Sequencing of individual chromosomes of plant pathogenic Fusarium oxysporum

Abstract A small chromosome in reference isolate 4287 of F. oxysporum f. sp. lycopersici ( Fol ) has been designated as a ‘pathogenicity chromosome’ because it carries several pathogenicity related genes such as the Secreted In Xylem ( SIX ) genes. Sequence assembly of small chromosomes in other isolates, based on a reference genome template, is difficult because of karyotype variation among isolates and a high number of sequences associated with transposable elements. These factors often result in misassembly of sequences, making it unclear whether other isolates possess the same pathogenicity chromosome harboring SIX genes as in the reference isolate. To overcome this difficulty, single chromosome sequencing after Contour-clamped Homogeneous Electric Field (CHEF) separation of chromosomes was performed, followed by de novo assembly of sequences. The assembled sequences of individual chromosomes were consistent with results of probing gels of CHEF separated chromosomes with SIX genes. Individual chromosome sequencing revealed that several SIX genes are located on a single small chromosome in two pathogenic forms of F. oxysporum , beyond the reference isolate 4287, and in the cabbage yellows fungus F. oxysporum f. sp. conglutinans . The particular combination of SIX genes on each small chromosome varied. Moreover, not all SIX genes were found on small chromosomes; depending on the isolate, some were on big chromosomes. This suggests that recombination of chromosomes and/or translocation of SIX genes may occur frequently. Our method improves sequence comparison of small chromosomes among isolates.