Abstract
Rubber tree Corynespora leaf fall (CLF) disease, caused by the fungus Corynespora cassiicola, is one of the most damaging diseases in rubber tree plantations in Asia and Africa, and this disease also threatens rubber nurseries and young rubber plantations in China. C. cassiicola isolates display high genetic diversity, and virulence profiles vary significantly depending on cultivar. Although one phytotoxin (cassicolin) has been identified, it cannot fully explain the diversity in pathogenicity between C. cassiicola species, and some virulent C. cassiicola strains do not contain the cassiicolin gene. In the present study, we report high-quality gapless genome sequences, obtained using short-read sequencing and single-molecule long-read sequencing, of two Chinese C. cassiicola virulent strains. Comparative genomics of gene families in these two stains and a virulent CPP strain from the Philippines showed that all three strains experienced different selective pressures, and metabolism-related gene families vary between the strains. Secreted protein analysis indicated that the quantities of secreted cell wall-degrading enzymes were correlated with pathogenesis, and the most aggressive CCP strain (cassiicolin toxin type 1) encoded 27.34% and 39.74% more secreted carbohydrate-active enzymes (CAZymes) than Chinese strains YN49 and CC01, respectively, both of which can only infect rubber tree saplings. The results of antiSMASH analysis showed that all three strains encode ~60 secondary metabolite biosynthesis gene clusters (SM BGCs). Phylogenomic and domain structure analyses of core synthesis genes, together with synteny analysis of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) gene clusters, revealed diversity in the distribution of SM BGCs between strains, as well as SM polymorphisms, which may play an important role in pathogenic progress. The results expand our understanding of the C. cassiicola genome. Further comparative genomic analysis indicates that secreted CAZymes and SMs may influence pathogenicity in rubber tree plantations. The findings facilitate future exploration of the molecular pathogenic mechanism of C. cassiicola.
Highlights
The fungus Corynespora cassiicola (Berk. and Curt) C
Based on the sequence of the cassicolin-encoding gene, the YN49 strain belongs to Cas5 isolates and CC01 belongs to Cas2 isolates (Figure S1, Supplementary Materials File S7)
Compared with CC01, YN49 was more pathogenic toward Reyan7-33-97 (Figure 1)
Summary
The fungus Corynespora cassiicola (Berk. and Curt) C. T. Wei, belonging to the Ascomycota phylum, Dothideomycetes class, and Pleosporales order, is responsible for diseases in a wide range of plants, including rubber tree, tomato, cucumber, soybean, cotton, and various others [1]. Wei, belonging to the Ascomycota phylum, Dothideomycetes class, and Pleosporales order, is responsible for diseases in a wide range of plants, including rubber tree, tomato, cucumber, soybean, cotton, and various others [1] This fungus has been isolated from sponges, nematodes, and rare human infections [2,3,4]. Arg.), until Corynespora leaf fall (CLF) disease was first reported in Sierra Leone, which devastated more than 4000 ha of the highly susceptible rubber cultivar RRIC103 in the 1980s [5,6]. CFL disease has rapidly spread through most rubber-producing countries in Asia and Africa, causing severe sporadic epidemics and damaging losses to natural rubber yields, making it among the most important cryptogamic diseases of rubber plantations [7]
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