Ancestral polyploidy in seed plants and angiosperms (original) (raw)

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Acknowledgements

This work was supported primarily by NSF Plant Genome Research Program (DEB 0638595, The Ancestral Angiosperm Genome Project) and in part by the Department of Biology and by the Huck Institutes of Life Sciences of the Pennsylvania State University. H.M. was also supported by funds from Fudan University. We thank J. Carlson, M. Frohlich, S. DiLoretto, L. Warg, S. Crutchfield, C. Johnson, N. Naznin, X. Zhou, J. Duarte, B. J. Bliss, J. Der and E. Wafula for help and discussion, D. Stevenson and C. Schultz for Zamia samples, J. McNeal, S. Kim and M. Axtell for photographs, and all the members of The Genome Center at Washington University production team, especially L. Fulton, K. Delehaunty and C. Fronick.

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Authors and Affiliations

1. Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, 16802, Pennsylvania, USA
   Yuannian Jiao, Hong Ma & Claude W. dePamphilis
2. Department of Biology, Institute of Molecular Evolutionary Genetics, and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, 16802, Pennsylvania, USA
   Yuannian Jiao, Norman J. Wickett, Lena Landherr, Paula E. Ralph, Yi Hu, Hong Ma & Claude W. dePamphilis
3. Department of Plant Biology, University of Georgia, Athens, 30602, Georgia, USA
   Saravanaraj Ayyampalayam & Jim Leebens-Mack
4. Department of Biology, University of Florida, Gainesville, 32611, Florida, USA
   André S. Chanderbali & Douglas E. Soltis
5. Center for Comparative Genomics, Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, 16802, Pennsylvania, USA
   Lynn P. Tomsho & Stephan C. Schuster
6. Department of Genetics and Biochemistry, Clemson University, Clemson, 29634, South Carolina, USA
   Haiying Liang
7. Florida Museum of Natural History, University of Florida, Gainesville, 32611, Florida, USA
   Pamela S. Soltis
8. The Genome Center at Washington University, Saint Louis, 63108, Missouri, USA
   Sandra W. Clifton
9. Department of Forestry, Wildlife & Fisheries, Institute of Agriculture, The University of Tennessee, Knoxville, 37996, Tennessee, USA
   Scott E. Schlarbaum
10. State Key Laboratory of Genetic Engineering, School of Life Sciences, Institute of Plant Biology, Center for Evolutionary Biology, Fudan University, Shanghai, 200433, China
    Hong Ma
11. Institute of Biomedical Sciences, Fudan University, Shanghai, 200433, China
    Hong Ma

Authors

1. Yuannian Jiao
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2. Norman J. Wickett
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3. Saravanaraj Ayyampalayam
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4. André S. Chanderbali
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5. Lena Landherr
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6. Paula E. Ralph
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7. Lynn P. Tomsho
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8. Yi Hu
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9. Haiying Liang
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10. Pamela S. Soltis
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11. Douglas E. Soltis
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12. Sandra W. Clifton
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13. Scott E. Schlarbaum
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14. Stephan C. Schuster
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15. Hong Ma
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16. Jim Leebens-Mack
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17. Claude W. dePamphilis
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Contributions

Y.J. and C.W.d. designed the study and Y.J. performed the principal data analyses. A.S.C., L.L., P.E.R., Y.H., S.E.S. and H.L. prepared tissues, RNAs, and/or libraries. S.W.C., L.P.T. and S.C.S. generated sequence data. S.A. and J.L.-M. performed the Ancestral Angiosperm Genome Project transcriptome assemblies and MAGIC database construction. Y.J. and C.W.d. drafted the manuscript, and N.J.W., A.S.C., L.L. P.E.R., P.S.S., D.E.S., H.M. and J.L-M. contributed to the planning and discussion of the research and the editing of the manuscript. All authors contributed to and approved the final manuscript.

Corresponding author

Correspondence toClaude W. dePamphilis.

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Competing interests

The authors declare no competing financial interests.

Additional information

Alignments and phylogenetic trees have been deposited in Dryad with package identifier doi:10.5061/dryad.8546.

Supplementary information

Supplementary Information 1

The file contains a Supplementary Discussion, Supplementary References, Supplementary Tables 1-5 and Supplementary Figures 1-8 with legends. (PDF 2117 kb)

Supplementary Table 1

Additional File 1 displays a list of 799 orthogroups with Monocot + Eudicot duplication. (XLS 1635 kb)

Supplementary Table 2

Additional File 2 displays the number of ancient duplications found in orthogroups in all four analyses. (XLS 124 kb)

Supplementary Table 3

Additional File 3 displays data on significant enrichment of GO-SLIM term for the orthogroups with ancient duplication measured by Fisher’s exact test followed by multiple testing corrections. (XLS 27 kb)

Supplementary Information 2

Additional File 4 shows plot of the genomic positions of paralogous pairs of Vitis vinifera genes that arose from duplications prior to the divergence of monocots and eudicots. (PDF 11308 kb)

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Jiao, Y., Wickett, N., Ayyampalayam, S. et al. Ancestral polyploidy in seed plants and angiosperms.Nature 473, 97–100 (2011). https://doi.org/10.1038/nature09916

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• Received: 29 August 2010
• Accepted: 10 February 2011
• Published: 10 April 2011
• Issue Date: 05 May 2011
• DOI: https://doi.org/10.1038/nature09916