MBE Advance Access published online on August 17, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl089
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1 The University of Texas at Austin, Austin, Texas
* To whom correspondence should be addressed. The chloroplast genome of Pelargonium x hortorum has been completely sequenced. It maps as a circular molecule of 217,942 bp, and is both the largest and most rearranged land plant chloroplast genome yet sequenced. It features two copies of a greatly expanded inverted repeat (IR) of 75,741 bp each, and consequently diminished single copy regions of 59,710 bp and 6,750 bp. Despite the increase in size and complexity of the genome, the gene content is similar to that of other angiosperms, with the exceptions of a large number of pseudogenes, the recognition of two open reading frames (ORF56 and ORF42) in the trnA intron with similarities to previously identified mitochondrial products (ACRS and pvs-trnA), the losses of accD and trnT-ggu, and in particular, the presence of a highly divergent set of rpoA-like ORFs rather than a single, easily recognized gene for rpoA. The three-fold expansion of the IR (relative to most angiosperms) accounts for most of the size increase of the genome, but an additional 10% of the size increase is related to the large number of repeats found. The Pelargonium genome contains 35 times as many 31 bp or larger repeats than the unrearranged genome of Spinacia. Most of these repeats occur near rearrangement hotspots, and two different associations of repeats are localized in these regions. These associations are characterized by full or partial duplications of several genes, most of which appear to be nonfunctional copies or pseudogenes. These duplications may also be linked to the disruption of at least one but possibly two or three operons. We propose simple models that account for the major rearrangements with a minimum of eight IR boundary changes and 12 inversions in addition to several insertions of duplicated sequence.
Accepted August 14, 2006
Research Article
The Complete Chloroplast Genome Sequence of Pelargonium x hortorum: Organization and Evolution of the Largest and Most Highly Rearranged Chloroplast Genome of Land Plants
Timothy W. Chumley 1 *, Jeffrey D. Palmer 2, Jeffrey P. Mower 2, H. Matthew Fourcade 3, Patrick J. Calie 4, Jeffrey L. Boore 5, and Robert K. Jansen 1
2 Indiana University, Bloomington, Indiana
3 DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, Walnut Creek, California
4 Eastern Kentucky University, Richmond, Kentucky
5 DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, Walnut Creek, California; University of California, Berkeley, California
Timothy W. Chumley, E-mail: tchumley{at}mail.utexas.edu
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