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Open Access Highly Accessed Research article

Molecular evolution of pentatricopeptide repeat genes reveals truncation in species lacking an editing target and structural domains under distinct selective pressures

Michael L Hayes1, Karolyn Giang1 and R Michael Mulligan12*

Author Affiliations

1 Developmental & Cell Biology, University of California, Irvine, USA

2 University of California, 5217 McGaugh Hall, Irvine, CA 92697, USA

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BMC Evolutionary Biology 2012, 12:66  doi:10.1186/1471-2148-12-66

Published: 14 May 2012

Additional files

Additional file 1:

Distribution of putative editing sites in selected Brassicaceae linages. A table depicts the nucleotide that aligns with an editing site in A. thaliana derived from chloroplast sequences for Brassicaceae species.

Format: XLS Size: 38KB Download file

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Additional file 2:

Alignment ofcis-elements for CRR4, CRR21, CLB19, and OTP82. A figure illustrates nucleotide sequences around editing sites targeted by four PPR proteins. Each sequence represents 20 nucleotides upstream and 5 nucleotides downstream of the editing site. The editing sites are indicated capitalized characters. Nucleotides that are 100% conserved are blocked in black.

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Additional file 3:

Genebank accession numbers of analyzed sequences. Genebank accession numbers for sequences of PPR genes determined by this work are provided in a single table.

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Additional file 4:

Examination of species with truncatedCRR21genes for potential duplicate copies ofCRR21.

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Additional file 5:

Rate of evolution of theCRR4 genes in Brassicaceae and PTCD3 in mammals. The dN/dS values for a 27nt window are plotted versus the midpoint position of each window for CRR4 (at top) and PTCD3 (at bottom). Below the nucleotide positions the respective positions of predicted helices are indicated by labeled boxes.

Format: TIFF Size: 3.9MB Download file

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Additional file 6:

Primers used in this survey.

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