Abstract
The nuclear genome of eukaryotes contains large amounts of cytoplasmic organelle DNA (nuclear integrants of organelle DNA [norgs]). The recent sequencing of many mitochondrial and chloroplast genomes has enabled investigation of the potential role of norgs in endosymbiotic evolution. In this article, we describe a new polymerase chain reaction-based method that allows the identification and evolutionary study of recent and older norgs in a range of eukaryotes. We tested this method in the genus Nicotiana and obtained sequences from seven nuclear integrants of plastid DNA (nupts) totaling 25 kb in length. These nupts were estimated to have been transferred 0.033 to 5.81 million years ago. The spectrum of mutations present in the potential protein-coding sequences compared with the noncoding sequences of each nupt revealed that nupts evolve in a nuclear-specific manner and are under neutral evolution. Indels were more frequent in noncoding regions than in potential coding sequences of former chloroplastic DNA, most probably due to the presence of a higher number of homopolymeric sequences. Unexpectedly, some potential protein-coding sequences within the nupts still contained intact open reading frames for up to 5.81 million years. These results suggest that chloroplast genes transferred to the nucleus have in some cases several millions of years to acquire nuclear regulatory elements and become functional. The different factors influencing this time frame and the potential role of nupts in endosymbiotic gene transfer are discussed.
Highlights
We identified deletion events larger than 20 bp that were unique to the chloroplast genome of Nicotiana tomentosiformis by aligning the plastome sequence of Nicotiana sylvestris, N. tomentosiformis, N. tabacum, Atropa belladona, and Solanum lycopersicum
These two species contain the same deletions when compared with other Solanaceae since N. sylvestris was the maternal diploid parent of the allotetraploid N. tabacum, which was formed,0.2 million years ago (Mya; Clarkson et al, 2005), and the plastomes of these two species only differ by nine nucleotides (Yukawa et al, 2006)
Such comparisons revealed seven deletions that were unique to the plastome of N. tomentosiformis and two that characterized the plastomes of N. sylvestris and N. tabacum
Summary
We describe a new polymerase chain reaction-based method that allows the identification and evolutionary study of recent and older norgs in a range of eukaryotes We tested this method in the genus Nicotiana and obtained sequences from seven nuclear integrants of plastid DNA (nupts) totaling 25 kb in length. Some potential protein-coding sequences within the nupts still contained intact open reading frames for up to 5.81 million years These results suggest that chloroplast genes transferred to the nucleus have in some cases several millions of years to acquire nuclear regulatory elements and become functional.
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