Open Access Highly Accessed Research article

Horizontal transfer of expressed genes in a parasitic flowering plant

Zhenxiang Xi1, Robert K Bradley23, Kenneth J Wurdack4, KM Wong5, M Sugumaran6, Kirsten Bomblies1, Joshua S Rest7* and Charles C Davis1*

Author Affiliations

1 Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA, 02138, USA

2 Computational Biology Program, Public Health Sciences Division, Fred, Hutchinson Cancer Research Center, Seattle, WA, 98109, USA

3 Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA

4 Department of Botany, Smithsonian Institution, Washington, DC, 20013, USA

5 Singapore Botanic Gardens, Singapore, 259569, Singapore

6 Rimba Ilmu Botanic Garden, Institute of Biological Sciences, University of Malaya, 50603, Kuala Lumpur, Malaysia

7 Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA

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BMC Genomics 2012, 13:227  doi:10.1186/1471-2164-13-227

Published: 8 June 2012

Additional files

Additional file 1:

Figure S1. Histogram of the assembled cDNA transcript lengths from Illumina Genome Analyzer II sequencing of Rafflesia cantleyi .

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Additional file 2:

Figure S2. Histogram of the assembled cDNA transcript lengths from GS-FLX 454-sequencing of Tetrastigma rafflesiae .

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Additional file 3:

Table S1. Data sources of protein coding DNA sequences from whole genome sequencing used in the comparative phylogenomic analyses.

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Additional file 4:

Figure S3. Bar chart showing the distribution of bootstrap support for putative VGT (dark grey) and HGT (light grey) transcripts identified for Rafflesia cantleyi .

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Additional file 5:

Figure S4. Elevated inference of HGT genes in Rafflesia cantleyi is not sensitive to our bootstrap cutoff thresholds. The percentage of HGT genes in Malpighiales (Rafflesia, Manihot esculenta, and Ricinus communis) was the number of genes sister to Vitis vinifera, in proportion to the total number of genes with resolved relationships, at the specified bootstrap thresholds. For Tetrastigma rafflesiae, HGT percentage is the number of genes that are sister to Malpighiales in proportion to the total number of genes with resolved relationships, at the specified bootstrap thresholds.

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Additional file 6:

Figure S5. (A) Summary of nucleotide substitution rates in Rafflesia cantleyi HGT transcripts versus homologous Vitis vinifera transcripts; (B) Summary of nucleotide substitution rates in Rafflesia cantleyi VGT transcripts versus homologous Manihot esculenta and Ricinus communis transcripts. The boxplot was truncated so that the median can be better visualized. The number of transcripts used to construct each boxplot is shown in parentheses.

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Additional file 7:

Table S2. Putative gene location and function of Rafflesia cantleyi HGT transcripts based on NCBI BLAST search results.

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Additional file 8:

Figure S6. Percentages of Rafflesia cantleyi HGTs (dark grey) and VGTs (light grey) for which gDNA Illumina reads can be positively mapped onto the assembled transcripts, as a function of bootstrap support for the VGT and HGT inference.

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Additional file 9:

Figure S7. Percentages of Rafflesia cantleyi HGTs (dark grey) and VGTs (light grey) for which gDNA Illumina reads can be positively mapped onto the assembled transcripts, as a function of transcript length for the VGT and HGT inference.

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Additional file 10:

Figure S8. Nucleotide sequence alignment for a typical intron-bearing HGT transcript identified from Rafflesia cantleyi genomic DNA sequencing. Nucleotides are denoted as dots when identical to the consensus sequence. The Rafflesia HGT transcript is printed in red, and sequences from genomic DNA are marked with asterisks. The intron is highlighted in grey for Rafflesia.

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Additional file 11:

Figure S9. Summary of the number of Rafflesia cantleyi cDNA Illumina reads re-mapped onto the assembled VGT and HGT transcripts. The boxplot was truncated so that the median can be better visualized. The number of transcripts used to construct each boxplot is shown in parentheses. (RPKM = reads per kilobase per million reads).

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