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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  d  N / d  S,  comparisons within trios show strong evidence for purifying selection acting on all three members. However,  d  N / d  S  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.

genome research

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

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