<p>Abstract</p> <p>Background</p> <p>Plastid genome content and protein sequence are highly conserved across land plants and their closest algal relatives. Parasitic plants, which obtain some or all of their nutrition through an attachment to a host plant, are often a striking exception. Heterotrophy can lead to relaxed constraint on some plastid genes or even total gene loss. We sequenced plastid genomes of two species in the parasitic genus <it>Cuscuta </it>along with a non-parasitic relative, <it>Ipomoea purpurea</it>, to investigate changes in the plastid genome that may result from transition to the parasitic lifestyle.</p> <p>Results</p> <p>Aside from loss of all <it>ndh </it>genes, <it>Cuscuta exaltata </it>retains photosynthetic and photorespiratory genes that evolve under strong selective constraint. <it>Cuscuta obtusiflora </it>has incurred substantially more change to its plastid genome, including loss of all genes for the plastid-encoded RNA polymerase. Despite extensive change in gene content and greatly increased rate of overall nucleotide substitution, <it>C. obtusiflora </it>also retains all photosynthetic and photorespiratory genes with only one minor exception.</p> <p>Conclusion</p> <p>Although <it>Epifagus virginiana</it>, the only other parasitic plant with its plastid genome sequenced to date, has lost a largely overlapping set of transfer-RNA and ribosomal genes as <it>Cuscuta</it>, it has lost all genes related to photosynthesis and maintains a set of genes which are among the most divergent in <it>Cuscuta</it>. Analyses demonstrate photosynthetic genes are under the highest constraint of any genes within the plastid genomes of <it>Cuscuta</it>, indicating a function involving RuBisCo and electron transport through photosystems is still the primary reason for retention of the plastid genome in these species.</p
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