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Genomic Characteristics and Comparative Genomics Analysis of Two Chinese Corynespora cassiicola Strains Causing Corynespora Leaf Fall (CLF) Disease

by 1,2, 1,2, 1,2, 1,2, 1,2, 1,2, 1,2, 3 and 1,2,*
1
Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou 571101, China
2
College of Grassland Agriculture Science and Technology, Lanzhou University, 222 Tianshui South Road, Lanzhou 730000, China
3
Key Laboratory of Integrated Pest Management on Tropical Grops, Ministry of Agriculture and Rural Affairs, Beijing 100020, China
*
Author to whom correspondence should be addressed.
Academic Editor: Willem Melchers
J. Fungi 2021, 7(6), 485; https://doi.org/10.3390/jof7060485
Received: 27 May 2021 / Revised: 8 June 2021 / Accepted: 8 June 2021 / Published: 16 June 2021
(This article belongs to the Section Fungi in Agriculture and Biotechnology)
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. View Full-Text
Keywords: comparative genomics; Corynespora cassiicola; pathogenicity; Corynespora leaf fall disease; rubber tree; secondary metabolites comparative genomics; Corynespora cassiicola; pathogenicity; Corynespora leaf fall disease; rubber tree; secondary metabolites
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MDPI and ACS Style

Li, B.; Yang, Y.; Cai, J.; Liu, X.; Shi, T.; Li, C.; Chen, Y.; Xu, P.; Huang, G. Genomic Characteristics and Comparative Genomics Analysis of Two Chinese Corynespora cassiicola Strains Causing Corynespora Leaf Fall (CLF) Disease. J. Fungi 2021, 7, 485. https://doi.org/10.3390/jof7060485

AMA Style

Li B, Yang Y, Cai J, Liu X, Shi T, Li C, Chen Y, Xu P, Huang G. Genomic Characteristics and Comparative Genomics Analysis of Two Chinese Corynespora cassiicola Strains Causing Corynespora Leaf Fall (CLF) Disease. Journal of Fungi. 2021; 7(6):485. https://doi.org/10.3390/jof7060485

Chicago/Turabian Style

Li, Boxun, Yang Yang, Jimiao Cai, Xianbao Liu, Tao Shi, Chaoping Li, Yipeng Chen, Pan Xu, and Guixiu Huang. 2021. "Genomic Characteristics and Comparative Genomics Analysis of Two Chinese Corynespora cassiicola Strains Causing Corynespora Leaf Fall (CLF) Disease" Journal of Fungi 7, no. 6: 485. https://doi.org/10.3390/jof7060485

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