Comparative genomic and transcriptomic analyses reveal different pathogenicity-related genes among three eucalyptus fungal pathogens

• Published in: Fungal genetics and biology 2020-04, Vol.137, p.103332-103332, Article 103332
• Main Authors: Santos, Samuel A., Vidigal, Pedro M.P., Thrimawithana, Amali, Betancourth, Blanca M.L., Guimarães, Lúcio M.S., Templeton, Matthew D., Alfenas, Acelino C.
• Format: Article
• Language: English
• Subjects: Calonectria pseudoreteaudii; Ceratocystis eucalypticola; Ceratocystis fimbriata; Ceratocystis Wilt; RNA-Seq
• ISSN: 1087-1845; 1096-0937
• DOI: 10.1016/j.fgb.2019.103332

•Ceratocystis fimbriata LPF1912 has a compact genome with 43% as coding sequencing.•A set of 4919 orthologous gene clusters represent the minimum quorum for the three pathogens.•Two Ceratocystis pathogens showed a different pathogenicity-related genes compared to Calonectria pseudoreteaudii.•The most of DEGs of C. fimbriata LPF1912 is related to its pathogenicity in Eucalyptus spp. Ceratocystis fimbriata is an important plant pathogen known to cause Ceratocystis Wilt (CW), a prevalent fungal disease known to affect Eucalyptus spp. plantations in Brazil. To better understand the molecular mechanisms related to pathogenicity in eucalyptus, we generated a high-quality assembly and annotation of the Ce. fimbriata LPF1912 isolate (LPF1912) genome, as well as the first transcriptome of LPF1912 from 16 eucalyptus clones at three infection incubation periods (12, 18, and 24 h). The LPF1912 genome assembly contains 805 scaffolds, totaling 31.8 Mb, with 43% of the genome estimated to be coding sequence comprised of 7,390 protein-coding genes of which 626 (8.5%) were classified as secreted proteins, 120 ribosomal RNAs, and 532 transfer RNAs. Comparative genomic analysis among three eucalyptus fungal pathogens (Ce. fimbriata, Ce. eucalypticola, and Calonectria pseudoreteaudii), showed high similarity in the proteome (21.81%) and secretome (52.01%) of LPF1912 and Ce. eucalypticola. GO annotation of pathogenicity-related genes of LPF1912 and Ce. eucalypticola, revealed enrichment in cell wall degrading enzymes (CWDEs), and lipid/cutin metabolism for Ca. pseudoreteaudii. Additionally, a transcriptome analysis between resistant and susceptible eucalyptus clones to CW infection indicated that a majority (11) of LPF1912 differentially expressed genes had GO terms associated with enzymatic functions, such as the polygalacturonase gene family, confirming the crucial role of CWDEs for Ce. fimbriata pathogenicity. Finally, our genomic and transcriptomic analysis approach provides a better understanding of the mechanisms involved in Ce. fimbriata pathogenesis, as well as a framework for further studies.