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

doi:10.1186/1471-2148-6-13

BMC Evolutionary Biology

Volume 6

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Wang LS
Tang J
Rymarquis L
Stern DB
dePamphilis CW

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Wang LS
Tang J
Rymarquis L
Stern DB
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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

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

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

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

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

author email corresponding author email

BMC Evolutionary Biology 2006, 6:13doi: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

Additional File 3:

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

Format: TXT Size: 6KB Download file

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

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

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