Publications by authors named "Luis E A Camargo"

10 Publications

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Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut-resistant genotype.

BMC Genomics 2019 Nov 6;20(1):809. Epub 2019 Nov 6.

Escola Superior de Agricultura "Luiz de Queiroz", Departamento de Genética, Universidade de São Paulo, Piracicaba, São Paulo, Brazil.

Background: Resistance genes composing the two-layer immune system of plants are thought as important markers for breeding pathogen-resistant crops. Many have been the attempts to establish relationships between the genomic content of Resistance Gene Analogs (RGAs) of modern sugarcane cultivars to its degrees of resistance to diseases such as smut. However, due to the highly polyploid and heterozygous nature of sugarcane genome, large scale RGA predictions is challenging.

Results: We predicted, searched for orthologs, and investigated the genomic features of RGAs within a recently released sugarcane elite cultivar genome, alongside the genomes of sorghum, one sugarcane ancestor (Saccharum spontaneum), and a collection of de novo transcripts generated for six modern cultivars. In addition, transcriptomes from two sugarcane genotypes were obtained to investigate the roles of RGAs differentially expressed (RGADE) in their distinct degrees of resistance to smut. Sugarcane references lack RGAs from the TNL class (Toll-Interleukin receptor (TIR) domain associated to nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains) and harbor elevated content of membrane-associated RGAs. Up to 39% of RGAs were organized in clusters, and 40% of those clusters shared synteny. Basically, 79% of predicted NBS-encoding genes are located in a few chromosomes. S. spontaneum chromosome 5 harbors most RGADE orthologs responsive to smut in modern sugarcane. Resistant sugarcane had an increased number of RGAs differentially expressed from both classes of RLK (receptor-like kinase) and RLP (receptor-like protein) as compared to the smut-susceptible. Tandem duplications have largely contributed to the expansion of both RGA clusters and the predicted clades of RGADEs.

Conclusions: Most of smut-responsive RGAs in modern sugarcane were potentially originated in chromosome 5 of the ancestral S. spontaneum genotype. Smut resistant and susceptible genotypes of sugarcane have a distinct pattern of RGADE. TM-LRR (transmembrane domains followed by LRR) family was the most responsive to the early moment of pathogen infection in the resistant genotype, suggesting the relevance of an innate immune system. This work can help to outline strategies for further understanding of allele and paralog expression of RGAs in sugarcane, and the results should help to develop a more applied procedure for the selection of resistant plants in sugarcane.
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http://dx.doi.org/10.1186/s12864-019-6207-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6836459PMC
November 2019

Infection Results in Hypersensitive-Like Response, Suppression of the JA/ET Plant Defense Pathway and Promotion of the Colonization of Its Mite Vector.

Front Plant Sci 2016 25;7:1757. Epub 2016 Nov 25.

Laboratório de Bioquímica Fitopatológica, Instituto BiológicoSão Paulo, Brazil; Embrapa Mandioca e FruticulturaCruz das Almas, Brazil.

Leprosis is a serious disease of citrus caused by (CiLV-C, genus ) whose transmission is mediated by false spider mites of the genus . CiLV-C infection does not systemically spread in any of its known host plants, thus remaining restricted to local lesions around the feeding sites of viruliferous mites. To get insight into this unusual pathosystem, we evaluated the expression profiles of genes involved in defense mechanisms of and upon infestation with non-viruliferous and viruliferous mites by using reverse-transcription qPCR. These results were analyzed together with the production of reactive oxygen species (ROS) and the appearance of dead cells as assessed by histochemical assays. After interaction with non-viruliferous mites, plants locally accumulated ROS and triggered the salicylic acid (SA) and jasmonate/ethylene (JA/ET) pathways. ERF branch of the JA/ET pathways was highly activated. In contrast, JA pathway genes were markedly suppressed upon the CiLV-C infection mediated by viruliferous mites. Viral infection also intensified the ROS burst and cell death, and enhanced the expression of genes involved in the RNA silencing mechanism and SA pathway. After 13 days of infestation of two sets of Arabidopsis plants with non-viruliferous and viruliferous mites, the number of mites in the CiLV-C infected Arabidopsis plants was significantly higher than in those infested with the non-viruliferous ones. Oviposition of the viruliferous mites occurred preferentially in the CiLV-C infected leaves. Based on these results, we postulated the first model of plant/ mite/cilevirus interaction in which cells surrounding the feeding sites of viruliferous mites typify the outcome of a hypersensitive-like response, whereas viral infection induces changes in the behavior of its vector.
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http://dx.doi.org/10.3389/fpls.2016.01757DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5122717PMC
November 2016

Common bean reaction to angular leaf spot comprises transcriptional modulation of genes in the ALS10.1 QTL.

Front Plant Sci 2015 12;6:152. Epub 2015 Mar 12.

Department of Plant Sciences, University of California, Davis Davis, CA, USA.

Genetic resistance of common bean (Phaseolus vulgaris L.) against angular leaf spot (ALS), caused by the fungus Pseudocercospora griseola, is conferred by quantitative trait loci (QTL). In this study, we determined the gene content of the major QTL ALS10.1 located at the end of chromosome Pv10, and identified those that are responsive to ALS infection in resistant (CAL 143) and susceptible (IAC-UNA) genotypes. Based on the current version of the common bean reference genome, the ALS10.1 core region contains 323 genes. Gene Ontology (GO) analysis of these coding sequences revealed the presence of genes involved in signal perception and transduction, programmed cell death (PCD), and defense responses. Two putative R gene clusters were found at ALS10.1 containing evolutionary related coding sequences. Among them, the Phvul.010G025700 was consistently up-regulated in the infected IAC-UNA suggesting its contribution to plant susceptibility to the fungus. We identified six other genes that were regulated during common bean response to P. griseola; three of them might be negative regulators of immunity as they showed opposite expression patterns during resistant and susceptible reactions at the initial phase of fungal infection. Taken together, these findings suggest that common bean reaction to P. griseola involves transcriptional modulation of defense genes in the ALS10.1 locus, contributing to resistance or susceptibility depending on the plant-pathogen interaction.
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http://dx.doi.org/10.3389/fpls.2015.00152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4357252PMC
March 2015

Molecular and Pathogenic Diversity Among Brazilian Isolates of Xanthomonas albilineans Assessed with SSR Marker Loci.

Plant Dis 2014 Apr;98(4):540-546

Centro de Cana, Instituto Agronômico, Campinas-IAC, Rod. Antonio Duarte Nogueira Km 321, CP 206, Ribeirão Preto, SP, Brazil.

Leaf scald is one of the most important diseases of sugarcane in Brazil. Despite its importance, little is known about the genetic and pathogenic variability of its causal agent, Xanthomonas albilineans. The genetic diversity of 44 X. albilineans isolates from diverse geographic regions of Brazil was assessed using 15 newly developed short sequence repeat (SSR) loci designed from the genome sequence of X. albilineans strain GPE PC73. In addition, the aggressiveness of each isolate was evaluated by inoculating on a susceptible sugarcane cultivar and scoring the disease severity. Of the 15 SSR loci, 12 were polymorphic and produced 54 polymorphic alleles. The average number of polymorphic alleles per locus was 4.5, and ranged from 2 to 12 alleles. Phenetic analysis based on Nei's unbiased genetic distance, clustered the isolates into two major groups. Group I included 32 isolates from all four geographic regions studied, whereas group II included 9 isolates from two regions. Three isolates did not cluster within these groups. Analysis of disease severity data also revealed variability in aggressiveness among isolates but no correlation could be established with either SSR haplotypes or phenetic groups. Isolates with identical haplotypes differed in aggressiveness and vice versa. However, single marker-trait analysis revealed two markers associated with this trait.
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http://dx.doi.org/10.1094/PDIS-07-13-0762-REDOI Listing
April 2014

Comparative bioinformatic analysis of genes expressed in common bean (Phaseolus vulgaris L.) seedlings.

Genome 2005 Jun;48(3):562-70

Department de Fitopatologia, Laboratório de Genética Molecular, ESALQ, Universidade de São Paulo, Brazil.

To rapidly and cost-effectively generate gene expression data, we developed an annotated unigene database of common bean (Phaseolus vulgaris L.). In this study, 3 cDNA libraries were constructed from the bean breeding line SEL1308, 1 from young leaf and 2 from seedlings inoculated or not inoculated with the fungal pathogen Colletotrichum lindemuthianum (Sacc. & Magnus) Briosi & Cavara, which causes anthracnose in common bean. To this date, 5255 single-pass sequences have been included in the database after selection based on sequence quality. These ESTs were trimmed and clustered using the computer programs Phred and CAP3 to form a unigene collection of 3126 unique sequences. Within clusters, 318 single nucleotide polymorphisms (SNPs) and 68 insertions-deletions (indels) were found, indicating the presence of paralogous gene families in our database. Each unigene sequence was analyzed for possible function using their similarity to known genes represented in the GenBank database and classified into 14 categories. Only 314 unigenes showed significant similarities to Phaseolus genomic sequences and P. vulgaris ESTs, which indicates that 90% (2818 unigenes) of our database represent newly discovered common bean genes. In addition, 12% (387 unigenes) were shown to be specific to common bean. This study represents a first step towards the discovery of novel genes in beans and a valuable source of molecular markers for expressed gene tagging and mapping.
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http://dx.doi.org/10.1139/g05-010DOI Listing
June 2005

The genome sequence of the gram-positive sugarcane pathogen Leifsonia xyli subsp. xyli.

Mol Plant Microbe Interact 2004 Aug;17(8):827-36

Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av. Pádua Dias, 11, 13418-900, Piracicaba, SP, Brazil.

The genome sequence of Leifsonia xyli subsp. xyli, which causes ratoon stunting disease and affects sugarcane worldwide, was determined. The single circular chromosome of Leifsonia xyli subsp. xyli CTCB07 was 2.6 Mb in length with a GC content of 68% and 2,044 predicted open reading frames. The analysis also revealed 307 predicted pseudogenes, which is more than any bacterial plant pathogen sequenced to date. Many of these pseudogenes, if functional, would likely be involved in the degradation of plant heteropolysaccharides, uptake of free sugars, and synthesis of amino acids. Although L. xyli subsp. xyli has only been identified colonizing the xylem vessels of sugarcane, the numbers of predicted regulatory genes and sugar transporters are similar to those in free-living organisms. Some of the predicted pathogenicity genes appear to have been acquired by lateral transfer and include genes for cellulase, pectinase, wilt-inducing protein, lysozyme, and desaturase. The presence of the latter may contribute to stunting, since it is likely involved in the synthesis of abscisic acid, a hormone that arrests growth. Our findings are consistent with the nutritionally fastidious behavior exhibited by L. xyli subsp. xyli and suggest an ongoing adaptation to the restricted ecological niche it inhabits.
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http://dx.doi.org/10.1094/MPMI.2004.17.8.827DOI Listing
August 2004

Interleukin 10 gene promoter polymorphisms are associated with chronic periodontitis.

J Clin Periodontol 2004 Jun;31(6):443-8

Department of Morphology, Dental School of Piracicaba-FOP/UNICAMP, Piracicaba, SP, Brazil.

Background: Chronic periodontitis (CP) is characterized by an inflammation in the supporting tissues of the teeth caused primarily by bacterial infection. Interleukin 10 (IL10) is an anti-inflammatory cytokine whose genetic polymorphisms may influence the expression of the protein.

Objective: In this study we investigated the hypothesis that single-nucleotide polymorphisms (SNPs) in the promoter of IL10 gene might be related to CP.

Materials And Methods: DNA was obtained from n=67 CP patients and n=43 control subjects. All studied individuals were non-smokers. The -1087 SNP was investigated by DNA sequencing, and the -819 and -592 SNPs by restriction fragment length polymorphism of PCR products.

Results: Frequencies of -819 and -592 SNPs showed differences between the control and CP groups. The ACC haplotype was more prevalent in the control group and the ATA haplotype more prevalent in the CP group. The ATA haplotype seemed to increase susceptibility to CP in women (odds ratio (OR)=2.57). The heterozygous haplotype GCC/ACC was predominant in the control group (OR=8.26; p=0.001).

Conclusions: Specific haplotypes and SNPs in IL10 gene are associated with susceptibility to CP in Brazilian patients.
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http://dx.doi.org/10.1111/j.1600-051X.2004.00500.xDOI Listing
June 2004

Evaluation of monocot and eudicot divergence using the sugarcane transcriptome.

Plant Physiol 2004 Mar;134(3):951-9

Centro de Biologia Molecular e Engenharia Genética, Universidade de Campinas, Caixa Postal 6010, 13083-970, Campinas SP, Brazil.

Over 40,000 sugarcane (Saccharum officinarum) consensus sequences assembled from 237,954 expressed sequence tags were compared with the protein and DNA sequences from other angiosperms, including the genomes of Arabidopsis and rice (Oryza sativa). Approximately two-thirds of the sugarcane transcriptome have similar sequences in Arabidopsis. These sequences may represent a core set of proteins or protein domains that are conserved among monocots and eudicots and probably encode for essential angiosperm functions. The remaining sequences represent putative monocot-specific genetic material, one-half of which were found only in sugarcane. These monocot-specific cDNAs represent either novelties or, in many cases, fast-evolving sequences that diverged substantially from their eudicot homologs. The wide comparative genome analysis presented here provides information on the evolutionary changes that underlie the divergence of monocots and eudicots. Our comparative analysis also led to the identification of several not yet annotated putative genes and possible gene loss events in Arabidopsis.
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http://dx.doi.org/10.1104/pp.103.033878DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC389918PMC
March 2004

Outbreaks of Bacterial Spot Caused by Xanthomonas gardneri on Processing Tomato in Central-West Brazil.

Plant Dis 2004 Feb;88(2):157-161

Universidade de São Paulo-Escola Superior de Agricultura "Luiz de Queiroz", Caixa Postal 09, CEP-13418-900, Piracicaba, SP, Brazil.

Severe epidemics of bacterial spot have been observed in central-west Brazil in fields of processing tomato. Several xanthomonads, Xanthomonas axonopodis pv. vesicatoria, X. vesicatoria, or X. gardneri, can cause the disease; therefore, attempts were made to identify the pathogen species present in this region. A total of 215 strains were obtained from 10 commercial areas in 1997, 1998, and 2000. The strains were characterized using pulsed-field gel electrophoresis (PFGE) and by their amylolytic and pectolytic activities. Representative strains from each PFGE haplotype then were tested for pathogenicity on tomato and pepper, carbon source utilization, and whole protein sodium dodecyl sulfate-polyacrylamide gel electrophoresis. rRNA sequence comparisons also were performed. All strains recovered from six fields were classified as X. gardneri, whereas X. vesicatoria and X. axonopodis pv. vesicatoria also were detected in the remaining four fields. Strains of X. gardneri, which could be grouped into two PFGE haplotypes, were unable to hydrolyze starch and pectate and to utilize gentiobiose and maltose. They expressed the β protein of 27 kDa and were pathogenic on tomato but variable on pepper. This is the first report of outbreaks of bacterial spot on tomato caused by X. gardneri.
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http://dx.doi.org/10.1094/PDIS.2004.88.2.157DOI Listing
February 2004

Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane.

Genome Res 2003 Dec 12;13(12):2725-35. Epub 2003 Nov 12.

Centro de Biologia Molecular e Engenharia Genética, Instituto da Computação, Universidade Estadual de Campinas, 13083-970 Campinas-SP, Brazil.

To contribute to our understanding of the genome complexity of sugarcane, we undertook a large-scale expressed sequence tag (EST) program. More than 260,000 cDNA clones were partially sequenced from 26 standard cDNA libraries generated from different sugarcane tissues. After the processing of the sequences, 237,954 high-quality ESTs were identified. These ESTs were assembled into 43,141 putative transcripts. Of the assembled sequences, 35.6% presented no matches with existing sequences in public databases. A global analysis of the whole SUCEST data set indicated that 14,409 assembled sequences (33% of the total) contained at least one cDNA clone with a full-length insert. Annotation of the 43,141 assembled sequences associated almost 50% of the putative identified sugarcane genes with protein metabolism, cellular communication/signal transduction, bioenergetics, and stress responses. Inspection of the translated assembled sequences for conserved protein domains revealed 40,821 amino acid sequences with 1415 Pfam domains. Reassembling the consensus sequences of the 43,141 transcripts revealed a 22% redundancy in the first assembling. This indicated that possibly 33,620 unique genes had been identified and indicated that >90% of the sugarcane expressed genes were tagged.
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http://dx.doi.org/10.1101/gr.1532103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403815PMC
December 2003