An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora

Background: Coffee is one of the world’s most important crops; it is consumed worldwide and plays a significant role in the economy of producing countries. Coffea arabica and C. canephora are responsible for 70 and 30% of commercial production, respectively. C. arabica is an allotetraploid from a recent hybridization of the diploid species, C. canephora and C. eugenioides. C. arabica has lower genetic diversity and results in a higher quality beverage than C. canephora. Research initiatives have been launched to produce genomic and transcriptomic data about Coffea spp. as a strategy to improve breeding efficiency. Results: Assembling the expressed sequence tags (ESTs) of C. arabica and C. canephora produced by the Brazilian Coffee Genome Project and the Nestlé-Cornell Consortium revealed 32,007 clusters of C. arabica and 16,665 clusters of C. canephora. We detected different GC3 profiles between these species that are related to their genome structure and mating system. BLAST analysis revealed similarities between coffee and grape (Vitis vinifera) genes. Using KA/KS analysis, we identified coffee genes under purifying and positive selection. Protein domain and gene ontology analyses suggested differences between Coffea spp. data, mainly in relation to complex sugar synthases and nucleotide binding proteins. OrthoMCL was used to identify specific and prevalent coffee protein families when compared to five other plant species. Among the interesting families annotated are new cystatins, glycine-rich proteins and RALF-like peptides. Hierarchical clustering was used to independently group C. arabica and C. canephora expression clusters according to expression data extracted from EST libraries, resulting in the identification of differentially expressed genes. Based on these results, we emphasize gene annotation and discuss plant defenses, abiotic stress and cup quality-related functional categories. Conclusion: We present the first comprehensive genome-wide transcript profile study of C. arabica and C. canephora, which can be freely assessed by the scientific community at http://www.lge.ibi.unicamp.br/ coffea. Our data reveal the presence of species-specific/prevalent genes in coffee that may help to explain particular characteristics of these two crops. The identification of differentially expressed transcripts offers a starting point for the correlation between gene expression profiles and Coffea spp. developmental traits, providing valuable insights for coffee breeding and biotechnology, especially concerning sugar metabolism and stress tolerance

The Genome Sequence Of Leishmania (leishmania) Amazonensis: Functional Annotation And Extended Analysis Of Gene Models

We present the sequencing and annotation of the Leishmania (Leishmania) amazonensis genome, an etiological agent of human cutaneous leishmaniasis in the Amazon region of Brazil. L. (L.) amazonensis shares features with Leishmania (L.) mexicana but also exhibits unique characteristics regarding geographical distribution and clinical manifestations of cutaneous lesions (e.g. borderline disseminated cutaneous leishmaniasis). Predicted genes were scored for orthologous gene families and conserved domains in comparison with other human pathogenic Leishmania spp. Carboxypeptidase, aminotransferase, and 3′-nucleotidase genes and ATPase, thioredoxin, and chaperone-related domains were represented more abundantly in L. (L.) amazonensis and L. (L.) mexicana species. Phylogenetic analysis revealed that these two species share groups of amastin surface proteins unique to the genus that could be related to specific features of disease outcomes and host cell interactions. Additionally, we describe a hypothetical hybrid interactome of potentially secreted L. (L.) amazonensis proteins and host proteins under the assumption that parasite factors mimic their mammalian counterparts. The model predicts an interaction between an L. (L.) amazonensis heat-shock protein and mammalian Toll-like receptor 9, which is implicated in important immune responses such as cytokine and nitric oxide production. The analysis presented here represents valuable information for future studies of leishmaniasis pathogenicity and treatment. © The Author 2013.206567581(2010) Control of the Leishmaniasis WHOTechnical Report Series, , WHO. WHO Press: GenevaLainson, R., Shaw, J.J., (1987) The leishmaniases in biology and medicine. Evolution, classification and geographical distributionBates, P.A., Transmission of Leishmania metacyclic promastigotes by phlebotomine sand flies (2007) Int. J. 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The Roles Of Auxin During Plant-microbe Interactions

Among all the phytohormones, auxin likely plays the most roles in plant physiology. With an intricate biosynthesis pathway and a complex gene signaling cascade, auxin is involved in many biological processes, including plant growth and responses against potential pathogens. It has been extensively documented that some microorganisms are capable of synthesizing this phytohormone, especially indole-3-acetic acid (IAA), the major naturally occurring auxin. In an environmental scenario consisting of bacteria and fungi interacting with plants, the production of auxin by such microorganisms may lead to hormonal imbalances in the host. This disturbance in plant hormonal status can modulate plant metabolism and defense systems, favoring symbiosis or pathogenesis. The basic mechanism of IAA as a modulator of plant gene expression is well understood, and new evidence about the mechanisms by which microbes affect plant auxin activities is now emerging. This review focuses on the effects of auxins produced by microorganisms during plant-microbe interactions. The routes of auxin biosynthesis in bacteria and fungi are described for some organisms. We also give examples of the effects of microbe-produced auxin in symbiotic and pathogenic events and describe how plants modulate IAA signaling to counteract infection by biotrophic pathogens. © 2012 Nova Science Publishers, Inc. 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Genomics, Transcriptomics, And Beyond: The Fifteen Years Of Cacao’s Witches’ Broom Disease Genome Project

Cacao production in Brazil was severely affected by the outbreak of witches’ broom disease (WBD) in the late 1980s. WBD is caused by the basidiomycete fungus Moniliophthora perniciosa, a hemibiotrophic pathogen that displays an uncommonly long-lasting biotrophic stage during which the host cacao suffers intense morphologic alterations in the infected shoots, giving rise to “green brooms.” Two months after infection, the fungus becomes necrotrophic resulting in the necrosis and destruction of the infected tissues that turn into a “dry broom.” During the last 15 years, the knowledge of this devastating and intriguing disease has been growing due to initiatives such as the WBD genome project. By using genomics and transcriptomics as tools to obtain insights about this disease, the WBD project has been elucidating the biochemistry and physiology of both plant host and pathogen, paving the way for practical applications to combat the fungus. In this chapter we present an overview of progress in the understanding of M. perniciosa genetics and the molecular mechanisms governing WBD, provide a model for the M. perniciosa–cacao interaction, and point to new directions to fight this disease. © Springer International Publishing Switzerland 2016.17921

Novel Receptor-like Kinases In Cacao Contain Pr-1 Extracellular Domains

Members of the pathogenesis-related protein 1 (PR-1) family are well-known markers of plant defence responses, forming part of the arsenal of the secreted proteins produced on pathogen recognition. Here, we report the identification of two cacao (Theobroma cacaoL.) PR-1s that are fused to transmembrane regions and serine/threonine kinase domains, in a manner characteristic of receptor-like kinases (RLKs). These proteins (TcPR-1f and TcPR-1g) were named PR-1 receptor kinases (PR-1RKs). Phylogenetic analysis of RLKs and PR-1 proteins from cacao indicated that PR-1RKs originated from a fusion between sequences encoding PR-1 and the kinase domain of a LecRLK (Lectin Receptor-Like Kinase). Retrotransposition marks surround TcPR-1f, suggesting that retrotransposition was involved in the origin of PR-1RKs. Genes with a similar domain architecture to cacao PR-1RKs were found in rice (Oryza sativa), barrel medic (Medicago truncatula) and a nonphototrophic bacterium (Herpetosiphon aurantiacus). 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Increasing The Density Of Markers Around A Major Qtl Controlling Resistance To Angular Leaf Spot In Common Bean

Angular leaf spot (ALS) causes major yield losses in the common bean (Phaseolus vulgaris L.), an important protein source in the human diet. This study describes the saturation around a major quantitative trait locus (QTL) region, ALS10.1, controlling resistance to ALS located on linkage group Pv10 and explores the genomic context of this region using available data from the P. vulgaris genome sequence. DArT-derived markers (STS-DArT) selected by bulk segregant analysis and SCAR and SSR markers were used to increase the resolution of the QTL, reducing the confidence interval of ALS10.1 from 13.4 to 3.0 cM. The position of the SSR ATA220 coincided with the maximum LOD score of the QTL. Moreover, a new QTL (ALS10.2UC) was identified at the end of the same linkage group. Sequence analysis using the P. vulgaris genome located ten SSRs and seven STS-DArT on chromosome 10 (Pv10). Coincident linkage and genome positions of five markers enabled the definition of a core region for ALS10.1 spanning 5.3 Mb. These markers are linked to putative genes related to disease resistance such as glycosyl transferase, ankyrin repeat-containing, phospholipase, and squamosa-promoter binding protein. Synteny analysis between ALS10.1 markers and the genome of soybean suggested a dynamic evolution of this locus in the common bean. The present study resulted in the identification of new candidate genes and markers closely linked to a major ALS disease resistance QTL, which can be used in marker-assisted selection, fine mapping and positional QTL cloning. © 2013 Springer-Verlag Berlin Heidelberg.11

Molecular Characterization Of A Miraculin-like Gene Differentially Expressed During Coffee Development And Coffee Leaf Miner Infestation

The characterization of a coffee gene encoding a protein similar to miraculin-like proteins, which are members of the plant Kunitz serine trypsin inhibitor (STI) family of proteinase inhibitors (PIs), is described. PIs are important proteins in plant defence against insects and in the regulation of proteolysis during plant development. This gene has high identity with the Richadella dulcifica taste-modifying protein miraculin and with the tomato protein LeMir; and was named as CoMir (Coffea miraculin). Structural protein modelling indicated that CoMir had structural similarities with the Kunitz STI proteins, but suggested specific folding structures. CoMir was up-regulated after coffee leaf miner (Leucoptera coffella) oviposition in resistant plants of a progeny derived from crosses between C. racemosa (resistant) and C. arabica (susceptible). Interestingly, this gene was down-regulated during coffee leaf miner herbivory in susceptible plants. 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High-resolution Transcript Profiling Of The Atypical Biotrophic Interaction Between Theobroma Cacao And The Fungal Pathogen Moniliophthora Perniciosa

Witches’ broom disease (WBD), caused by the hemibiotrophic fungus Moniliophthora perniciosa, is one of the most devastating diseases of Theobroma cacao, the chocolate tree. In contrast to other hemibiotrophic interactions, the WBD biotrophic stage lasts for months and is responsible for the most distinctive symptoms of the disease, which comprise drastic morphological changes in the infected shoots. Here, we used the dual RNA-seq approach to simultaneously assess the transcriptomes of cacao and M. perniciosa during their peculiar biotrophic interaction. Infection with M. perniciosa triggers massive metabolic reprogramming in the diseased tissues. Although apparently vigorous, the infected shoots are energetically expensive structures characterized by the induction of ineffective defense responses and by a clear carbon deprivation signature. Remarkably, the infection culminates in the establishment of a senescence process in the host, which signals the end of the WBD biotrophic stage. 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