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Colletotrichum species can infect a wide range of hosts and cause the economically important disease anthracnose.Species of Colletotrichum use diverse strategies for invading host tissue, ranging from intracellular hemibiotrophy to subcuticular intramural necrotrophy.For example, C.higginsianum on cruciferous plants uses localized hemibiotrophic infection strategy and its biotrophic phase is restricted to the initially infected epidermal cells, whilc the biotrophic phase of C.graminicola from maize may extend to many host cells.Comparative genomic analysis was conducted by Mummer 3.22 using projection method.However, genomic analysis revealed that only 34% of the two genomes are syntenic.Althought number of core chromosomes was almost the same,maximum matching fragments among chromosomes were not consistent with the order of corresponding chromosomes between two genomes.The low identity between two genomes is rare in sequencing fungal species in the same genus.This provide a new prospect for understanding species diversity of Collectotrichum from genomic data.