Moniliophthora roreri strain:MCA 2952
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ABSTRACT:
PROVIDER: PRJNA279170 | ENA |
REPOSITORIES: ENA
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Project description:Moniliophthora roreri MCA 2997 Genome sequencing and assembly
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Project description:The basidiomycete Moniliophthora roreri causes frosty pod rot of cacao (Theobroma cacao) in the Western hemisphere. M. roreri is considered asexual and haploid throughout its hemibiotrophic lifecycle. To understand the processes driving genome modification, using long-read sequencing technology we sequenced and assembled five high quality M. roreri genomes out of a collection of ninety-nine isolates collected throughout the pathogen's range. We obtained chromosome-scale assemblies composed of eleven scaffolds. We used short-read technology to sequence the genomes of twenty-two similarly chosen isolates. Alignments among the five reference assemblies revealed inversions and segmental translocations and duplications between and within scaffolds. Isolates at the front of the pathogens’ expanding range tend to share lineage-specific structural variants, as confirmed by short-read sequencing. We identified, for the first time, three new mating type A locus alleles (five in total) and one new potential mating type B locus allele (three in total). Currently only two mating type combinations, A1B1 and A2B2, are known to exist outside of Colombia. A systematic survey of the M. roreri transcriptome across twenty-two isolates identified an expanded candidate effector pool and provided evidence that effector candidate genes unique to the Moniliophthoras have been selected for preferential expression during the biotrophic phase of disease. Notably, M. roreri isolates in Costa Rica carry a chromosome segment duplication that has doubled the associated gene complement and includes secreted proteins and candidate effectors. Clonal propagation of the haploid M. roreri genome has allowed lineages with unique genome structures and compositions to dominate as it expands its range, displaying a significant founder effect.
2023-06-01 | GSE226814 | GEO
Project description:BackgroundThe 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.ResultsCandidate 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.ConclusionsThe 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.
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Project description:Clonal propagation of Moniliophthora roreri and the emergence of unique lineages with distinct genomes during range expansion
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