Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling

Xenopus
  1. Ryan D. Morin1,
  2. Elbert Chang1,
  3. Anca Petrescu1,
  4. Nancy Liao1,
  5. Malachi Griffith1,
  6. Robert Kirkpatrick1,
  7. Yaron S. Butterfield1,
  8. Alice C. Young3,
  9. Jeffrey Stott1,
  10. Sarah Barber1,
  11. Ryan Babakaiff1,
  12. Mark C. Dickson2,
  13. Corey Matsuo1,
  14. David Wong1,
  15. George S. Yang1,
  16. Duane E. Smailus1,
  17. Keith D. Wetherby3,
  18. Peggy N. Kwong3,
  19. Jane Grimwood2,
  20. Charles P. Brinkley III3,
  21. Mabel Brown-John1,
  22. Natalie D. Reddix-Dugue3,
  23. Michael Mayo1,
  24. Jeremy Schmutz2,
  25. Jaclyn Beland1,
  26. Morgan Park3,
  27. Susan Gibson1,
  28. Teika Olson1,
  29. Gerard G. Bouffard3,
  30. Miranda Tsai1,
  31. Ruth Featherstone1,
  32. Steve Chand1,
  33. Asim S. Siddiqui1,
  34. Wonhee Jang7,
  35. Ed Lee7,
  36. Steven L. Klein6,
  37. Robert W. Blakesley3,
  38. Barry R. Zeeberg4,
  39. Sudarshan Narasimhan9,
  40. John N. Weinstein4,
  41. Christa Prange Pennacchio8,
  42. Richard M. Myers2,
  43. Eric D. Green3,
  44. Lukas Wagner7,
  45. Daniela S. Gerhard5,
  46. Marco A. Marra1,
  47. Steven J.M. Jones1, and
  48. Robert A. Holt1,10
  1. 1 British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada;
  2. 2 Stanford Human Genome Center and Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA;
  3. 3 NIH Intramural Sequencing Center, National Human Genome Research Institute,
  4. 4 Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology,
  5. 5 National Cancer Institute, and
  6. 6 National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA;
  7. 7 National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20894, USA;
  8. 8 The I.M.A.G.E Consortium, Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, California 94550, USA;
  9. 9 2SRA International, Fairfax, Virginia 22033, USA

Abstract

Sequencing of full-insert clones from full-length cDNA libraries from both Xenopus laevis and Xenopus tropicalis has been ongoing as part of the Xenopus Gene Collection Initiative. Here we present 10,967 full ORF verified cDNA clones (8049 from X. laevis and 2918 from X. tropicalis) as a community resource. Because the genome of X. laevis, but not X. tropicalis, has undergone allotetraploidization, comparison of coding sequences from these two clawed (pipid) frogs provides a unique angle for exploring the molecular evolution of duplicate genes. Within our clone set, we have identified 445 gene trios, each comprised of an allotetraploidization-derived X. laevis gene pair and their shared X. tropicalis ortholog. Pairwise dN/dS, comparisons within trios show strong evidence for purifying selection acting on all three members. However, dN/dS ratios between X. laevis gene pairs are elevated relative to their X. tropicalis ortholog. This difference is highly significant and indicates an overall relaxation of selective pressures on duplicated gene pairs. We have found that the paralogs that have been lost since the tetraploidization event are enriched for several molecular functions, but have found no such enrichment in the extant paralogs. Approximately 14% of the paralogous pairs analyzed here also show differential expression indicative of subfunctionalization.

Footnotes

  • 10

    ↵10 Corresponding author.

    ↵10 E-mail rholt{at}bcgsc.ca; fax (604) 877-6085.

  • [Supplemental material is available online at www.genome.org. The sequence data from this study have been submitted to GenBank under accession nos. BC040971–BC100665 (not exclusively). Keyword MGC and organism Xenopus will be required to get only the XGC sequences in the range.]

  • The content of this publication does not necessarily reflect the views or policies of the U.S. Department of Health and Human Services, nor does mention of trade names, commercial products, or organization imply endorsement by the U.S. Government.

  • Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.4871006

    • Received October 28, 2005.
    • Accepted March 16, 2006.
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  1. Published in Advance May 3, 2006, doi: 10.1101/gr.4871006 Genome Res. 16: 796-803 Cold Spring Harbor Laboratory Press

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