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Title:   Author  item
                                            Meinhardt, Lyndelitem
                                            THOMAZELLA, DANIELA - Universidade De Campinas (UNICAMP)item
                                            TEIXEIRA, PAULO - Universidade De Campinas (UNICAMP)item
                                            COSTA, GUSTAVO - Universidade De Campinas (UNICAMP)item
                                            CARAZZOLLE, MARCELO - Universidade De Campinas (UNICAMP)item
                                            SCHUSTER, STEPHEN - Pennsylvania State Universityitem
                                            CARLSON, JOHN - Pennsylvania State Universityitem
                                            GUILTINAN, MARK - Pennsylvania State Universityitem
                                            MIECZKOWSKI, PIOTR - University Of North Carolinaitem
                                            CROW, JOHN - Dupont Pioneer Hi-Breditem
                                            FARMER, ANDREW - National Center For Genome Researchitem
                                            RAMARAJ, THIRU - National Center For Genome Researchitem
                                            CROSIER, JANE - Commonwealth Agricultural Bureau International (CABI)item
                                            Davis, Robertitem
                                            Shao, Jonathanitem
                                            PEREIRA, GONCALO - Universidade De Campinas (UNICAMP)item
                                            Bailey, Bryan
  Submitted to: BMC Genomics
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 2/14/2014
                                    Publication  Date: 2/27/2014
                                    Citation: Meinhardt, L.W., Thomazella, D.P., Teixeira, P.J., Costa, G.G., Carazzolle, M., Schuster, S., Carlson, J.E., Guiltinan, M.J., Mieczkowski, P., Crow, J., Farmer, A., Ramaraj, T., Crosier, J., Davis, R.E., Shao, J.Y., Pereira, G.A., Bailey, B.A. 2014. 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. Biomed Central (BMC) Genomics. 15:164.Interpretive Summary: Moniliophthora roreri is the fungus that causes Frosty Pod Rot, a disease that has devastated cacao production in most of South and Central America. The region affected by this plant disease produces most of the world’s supply of fine flavored cacao, which is used in the making of fine flavored chocolates. To understand this disease at the molecular level we sequenced the genome of this fungus and looked at the gene expression during the disease cycle. This fungus is genetically related to another cacao fungal pathogen and we found 93% of their DNA matched even though they cause very different diseases. The expression data show different sets of genes are turned on at different times during the disease. This information is being used to identify key genes in the interaction that can be targeted to stop the disease or limit its effect. This information will be used by researchers, and plant breeders to improve cacao and by farmers through improved control methods or improved cacao varieties. Ultimately, the consumer could benefit through better quality and a more stable supply of fine flavored cacao.
                                Technical Abstract: Background: Moniliophthora roreri is the causal agent of Frosty pod rot (FPR) disease of Theobroma cacao, the source of chocolate and is one of the most destructive diseases of cacao in the Americas. This Basidiomycete only infects cacao pods and has an extended biotrophic phase lasting up to sixty days, which culminating in plant necrosis and sporulation of the fungus without the formation of a basidiocarp.  
Results: We sequenced and assembled 52.3Mb into 3298 contigs which represents the M. roreri genome. Seventeen thousand nine hundred and twenty open reading frames (OFRs) were predicted and 7638 were validated by RNAseq. The M. roreri genome has a high number of proteins encoding glycoside hydrolases, transporter proteins and cytochrome P450 as well as a multiple cell wall degrading enzymes. RNA sequencing of cacao pods at 30 days post infection and 60 days post infection reveals differential gene expression for the biotrophic and necrotrophic phases of this plant-pathogen interaction. The sequencing data was used to develop a genome–based secretome for the infected pods through the use of signal peptide detection software. The secretome data revealed gene expression that correlate with infection and intercellular growth in the biotrophic phase and invasive growth and plant cellular death in the necrotrophic phase.  
Conclusion: Genome sequencing and RNA-seq was used to determine and validate the Moniliophthora roreri genome. Gene homology supports the taxonomic relationship with Moniliophthora perniciosa and the relatedness of this fungus to other basidiomycetes. RNA-seq data from infected plant tissues revealed differentially expressed genes in the biotrophic and necrotrophic phases of this pathogen. These genes can be used to develop hypotheses of how this disease interaction functions and to identify potential targets to reduce the impact of this disease.


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