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

Ryan D. Morin, Elbert Chang, Anca Petrescu, Nancy Liao, Malachi Griffith, Robert Kirkpatrick, Yaron S. Butterfield, Alice C. Young, Jeffrey Stott, Sarah Barber, Ryan Babakaiff, Mark C. Dickson, Corey Matsuo, David Wong, George S. Yang, Duane E. Smailus, Keith D. Wetherby, Peggy N. Kwong, Jane Grimwood, Charles P. BrinkleyMabel Brown-John, Natalie D. Reddix-Dugue, Michael Mayo, Jeremy Schmutz, Jaclyn Beland, Morgan Park, Susan Gibson, Teika Olson, Gerard G. Bouffard, Miranda Tsai, Ruth Featherstone, Steve Chand, Asim S. Siddiqui, Wonhee Jang, Ed Lee, Steven L. Klein, Robert W. Blakesley, Barry R. Zeeberg, Sudarshan Narasimhan, John N. Weinstein, Christa Prange Pennacchio, Richard M. Myers, Eric D. Green, Lukas Wagner, Daniela S. Gerhard, Marco A. Marra, Steven J.M. Jones, Robert A. Holt

Research output: Contribution to journalArticlepeer-review

63 Scopus citations

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.

Original languageEnglish
Pages (from-to)796-803
Number of pages8
JournalGenome research
Volume16
Issue number6
DOIs
StatePublished - Jun 2006

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