Extent of rearrangements between the Scherffelia and Tetraselmis chloroplast genomes.

These genomes were aligned using Mauve 2.3.1. Only one copy of the IR (pink boxes) is shown for each genome. The blocks of colinear sequences containing two or more genes are numbered as in Fig 1. Gene clusters 5 and 6 were retrieved as a single locally colinear block because their very small sizes did not allow them to be resolved in Mauve. Conversely, the gene cluster spanning the LSC/IR junction (cluster 1) was fragmented into three colinear blocks in Mauve because only one copy of the IR was included in this analysis and also because the two genomes were treated as linear instead of circular molecules (the genomes were linearized at the LSC/IR junction).