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Abstract The infection process of the hemibiotrophic fungus Colletotrichum lindemuthianum has been independently studied at the microscopic and genomic levels. However, the relationship between the morphological changes and the pathogenicity mechanisms of the fungus at the early stages of the infection remains uncharacterized. Therefore, this study attempts to bridge this gap by integrating microscopic and transcriptional approaches to understand the infection process of C. lindemuthianum. Fungal structures were followed by fluorescence microscopy for 120 hours. Simultaneously, the transcriptomic profile was made using RNAseq. Morphological characterization shows that appressoria, infective vesicles, and secondary hypha formation occur before 72 hours. Additionally, we assembled 38,206 transcripts with lengths between 201 and 3,548 bp. The secretome annotation revealed the expression of 1,204 CAZymes, of which 17 exhibited secretion domains and were identified as chitinases and β-1,3-glucanases, 27 were effector candidates, and 30 were transport proteins mostly associated with ABC-type. Finally, we confirmed the presence and expression of CAC1 role during the appressoria formation of Clr7. This result represents the first report of adenylate cyclase expression evaluated under three different approaches. In conclusion, C. lindemuthianum colonizes the host through different infection structures complemented with the expression of multiple enzymes, where CAC1 favors disease development. levels However uncharacterized Therefore C 12 hours Simultaneously RNAseq vesicles 7 Additionally 38206 38 206 38,20 20 3548 3 548 3,54 bp 1204 1 204 1,20 CAZymes β1,3glucanases, β13glucanases βglucanases β 1,3 glucanases, glucanases β-1,3-glucanases 2 candidates ABCtype. ABCtype ABC type. type ABC-type Finally CAC Clr7 Clr conclusion enzymes development 3820 38,2 354 54 3,5 1,2 β1 3glucanases β1,3glucanases 13 1, 382 38, 35 5 3,
