Fig. 4

Highly differentiated haplotypes within the S. miscanthi LF1 clonal lineage differ in their in their divergence from S. avenae. a Sequence divergence distribution within and between phased haplotypes of JIC1 and LF1 for S. avenae chromosome (scaffold) 2. Comparing the LF1 haplotypes (LF1-H1 and LF1-H2) to either JIC1 haplotype reveals distinct patterns of divergence, with LF1-H1 diverged ~ 0.5% from either JIC1 haplotype, and LF1-H2 diverged by ~ 1%. b Haplotype divergence within and between JIC1 and LF1 in 100-kb fixed windows along S. avenae chromosome (scaffold) 2. The unusual pattern of haplotype divergence observed in LF1 is maintained across the full length of chromosome 2 indicating an absence of recombination. Divergence patterns for all chromosomes are shown in Additional File 2: Figure S12