CgT1: A non-LTR retrotransposon with restricted distribution in the fungal phytopathogen Colletotrichum gloeosporioides

Two genetically distinct biotypes (A and B) of Colletotrichum gloeosporioides that cause different anthracnose diseases on the legumes Stylosanthes spp. have been identified in Australia. A DNA sequence that was present in biotype B and absent in biotype A was isolated by differential hybridisation of a genomic library using total genomic DNA of each biotype as hybridisation probes. This sequence also failed to hybridise to DNA of three biotypes of C, gloeosporioides from other host species and to DNA of three other species of Colletotrichum. This clone was used to isolate two cosmid clones of biotype B. Sequence analysis of these clones revealed a repetitive element of approximately 5.7 kb in length. This element, termed CgT1, was dispersed in the genome and present in about 30 copies. The element contained open reading frames encoding deduced sequence motifs homologous to gag-like proteins, reverse transcriptase and RNase H domains of non-LTR retrotransposons. The termini of CgT1 lacked long terminal repeats (LTRs) but contained a 3' A-rich domain. The insertion site of one copy of the element was flanked by short 13-bp direct repeats. These characteristics of the termini, taken together with the overall structure and sequence homologies, indicate that CgT1 belongs to the non-LTR, LINE-like retrotransposon class of elements that are present in many eukaryotes. PCR primers designed to amplify regions of CgT1 can be used to distinguish biotypes A and B in Australia. DNA fingerprinting analysis of genomic DNA using hybridisation probes derived from the terminal regions of CgT1 revealed that Australian isolates of biotype B are monomorphic. CgT1 was not detected in some isolates causing Type B disease from other countries and when CgT1 was present there was considerable polymorphism in CgT1 organisation in the genome. CgT1 is the first transposon-like element to be identified in the genus Colletotrichum and has considerable potential as a tool for the study of population structure, genome dynamics and evolution in C. gloeosporioides