Pereira GA

References (8)

Title : Transcriptome analysis in Coffea eugenioides, an Arabica coffee ancestor, reveals differentially expressed genes in leaves and fruits - Yuyama_2016_Mol.Genet.Genomics_291_323
Author(s) : Yuyama PM , Reis Junior O , Ivamoto ST , Domingues DS , Carazzolle MF , Pereira GA , Charmetant P , Leroy T , Pereira LF
Ref : Mol Genet Genomics , 291 :323 , 2016
Abstract : Studies in diploid parental species of polyploid plants are important to understand their contributions to the formation of plant and species evolution. Coffea eugenioides is a diploid species that is considered to be an ancestor of allopolyploid Coffea arabica together with Coffea canephora. Despite its importance in the evolutionary history of the main economic species of coffee, no study has focused on C. eugenioides molecular genetics. RNA-seq creates the possibility to generate reference transcriptomes and identify coding genes and potential candidates related to important agronomic traits. Therefore, the main objectives were to obtain a global overview of transcriptionally active genes in this species using next-generation sequencing and to analyze specific genes that were highly expressed in leaves and fruits with potential exploratory characteristics for breeding and understanding the evolutionary biology of coffee. A de novo assembly generated 36,935 contigs that were annotated using eight databases. We observed a total of ~5000 differentially expressed genes between leaves and fruits. Several genes exclusively expressed in fruits did not exhibit similarities with sequences in any database. We selected ten differentially expressed unigenes in leaves and fruits to evaluate transcriptional profiles using qPCR. Our study provides the first gene catalog for C. eugenioides and enhances the knowledge concerning the mechanisms involved in the C. arabica homeologous. Furthermore, this work will open new avenues for studies into specific genes and pathways in this species, especially related to fruit, and our data have potential value in assisted breeding applications.
ESTHER : Yuyama_2016_Mol.Genet.Genomics_291_323
PubMedSearch : Yuyama_2016_Mol.Genet.Genomics_291_323
PubMedID: 26334613

Title : Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: mechanisms of the biotrophic and necrotrophic phases - Meinhardt_2014_BMC.Genomics_15_164
Author(s) : Meinhardt LW , Costa GG , Thomazella DP , Teixeira PJ , Carazzolle MF , Schuster SC , Carlson JE , Guiltinan MJ , Mieczkowski P , Farmer A , Ramaraj T , Crozier J , Davis RE , Shao J , Melnick RL , Pereira GA , Bailey BA
Ref : BMC Genomics , 15 :164 , 2014
Abstract : BACKGROUND: The basidiomycete Moniliophthora roreri is the causal agent of Frosty pod rot (FPR) disease of cacao (Theobroma cacao), the source of chocolate, and FPR is one of the most destructive diseases of this important perennial crop in the Americas. This hemibiotroph infects only cacao pods and has an extended biotrophic phase lasting up to sixty days, culminating in plant necrosis and sporulation of the fungus without the formation of a basidiocarp.
RESULTS: We sequenced and assembled 52.3 Mb into 3,298 contigs that represent the M. roreri genome. Of the 17,920 predicted open reading frames (OFRs), 13,760 were validated by RNA-Seq. Using read count data from RNA sequencing of cacao pods at 30 and 60 days post infection, differential gene expression was estimated for the biotrophic and necrotrophic phases of this plant-pathogen interaction. The sequencing data were used to develop a genome based secretome for the infected pods. Of the 1,535 genes encoding putative secreted proteins, 1,355 were expressed in the biotrophic and necrotrophic phases. Analysis of the data revealed secretome gene expression that correlated with infection and intercellular growth in the biotrophic phase and invasive growth and plant cellular death in the necrotrophic phase.
CONCLUSIONS: Genome sequencing and RNA-Seq was used to determine and validate the Moniliophthora roreri genome and secretome. High sequence identity between Moniliophthora roreri genes and Moniliophthora perniciosa genes supports the taxonomic relationship with Moniliophthora perniciosa and the relatedness of this fungus to other basidiomycetes. Analysis of RNA-Seq data from infected plant tissues revealed differentially expressed genes in the biotrophic and necrotrophic phases. The secreted protein genes that were upregulated in the biotrophic phase are primarily associated with breakdown of the intercellular matrix and modification of the fungal mycelia, possibly to mask the fungus from plant defenses. Based on the transcriptome data, the upregulated secreted proteins in the necrotrophic phase are hypothesized to be actively attacking the plant cell walls and plant cellular components resulting in necrosis. These genes are being used to develop a new understanding of how this disease interaction progresses and to identify potential targets to reduce the impact of this devastating disease.
ESTHER : Meinhardt_2014_BMC.Genomics_15_164
PubMedSearch : Meinhardt_2014_BMC.Genomics_15_164
PubMedID: 24571091
Gene_locus related to this paper: monro-v2wn76 , monro-v2xuz8 , monro-v2xl67 , monro-v2xnp4 , monro-v2wv67 , monro-v2wja9

Title : Genome Sequences of Avian Pathogenic Escherichia coli Strains Isolated from Brazilian Commercial Poultry - Rojas_2013_Genome.Announc_1_e0011013
Author(s) : Rojas TC , Maluta RP , Parizzi LP , Koenigkan LV , Yang J , Yu J , Pereira GA , Dias da Silveira W
Ref : Genome Announc , 1 :e0011013 , 2013
Abstract : Avian pathogenic Escherichia coli (APEC) infections are responsible for significant losses in the poultry industry worldwide. The disease might present as different local infections or as septicemia. Here, we present the draft genome sequences of three Brazilian APEC strains isolated from different kinds of infections. The availability of these APEC genome sequences is important for gaining a thorough understanding of the genomic features of E. coli, particularly those of this pathotype.
ESTHER : Rojas_2013_Genome.Announc_1_e0011013
PubMedSearch : Rojas_2013_Genome.Announc_1_e0011013
PubMedID: 23516222
Gene_locus related to this paper: ecoli-d7xp23 , ecoli-IROD , ecoli-IROE , ecoli-estX , ecoli-yaim , ecoli-ybff , ecoli-ycfp , ecoli-yiel , ecoli-ypt1 , ecoli-yqia , ecoli-Z1930 , ecoli-YfhR

Title : Draft genome of a Brazilian avian-pathogenic Escherichia coli strain and in silico characterization of virulence-related genes - Rojas_2012_J.Bacteriol_194_3023
Author(s) : Rojas TC , Parizzi LP , Tiba MR , Chen L , Pereira GA , Sangal V , Yang J , Yu J , Dias da Silveira W
Ref : Journal of Bacteriology , 194 :3023 , 2012
Abstract : Avian-pathogenic Escherichia coli (APEC) strains cause extraintestinal diseases in avian species. Here, we present the draft genome of an APEC strain (SCI-07) from Brazil that was isolated from skin lesions (gelatinous edema) on the head and periorbital tissues of a laying hen with swollen head syndrome.
ESTHER : Rojas_2012_J.Bacteriol_194_3023
PubMedSearch : Rojas_2012_J.Bacteriol_194_3023
PubMedID: 22582380
Gene_locus related to this paper: ecoli-IROD , ecoli-IROE , ecoli-ycfp , ecoli-YFBB , ecoli-ypt1 , ecoli-YfhR

Title : The genome sequence of Propionibacterium acidipropionici provides insights into its biotechnological and industrial potential - Parizzi_2012_BMC.Genomics_13_562
Author(s) : Parizzi LP , Grassi MC , Llerena LA , Carazzolle MF , Queiroz VL , Lunardi I , Zeidler AF , Teixeira PJ , Mieczkowski P , Rincones J , Pereira GA
Ref : BMC Genomics , 13 :562 , 2012
Abstract : BACKGROUND: Synthetic biology allows the development of new biochemical pathways for the production of chemicals from renewable sources. One major challenge is the identification of suitable microorganisms to hold these pathways with sufficient robustness and high yield. In this work we analyzed the genome of the propionic acid producer Actinobacteria Propionibacterium acidipropionici (ATCC 4875).
RESULTS: The assembled P. acidipropionici genome has 3,656,170 base pairs (bp) with 68.8% G + C content and a low-copy plasmid of 6,868 bp. We identified 3,336 protein coding genes, approximately 1000 more than P. freudenreichii and P. acnes, with an increase in the number of genes putatively involved in maintenance of genome integrity, as well as the presence of an invertase and genes putatively involved in carbon catabolite repression. In addition, we made an experimental confirmation of the ability of P. acidipropionici to fix CO2, but no phosphoenolpyruvate carboxylase coding gene was found in the genome. Instead, we identified the pyruvate carboxylase gene and confirmed the presence of the corresponding enzyme in proteome analysis as a potential candidate for this activity. Similarly, the phosphate acetyltransferase and acetate kinase genes, which are considered responsible for acetate formation, were not present in the genome. In P. acidipropionici, a similar function seems to be performed by an ADP forming acetate-CoA ligase gene and its corresponding enzyme was confirmed in the proteome analysis.
CONCLUSIONS: Our data shows that P. acidipropionici has several of the desired features that are required to become a platform for the production of chemical commodities: multiple pathways for efficient feedstock utilization, ability to fix CO2, robustness, and efficient production of propionic acid, a potential precursor for valuable 3-carbon compounds.
ESTHER : Parizzi_2012_BMC.Genomics_13_562
PubMedSearch : Parizzi_2012_BMC.Genomics_13_562
PubMedID: 23083487
Gene_locus related to this paper: proa4-k7rwz8

Title : Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production - Argueso_2009_Genome.Res_19_2258
Author(s) : Argueso JL , Carazzolle MF , Mieczkowski PA , Duarte FM , Netto OV , Missawa SK , Galzerani F , Costa GG , Vidal RO , Noronha MF , Dominska M , Andrietta MG , Andrietta SR , Cunha AF , Gomes LH , Tavares FC , Alcarde AR , Dietrich FS , McCusker JH , Petes TD , Pereira GA
Ref : Genome Res , 19 :2258 , 2009
Abstract : Bioethanol is a biofuel produced mainly from the fermentation of carbohydrates derived from agricultural feedstocks by the yeast Saccharomyces cerevisiae. One of the most widely adopted strains is PE-2, a heterothallic diploid naturally adapted to the sugar cane fermentation process used in Brazil. Here we report the molecular genetic analysis of a PE-2 derived diploid (JAY270), and the complete genome sequence of a haploid derivative (JAY291). The JAY270 genome is highly heterozygous (approximately 2 SNPs/kb) and has several structural polymorphisms between homologous chromosomes. These chromosomal rearrangements are confined to the peripheral regions of the chromosomes, with breakpoints within repetitive DNA sequences. Despite its complex karyotype, this diploid, when sporulated, had a high frequency of viable spores. Hybrid diploids formed by outcrossing with the laboratory strain S288c also displayed good spore viability. Thus, the rearrangements that exist near the ends of chromosomes do not impair meiosis, as they do not span regions that contain essential genes. This observation is consistent with a model in which the peripheral regions of chromosomes represent plastic domains of the genome that are free to recombine ectopically and experiment with alternative structures. We also explored features of the JAY270 and JAY291 genomes that help explain their high adaptation to industrial environments, exhibiting desirable phenotypes such as high ethanol and cell mass production and high temperature and oxidative stress tolerance. The genomic manipulation of such strains could enable the creation of a new generation of industrial organisms, ideally suited for use as delivery vehicles for future bioenergy technologies.
ESTHER : Argueso_2009_Genome.Res_19_2258
PubMedSearch : Argueso_2009_Genome.Res_19_2258
PubMedID: 19812109
Gene_locus related to this paper: yeast-AIM2 , yeast-BST1 , yeast-cbpy1 , yeast-cld1 , yeast-dap1 , yeast-dap2 , yeast-dlhh , yeast-ECM18 , yeast-FSH1 , yeast-FSH3 , yeast-ict1 , yeast-kex01 , yeast-LDH1 , yeast-MCFS1 , yeast-MCFS2 , yeast-met2 , yeast-mgll , yeast-pdat , yeast-ppme1 , yeast-ROG1 , yeast-SAY1 , yeast-tgl1 , yeast-tgl2 , yeast-yby9 , yeast-YDL109C , yeast-YDR428C , yeast-YDR444W , yeast-yg19 , yeast-yj77 , yeast-yjg8 , yeast-YLL012W , yeast-YLR020C , yeast-YLR118c , yeast-ym60 , yeast-ynl5 , yeast-yo059 , yeast-YPR147C , yeast-hda1

Title : A genome survey of Moniliophthora perniciosa gives new insights into Witches' Broom Disease of cacao - Mondego_2008_BMC.Genomics_9_548
Author(s) : Mondego JM , Carazzolle MF , Costa GG , Formighieri EF , Parizzi LP , Rincones J , Cotomacci C , Carraro DM , Cunha AF , Carrer H , Vidal RO , Estrela RC , Garcia O , Thomazella DP , de Oliveira BV , Pires AB , Rio MC , Araujo MR , de Moraes MH , Castro LA , Gramacho KP , Goncalves MS , Neto JP , Neto AG , Barbosa LV , Guiltinan MJ , Bailey BA , Meinhardt LW , Cascardo JC , Pereira GA
Ref : BMC Genomics , 9 :548 , 2008
Abstract : BACKGROUND: The basidiomycete fungus Moniliophthora perniciosa is the causal agent of Witches' Broom Disease (WBD) in cacao (Theobroma cacao). It is a hemibiotrophic pathogen that colonizes the apoplast of cacao's meristematic tissues as a biotrophic pathogen, switching to a saprotrophic lifestyle during later stages of infection. M. perniciosa, together with the related species M. roreri, are pathogens of aerial parts of the plant, an uncommon characteristic in the order Agaricales. A genome survey (1.9x coverage) of M. perniciosa was analyzed to evaluate the overall gene content of this phytopathogen. RESULTS: Genes encoding proteins involved in retrotransposition, reactive oxygen species (ROS) resistance, drug efflux transport and cell wall degradation were identified. The great number of genes encoding cytochrome P450 monooxygenases (1.15% of gene models) indicates that M. perniciosa has a great potential for detoxification, production of toxins and hormones; which may confer a high adaptive ability to the fungus. We have also discovered new genes encoding putative secreted polypeptides rich in cysteine, as well as genes related to methylotrophy and plant hormone biosynthesis (gibberellin and auxin). Analysis of gene families indicated that M. perniciosa have similar amounts of carboxylesterases and repertoires of plant cell wall degrading enzymes as other hemibiotrophic fungi. In addition, an approach for normalization of gene family data using incomplete genome data was developed and applied in M. perniciosa genome survey. CONCLUSION: This genome survey gives an overview of the M. perniciosa genome, and reveals that a significant portion is involved in stress adaptation and plant necrosis, two necessary characteristics for a hemibiotrophic fungus to fulfill its infection cycle. Our analysis provides new evidence revealing potential adaptive traits that may play major roles in the mechanisms of pathogenicity in the M. perniciosa/cacao pathosystem.
ESTHER : Mondego_2008_BMC.Genomics_9_548
PubMedSearch : Mondego_2008_BMC.Genomics_9_548
PubMedID: 19019209
Gene_locus related to this paper: monpe-e2l806 , monpe-e2lyh7 , monpe-e2lz46 , monro-v2x3v0 , monro-v2yx67 , monpe-e2lnh8

Title : The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis - Simpson_2000_Nature_406_151
Author(s) : Simpson AJ , Reinach FC , Arruda P , Abreu FA , Acencio M , Alvarenga R , Alves LM , Araya JE , Baia GS , Baptista CS , Barros MH , Bonaccorsi ED , Bordin S , Bove JM , Briones MR , Bueno MR , Camargo AA , Camargo LE , Carraro DM , Carrer H , Colauto NB , Colombo C , Costa FF , Costa MC , Costa-Neto CM , Coutinho LL , Cristofani M , Dias-Neto E , Docena C , El-Dorry H , Facincani AP , Ferreira AJ , Ferreira VC , Ferro JA , Fraga JS , Franca SC , Franco MC , Frohme M , Furlan LR , Garnier M , Goldman GH , Goldman MH , Gomes SL , Gruber A , Ho PL , Hoheisel JD , Junqueira ML , Kemper EL , Kitajima JP , Krieger JE , Kuramae EE , Laigret F , Lambais MR , Leite LC , Lemos EG , Lemos MV , Lopes SA , Lopes CR , Machado JA , Machado MA , Madeira AM , Madeira HM , Marino CL , Marques MV , Martins EA , Martins EM , Matsukuma AY , Menck CF , Miracca EC , Miyaki CY , Monteriro-Vitorello CB , Moon DH , Nagai MA , Nascimento AL , Netto LE , Nhani A, Jr. , Nobrega FG , Nunes LR , Oliveira MA , de Oliveira MC , de Oliveira RC , Palmieri DA , Paris A , Peixoto BR , Pereira GA , Pereira HA, Jr. , Pesquero JB , Quaggio RB , Roberto PG , Rodrigues V , de MRAJ , de Rosa VE, Jr. , de Sa RG , Santelli RV , Sawasaki HE , da Silva AC , da Silva AM , da Silva FR , da Silva WA, Jr. , da Silveira JF , Silvestri ML , Siqueira WJ , de Souza AA , de Souza AP , Terenzi MF , Truffi D , Tsai SM , Tsuhako MH , Vallada H , Van Sluys MA , Verjovski-Almeida S , Vettore AL , Zago MA , Zatz M , Meidanis J , Setubal JC
Ref : Nature , 406 :151 , 2000
Abstract : Xylella fastidiosa is a fastidious, xylem-limited bacterium that causes a range of economically important plant diseases. Here we report the complete genome sequence of X. fastidiosa clone 9a5c, which causes citrus variegated chlorosis--a serious disease of orange trees. The genome comprises a 52.7% GC-rich 2,679,305-base-pair (bp) circular chromosome and two plasmids of 51,158 bp and 1,285 bp. We can assign putative functions to 47% of the 2,904 predicted coding regions. Efficient metabolic functions are predicted, with sugars as the principal energy and carbon source, supporting existence in the nutrient-poor xylem sap. The mechanisms associated with pathogenicity and virulence involve toxins, antibiotics and ion sequestration systems, as well as bacterium-bacterium and bacterium-host interactions mediated by a range of proteins. Orthologues of some of these proteins have only been identified in animal and human pathogens; their presence in X. fastidiosa indicates that the molecular basis for bacterial pathogenicity is both conserved and independent of host. At least 83 genes are bacteriophage-derived and include virulence-associated genes from other bacteria, providing direct evidence of phage-mediated horizontal gene transfer.
ESTHER : Simpson_2000_Nature_406_151
PubMedSearch : Simpson_2000_Nature_406_151
PubMedID: 10910347
Gene_locus related to this paper: xylfa-ACVB , xylfa-cxest , xylfa-metx , xylfa-PD2024 , xylfa-pip , xylfa-q9pdj5 , xylfa-XF0015 , xylfa-XF0357 , xylfa-XF0358 , xylfa-XF0754 , xylfa-XF0863 , xylfa-XF0992 , xylfa-XF1029 , xylfa-XF1181 , xylfa-XF1253 , xylfa-XF1282 , xylfa-XF1356 , xylfa-XF1479 , xylfa-XF1743 , xylfa-XF1745 , xylfa-XF1750 , xylfa-XF1829 , xylfa-XF1965 , xylfa-XF2151 , xylfa-XF2260 , xylfa-XF2330 , xylfa-XF2551 , xylfa-XFA0032