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Background  The hemibiotrophic pathogens  Moniliophthora perniciosa  (witches’ broom disease) and  Moniliophthora roreri  (frosty pod rot disease) are among the most important pathogens of cacao.  Moniliophthora perniciosa  has a broad host range and infects a variety of meristematic tissues in cacao plants, whereas  M. roreri  infects only pods of  Theobroma  and  Herrania  genera. Comparative pathogenomics of these fungi is essential to understand  Moniliophthora  infection strategies, therefore the detection and in silico functional characterization of effector candidates are important steps to gain insight on their pathogenicity.    Results  Candidate secreted effector proteins repertoire were predicted using the genomes of five representative isolates of  M. perniciosa  subpopulations (three from cacao and two from solanaceous hosts), and one representative isolate of  M. roreri  from Peru. Many putative effectors candidates were identified in  M. perniciosa : 157 and 134 in cacao isolates from Bahia, Brazil; 109 in cacao isolate from Ecuador, 92 and 80 in wild solanaceous isolates from Minas Gerais (Lobeira) and Bahia (Caiçara), Brazil; respectively.  Moniliophthora roreri  showed the highest number of effector candidates, a total of 243. A set of eight core effectors were shared among all  Moniliophthora  isolates, while others were shared either between the wild solanaceous isolates or among cacao isolates. Mostly, candidate effectors of  M. perniciosa  were shared among the isolates, whereas in  M. roreri  nearly 50% were exclusive to the specie. In addition, a large number of cell wall-degrading enzymes characteristic of hemibiotrophic fungi were found. From these, we highlighted the proteins involved in cell wall modification, an enzymatic arsenal that allows the plant pathogens to inhabit environments with oxidative stress, which promotes degradation of plant compounds and facilitates infection.    Conclusions  The present work reports six genomes and provides a database of the putative effectorome of  Moniliophthora , a first step towards the understanding of the functional basis of fungal pathogenicity.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-4875-7) contains supplementary material, which is available to authorized users.

Genome sequence and effectorome of Moniliophthora perniciosa and Moniliophthora roreri subpopulations