TY  - JOUR
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
Y1  - 2006/06/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 796 
EP  - 803 
DO  - 10.1101/gr.4871006 
VL  - 16 
IS  - 6 
UR  - http://genome.cshlp.org/content/16/6/796.abstract 
N2  - 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. 
ER  -