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Fusarium wilt is one of the main limiting factors for tomato production in Mexico. One thousand and fifty isolates were obtained from vascular tissues tomato plants showing wilt and yellowing symptoms in Sinaloa, Mexico. The pathogenic isolates were evaluated through phylogenetic analysis of the TEF-1α gene and ITS region, morphological markers and pathogenicity tests. Within the 15 pathogenic Fusarium isolates, 7 were identified as F. oxysporum and 8 as F. falciforme. Phylogenetic analysis of Fusarium oxysporum f. sp. lycopersici and Fusarium falciforme isolates confirmed that both populations are constituted by distinct phylogenetic lineages. The isolates showed differences in aggressiveness; F. falciforme was the most aggressive. Isolates of both complexes triggered similar aerial symptoms of yellowing and darkening of the vascular tissues in tomato plants. But only F. falciforme isolates triggered necrosis in the plant crowns. Morphological markers allowed differentiating isolates from distinct complexes but not differentiating between lineages.

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