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Open Access Highly Accessed Methodology article

A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses

Philippa C Griffin1*, Charles Robin1 and Ary A Hoffmann12

Author Affiliations

1 Department of Genetics, University of Melbourne, Parkville 3010, Victoria, Australia

2 Department of Zoology, University of Melbourne, Parkville 3010, Victoria, Australia

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BMC Biology 2011, 9:19  doi:10.1186/1741-7007-9-19

Published: 23 March 2011

Additional files

Additional file 1:

Figure S1 - Alignment of partial trnH-psbA spacer region showing insertional mutation across the Poaceae. The predicted hairpin structure is shown in the upper panel, with conserved regions involved in hairpin binding colored as per the alignment in the lower panel. Species names are shaded according to subfamily: Arundinoideae (pink), Bambusoideae (light blue), Chloridoideae (green), Ehrhartoideae (Yellow), Panicoideae (dark blue), Pooideae (red), uncertain (grey). One Liliaceae sequence is included, outlined in black.

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Additional file 2:

Figure S2 - Spatial genetic autocorrelation plots for the chloroplast markers. The two markers that revealed spatial genetic structure are shown: rpl32-trnL (A-B, E-F) and rpoB-trnC (C-D, G-H). Analyses were repeated including (A, C, E, G) and excluding (B, D, F, H) the Tasmanian samples, and for large-scale (A-D) and small-scale (E-H) distances. Solid black line joins the mean r values for each distance class, with 95% CI shown by the error bars (determined by 999 bootstrap resampling repeats). The dotted red lines bound the 95% CI about the null hypothesis (determined by 999 permutations).

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Additional file 3:

Table SI - Primers and PCR details for the regions amplified. Table showing primer sequences and variation from the PCR protocol described in the text for each gene region amplified.

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Additional file 4:

Supplementary Text - Detailed instructions for barcode deconvolution in R. Text file including R code.

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