Characterization of Claviceps species pathogenic on sorghum by sequence analysis of the beta-tubulin gene intron 3 region and EF-1 alpha gene intron 4

The intron 3 region of the beta -tubulin gene, and intron 4 of the translat ion elongation factor gene were PCR-amplified, cloned, and sequenced to det ermine relationships among Claviceps species and characterize isolates of C laviceps causing ergot of sorghum in the USA and other countries. The beta -tubulin gene intron 3 region and intron 4 of the EF-1 alpha gene allowed c lear differentiation of five species (C. africana, C. sorghicola, C. purpur ea, C. fusiformis, and C. paspali), two of which (C. africana and C. sorghi cola) are pathogens of sorghum, with almost no intraspecific variation obse rved among isolates. Claviceps isolates obtained from sorghum in the USA co ntained beta -tubulin gene intron 3 region sequences identical to those, of C. africana isolates from India, Australia, and South Africa. PCR primers were designed from unique sequences within the beta -tubulin intron 3 regio n that can differentiate the five Claviceps species used in this study. We describe primers that allow direct PCR detection of C. africana from honeyd ew produced on infected sorghum plants, providing a useful tool for analysi s of field samples. The beta -tubulin gene intron 3 region and EF-1 alpha i ntron 4 should prove useful in phylogenetic and epidemiological studies of additional Claviceps species.