tereza Ribeiro de.

Mollicutes are cell wall-less bacteria with a genome characterized by its small size. Chromosomal rearrangements help these organisms evade host immune surveillance and hence cause disease. Our goal was to determine genes shared by Mollicutes genomes using the bidirectional best hit methodology. The twelve studied Mollicutes share 210 genes, most of which (> 60%) fall into the following COG categories: translation, ribosomal structure and biogenesis; DNA replication, recombination and repair; nucleotide transport and metabolism and energy production and conversion. Thirty Mollicute-specific genes were identified, 22 of them previously described as essential genes in Mycoplasma genitalium.

Regulation of gene expression in Mycoplasmas: contribution from Mycoplasma hyopneumoniae and Mycoplasma synoviae genome sequences

Palavras-chave: Mollicutes; Comparative genomics; Synteny; Bidirectional best hit.

Ano: 2007

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572007000200002

Madeira,Humberto Maciel França; Gabriel,Jane Eyre.

This report describes the transcription apparatus of Mycoplasma hyopneumoniae (strains J and 7448) and Mycoplasma synoviae, using a comparative genomics approach to summarize the main features related to transcription and control of gene expression in mycoplasmas. Most of the transcription-related genes present in the three strains are well conserved among mycoplasmas. Some unique aspects of transcription in mycoplasmas and the scarcity of regulatory proteins in mycoplasma genomes are discussed.

Tandem repeat distribution of gene transcripts in three plant families

Palavras-chave: Mycoplasma hyopneumoniae; Mycoplasma synoviae; Transcription; Comparative genomics.

Ano: 2007

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572007000200016

Maia,Luciano Carlos da; Souza,Velci Queiróz de; Kopp,Mauricio Marini; Carvalho,Fernando Irajá Félix de; Oliveira,Antonio Costa de.

Tandem repeats (microsatellites or SSRs) are molecular markers with great potential for plant genetic studies. Modern strategies include the transfer of these markers among widely studied and orphan species. In silico analyses allow for studying distribution patterns of microsatellites and predicting which motifs would be more amenable to interspecies transfer. Transcribed sequences (Unigene) from ten species of three plant families were surveyed for the occurrence of micro and minisatellites. Transcripts from different species displayed different rates of tandem repeat occurrence, ranging from 1.47% to 11.28%. Both similar and different patterns were found within and among plant families. The results also indicate a lack of association between genome size...

The genome sequence of Dyella jiangningensis FCAV SCS01 from a lignocellulose-decomposing microbial consortium metagenome reveals potential for biotechnological applications

Palavras-chave: SSR; EST; Comparative genomics; Molecular markers.

Ano: 2009

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572009000400025

Desiderato,Joana G.; Alvarenga,Danillo O.; Constancio,Milena T.L.; Alves,Lucia M.C.; Varani,Alessandro M..

Abstract Cellulose and its associated polymers are structural components of the plant cell wall, constituting one of the major sources of carbon and energy in nature. The carbon cycle is dependent on cellulose- and lignin-decomposing microbial communities and their enzymatic systems acting as consortia. These microbial consortia are under constant exploration for their potential biotechnological use. Herein, we describe the characterization of the genome of Dyella jiangningensis FCAV SCS01, recovered from the metagenome of a lignocellulose-degrading microbial consortium, which was isolated from a sugarcane crop soil under mechanical harvesting and covered by decomposing straw. The 4.7 Mbp genome encodes 4,194 proteins, including 36 glycoside hydrolases...

Vibrio tapetis Displays an Original Type IV Secretion System in Strains Pathogenic for Bivalve Molluscs

Palavras-chave: Plant cell wall polysaccharides; Glycoside hydrolases; Genome annotation; Comparative genomics; Rhodanobacteraceae.

Ano: 2018

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572018000300507

Dias, Graciela M.; Bidault, Adeline; Le Chevalier, Patrick; Choquet, Gwenaelle; Sarkissian, Clio Der; Orlando, Ludovic; Medigue, Claudine; Barbe, Valerie; Mangenot, Sophie; Thompson, Cristiane C.; Thompson, Fabiano L.; Jacq, Annick; Pichereau, Vianney; Paillard, Christine.

The Brown Ring Disease (BRD) caused high mortality rates since 1986 in the Manila clam Venerupis philippinarum introduced and cultured in Western Europe from the 1970s. The causative agent of BRD is a Gram-Negative bacterium, Vibrio tapetis, which is also pathogenic to fish. Here we report the first assembly of the complete genome of V. tapetis CECT4600T, together with the genome sequences of 16 additional strains isolated across a broad host and geographic range. Our extensive genome dataset allowed us to describe the pathogen pan-and core genomes and to identify putative virulence factors. The V. tapetis core genome consists of 3,352 genes, including multiple potential virulence factors represented by haemolysins, transcriptional regulators, Type I...

Tipo: Text

Palavras-chave: Vibrio tapetis; Venerupis philippinarum; Comparative genomics; Pathogenicity; T4SS; Pangenome; Core genome.

Ano: 2018

URL: https://archimer.ifremer.fr/doc/00429/54077/72091.pdf

Xylella fastidiosa comparative genomic database is an information resource to explore the annotation, genomic features, and biology of different strains

Varani,Alessandro M.; Monteiro-Vitorello,Claudia B.; Almeida,Luiz G.P. de; Souza,Rangel C.; Cunha,Oberdan L.; Lima,Wanessa C.; Civerolo,Edwin; Sluys,Marie-Anne Van; Vasconcelos,Ana T.R..

The Xylella fastidiosa comparative genomic database is a scientific resource with the aim to provide a user-friendly interface for accessing high-quality manually curated genomic annotation and comparative sequence analysis, as well as for identifying and mapping prophage-like elements, a marked feature of Xylella genomes. Here we describe a database and tools for exploring the biology of this important plant pathogen. The hallmarks of this database are the high quality genomic annotation, the functional and comparative genomic analysis and the identification and mapping of prophage-like elements. It is available from web site http://www.xylella.lncc.br.