The highly rearranged chloroplast genome of Trachelium caeruleum (Campanulaceae): multiple inversions, inverted repeat expansion and contraction, transposition, insertions/deletions, and several repeat families

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Abstract
Comprehensive gene mapping reveals that the chloroplast genome of Trachelium caeruleum is highly rearranged relative to those of other land plants. Evolutionary scenarios that consist of seven to ten inversions, one or two transpositions, both expansion and contraction of the typically size-conserved inverted repeat, a presumed gene loss, deletions within two large open reading frames and several insertions, are sufficient to derive the Trachelium arrangement from the ancestral angiosperm chloroplast DNA arrangement. Two of the rearrangements disrupt transcriptional units that are otherwise conserved among land plants. At least five families of small dispersed repeats exist in the Trachelium chloroplast genome. Most of the repeats are associated with inversion endpoints and may have facilitated inversions through recombination across homologous repeats.

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