Physical map of a conditionally dispensable chromosome in Nectria haematococca mating population VI and location of chromosome breakpoints

Certain isolates of the plant pathogenic fungus Nectria haematococca mating population (MP) VI contain a 1.6-Mb conditionally dispensable (CD) chromos ome carrying the phytoalexin detoxification genes MAK1 and PDA6-1. This chr omosome is structurally unstable during sexual reproduction. As a first ste p in our analysis of the mechanisms underlying this chromosomal instability , hybridization between overlapping cosmid clones was used to construct a m ap of the MAK1 PDA6-1 chromosome. The map consists of 33 probes that are li nked by 199 cosmid clones. The polymerase chain reaction and Southern analy sis of N. haematococca MP VI DNA digested with infrequently cutting restric tion enzymes were used to close gaps and order the hybridization-derived co ntigs. Hybridization to a probe extended from telomeric repeats was used to anchor the ends of the map to the actual chromosome ends. The resulting ma p is estimated to cover 95% of the MAK1 PDA6-1 chromosome and is composed o f two ordered contigs. Thirty-eight percent of the clones in the minimal ma p are known to contain repeated DNA. sequences. Three dispersed repeats wer e cloned during map construction; each is present in five to seven copies o n the chromosome. The cosmid clones representing the map were probed with d eleted forms of the CD chromosome and the results were integrated into the map. This allowed the identification of chromosome breakpoints and deletion s.