Figure 3.

Inverted repeat length variation in Medicago minima. Both polymorphisms extended the IR into the small single‐copy region (SSC). A schematic representing a single unit of the M. minima plastome is presented for context. Inverted repeat expansion to the A haplotype (A) included an additional 13 bp of single‐copy sequence (gray) in the IR. The expansion includes 10 bp upstream of J_SB (boxed) that were single copy in M. minima plastomes that lack the expansion (O). Five base pairs were inserted at J_SA (TTTAT), and five base pairs of formerly single‐copy sequence have likely undergone gene conversion (ATAGA ➔ TATGA) homogenizing the two repeats. The extension of the IR places both junctions adjacent to an existing three‐base sequence (TGG, gray, and black dots) that is present in near both ends of the SSC in M. minima plastomes that contain unexpanded IRs. The polymorphic expansion yielding haplotype B (B) included 11 bp in the M. minima IR relative to the unexpanded O haplotype. Gene conversion templates are boxed. bp; base pairs. LSC; large single‐copy region. SSC; small single‐copy region. IR; inverted repeat. J_SB and J_LB; boundary of IR_B with SSC and LSC, respectively. J_SA and J_LA; boundary of IRA with SSC and LSC, respectively