Open Access Highly Accessed Research article

Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach

Liying Cui1, Jim Leebens-Mack1, Li-San Wang2, Jijun Tang3, Linda Rymarquis4, David B Stern4 and Claude W dePamphilis1*

Author Affiliations

1 Department of Biology, Institute of Molecular Evolutionary Genetics, and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA

2 Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA

3 Department of Computer Science and Engineering, University of South Carolina, Columbia, SC 29208, USA

4 Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA

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BMC Evolutionary Biology 2006, 6:13  doi:10.1186/1471-2148-6-13

Published: 9 February 2006

Additional files

Additional File 1:

Gene coding and functional categories. Text file, lists the names of 85 genes included in the study and corresponding functional categories.

Format: TXT Size: 3KB Download file

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Additional File 3:

The gene order data set. Text file, contains gene orders of seven chloroplast genomes, computed Cs and Cf indices, and the inferred rearrangement phylogeny.

Format: TXT Size: 6KB Download file

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Additional File 2:

Protein alignment matrix. Text file, with a NEXUS format data matrix of concatenated proteins from seven chloroplast genomes and the outgroup, Cyanophora paradoxa.

Format: TXT Size: 169KB Download file

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Additional File 4:

Comparison of gene clusters. Text file, shows gene clusters shared between the inferred ancestral genome of C. reinhardtii and C. vulgaris to the cpDNA of C. vulgaris and N. olivacea.

Format: TXT Size: 2KB Download file

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Additional File 5:

Inversions separating N. tabacum and M. polymorpha cpDNA. Text file, shows the possible scenarios to transform the chloroplast gene order of N. tabacum to M. polymorpha cpDNA through inversions.

Format: TXT Size: 1KB Download file

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