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Extensive Rearrangements in the Chloroplast Genome of Trachelium caeruleum Are Associated with Repeats and tRNA Genes

Abstract

Chloroplast genome organization, gene order, and content are highly conserved among land plants. We sequenced the chloroplast genome of Trachelium caeruleum L. (Campanulaceae), a member of an angiosperm family known for highly rearranged genomes. The total genome size is 162,321 bp, with an inverted repeat (IR) of 27,273 bp, large single-copy (LSC) region of 100,114 bp, and small single-copy (SSC) region of 7,661 bp. The genome encodes 112 different genes, with 17 duplicated in the IR, a tRNA gene (trnI-cau) duplicated once in the LSC region, and a protein-coding gene (psbJ) with two duplicate copies, for a total of 132 putatively intact genes. ndhK may be a pseudogene with internal stop codons, and clpP, ycf1, and ycf2 are so highly diverged that they also may be pseudogenes. ycf15, rpl23, infA, and accD are truncated and likely nonfunctional. The most conspicuous feature of the Trachelium genome is the presence of 18 internally unrearranged blocks of genes inverted or relocated within the genome relative to the ancestral gene order of angiosperm chloroplast genomes. Recombination between repeats or tRNA genes has been suggested as a mechanism of chloroplast genome rearrangements. The Trachelium chloroplast genome shares with Pelargonium and Jasminum both a higher number of repeats and larger repeated sequences in comparison to eight other angiosperm chloroplast genomes, and these are concentrated near rearrangement endpoints. Genes for tRNAs occur at many but not all inversion endpoints, so some combination of repeats and tRNA genes may have mediated these rearrangements.

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Acknowledgments

Funding for this project was provided by a grant from the NSF (DEB 0120709) to R.K.J. and J.L.B. Part of this work was performed under the auspices of the U.S. Department of Energy, Office of Biological and Environmental Research, by the University of California, Lawrence Berkeley National Laboratory, under contract No. DE-AC02-05CH11231. The authors thank Stacia Wyman for computational assistance and Tim Chumley and Gwen Gage for technical assistance in generating figures. We also thank Andrew Alverson, Katie Hansen, Paul Wolf, and Elizabeth Ruck for their helpful comments and suggestions on an early version of the manuscript. This paper represents a portion of R.C.H.’s Ph.D. thesis in botany at the University of Texas at Austin.

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Correspondence to Rosemarie C. Haberle.

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Haberle, R.C., Fourcade, H.M., Boore, J.L. et al. Extensive Rearrangements in the Chloroplast Genome of Trachelium caeruleum Are Associated with Repeats and tRNA Genes. J Mol Evol 66, 350–361 (2008). https://doi.org/10.1007/s00239-008-9086-4

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  • DOI: https://doi.org/10.1007/s00239-008-9086-4

Keywords

  • Chloroplast genome evolution
  • Genome rearrangements
  • Repeated sequences
  • Trachelium caeruleum
  • Campanulaceae