RT Journal
A1 Morin, Ryan D.
A1 Chang, Elbert
A1 Petrescu, Anca
A1 Liao, Nancy
A1 Griffith, Malachi
A1 Kirkpatrick, Robert
A1 Butterfield, Yaron S.
A1 Young, Alice C.
A1 Stott, Jeffrey
A1 Barber, Sarah
A1 Babakaiff, Ryan
A1 Dickson, Mark C.
A1 Matsuo, Corey
A1 Wong, David
A1 Yang, George S.
A1 Smailus, Duane E.
A1 Wetherby, Keith D.
A1 Kwong, Peggy N.
A1 Grimwood, Jane
A1 Brinkley, Charles P.
A1 Brown-John, Mabel
A1 Reddix-Dugue, Natalie D.
A1 Mayo, Michael
A1 Schmutz, Jeremy
A1 Beland, Jaclyn
A1 Park, Morgan
A1 Gibson, Susan
A1 Olson, Teika
A1 Bouffard, Gerard G.
A1 Tsai, Miranda
A1 Featherstone, Ruth
A1 Chand, Steve
A1 Siddiqui, Asim S.
A1 Jang, Wonhee
A1 Lee, Ed
A1 Klein, Steven L.
A1 Blakesley, Robert W.
A1 Zeeberg, Barry R.
A1 Narasimhan, Sudarshan
A1 Weinstein, John N.
A1 Pennacchio, Christa Prange
A1 Myers, Richard M.
A1 Green, Eric D.
A1 Wagner, Lukas
A1 Gerhard, Daniela S.
A1 Marra, Marco A.
A1 Jones, Steven J.M.
A1 Holt, Robert A.
T1 Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling
JF Genome Research 
JO Genome Research 
YR 2006 
FD June 01 
VO 16 
IS 6 
SP 796 
OP 803 
DO 10.1101/gr.4871006 
UL http://genome.cshlp.org/content/16/6/796.abstract 
AB 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.