Additional file 1.

Table S1. DNA sequencing information. Table S2. Genome sequences used in this study. Figure S1. Alignment of plastid trnR-CCG in monilophytes. Selected trnR-CCG sequences from representative monilophyte taxa were aligned to the sequences from the lycophytes Huperzia lucidula and Isoetes flaccida. Alignment positions with >70% identity among sequences are shaded in grey. Predicted tRNA secondary structure is depicted in dot-bracket format above and below the alignment. The tRNA anticodon position is indicated by “AAA” and highlighted in yellow. A deletion in the Cryptogramma gene is indicated by dashes, whereas two insertion sequences (the first in the top five Polypodiopsida species and the second in Polybotrya only) are boxed in red with a red bar indicating their position within the gene sequences. Figure S2. Additional phylogenetic analyses. A) Nt - all positions for MrBayes (RAxML and PhyloBayes results shown in Figure  5). B) Nt - 1st and 2nd positions. C) Nt - 3rd positions. D) Nt - reduced taxon sampling. E) AA - reduced taxon sampling. Figure S3. Depth of sequencing coverage for fern plastomes. Illumina sequencing reads were mapped onto the finished genomes using Bowtie 2.0.0 [47]. Depth of coverage was estimated using a window size of 100 and a step size of 10; it is reported on a logarithmic base 2 scale. Mean coverage for each genome is indicated by the dashed horizontal line. Genome position is given in kilobases.

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Grewe et al. BMC Evolutionary Biology 2013 13:8   doi:10.1186/1471-2148-13-8