Abstract
Thread blight disease has recently been described as an emerging disease on cacao (Theobroma cacao) in Ghana. In Ghana, thread blight disease is caused by multiple species of the Marasmiaceae family: Marasmius tenuissimus, M. crinis-equi, M. palmivorus, and Marasmiellus scandens. Interestingly, two additional members of the Marasmiaceae; Moniliophthora roreri (frosty pod rot) and Moniliophthora perniciosa (witches’ broom disease), are major pathogens of cacao in the Western hemisphere. It is important to accurately characterize the genetic relationships among these economically important species in support of their disease management. We used data from Illumina NGS-based genome sequencing efforts to study the mitochondrial genomes (mitogenomes) of the four cacao thread blight associated pathogens from Ghana and compared them with published mitogenomes of Mon. roreri and Mon. perniciosa. There is a remarkable interspecies variation in mitogenome size within the six cacao-associated Marasmiaceae species, ranging from 43,121 to 109,103 bp. The differences in genome lengths are primarily due to the number and lengths of introns, differences in intergenic space, and differences in the size and numbers of unidentified ORFs (uORF). Among seven M. tenuissimus mitogenomes sequenced, there is variation in size and sequence pointing to divergent evolution patterns within the species. The intronic regions show a high degree of sequence variation compared to the conserved sequences of the 14 core genes. The intronic ORFs identified, regardless of species, encode GIY-YIG or LAGLIDADG domain-containing homing endonuclease genes. Phylogenetic relationships using the 14 core proteins largely mimic the phylogenetic relationships observed in gene order patterns, grouping M. tenuissimus with M. crinis-equi, and M. palmivorus with Mon. roreri and Mon. perniciosa, leaving Mar. scandens as an outlier. The results from this study provide evidence of independent expansion/contraction events and sequence diversification in each species and establish a foundation for further exploration of the evolutionary trajectory of the fungi in Marasmiaceae family.
Highlights
There are more than 1,000 species of fungi in the family Marasmiaceae, which includes the genus Marasmius Fr. (1836: 339) (Agaricales, Basidiomycota)
Based on that previous study (Amoako-Attah et al, 2020), one strain each from M. crinis-equi, M. palmivorus and Mar. scandens, and seven isolates from M. tenuissimus (Table 1) were chosen for whole genome Illumina sequencing and their complete mitogenomes were assembled for this study
Most of the intronic open reading frames (ORFs) of the Thread blight disease (TBD)-associated pathogens share sequence homology with intronic ORFs found in the Mon. perniciosa and Mon. roreri mitogenomes, exceptions exist
Summary
There are more than 1,000 species of fungi in the family Marasmiaceae, which includes the genus Marasmius Fr. (1836: 339) (Agaricales, Basidiomycota). Thread blight disease (TBD) is an emerging threat to cacao production in Ghana (Amoako-Attah et al, 2016, 2020). It is caused by canopy-dwelling basidiomycetes and mostly seen as a network of mycelial rhizomorphs, often called “threads,” that grow along twigs and branches covering leaves creating distinctive leaf blight symptoms. Recent morphological and molecular analyses identified four different fungal species, of the Marasmiaceae, causing TBD- like symptoms on cacao in Ghana (Amoako-Attah et al, 2020). When considered with the Moniliophthora spp. that cause disease on cacao, these six species within the Marasmiaceae create a fertile ground for dissection of genetic diversity in association with varied disease processes in a single crop
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