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Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus
tropicalis reveals post-tetraploidization transcriptome remodeling.
Morin RD, Chang E, Petrescu A, Liao N, Griffith M, Kirkpatrick R, Butterfield YS, Young AC, Stott J,
Barber S, Babakaiff R, Dickson MC, Matsuo C, Wong D, Yang GS, Smailus DE, Wetherby KD, Kwong PN, Grimwood J, Brinkley CP 3rd,
Brown-John M, Reddix-Dugue ND, Mayo M, Schmutz J, Beland J, Park M, Gibson S, Olson T, Bouffard GG, Tsai M, Featherstone R,
Chand S, Siddiqui AS, Jang W, Lee E, Klein SL, Blakesley RW, Zeeberg BR, Narasimhan S, Weinstein JN, Pennacchio CP,
Myers RM, Green ED, Wagner L, Gerhard DS, Marra MA, Jones SJ, Holt RA.
Genome Res. 2006 Jun;16(6):796-803.
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.
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