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

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.

Figure 1.

Frequencies of d_N/d_S ratio (ω) for pairwise comparisons between X. laevis and X. tropicalis genes. The distribution of d_N/d_S from pairwise comparisons of genes within gene trios is shown. ωs from X. laevis paralog pairs (shown in red) indicate a weaker selective constraint than the ω obtained from the comparisons of X. laevis paralogs with their X. tropicalis ortholog (shown in gray and blue). The ωs from both paralog–ortholog pairs follow a similar distribution with a lower median than the ω obtained from the paralogs in each trio (P = 2.184 × 10⁻⁷).

Figure 2.

Distribution of d_S for pairwise comparisons between paralogs and orthologs. Distribution of d_S from pairwise comparison between X. laevis paralogs (red) and from pairwise comparisons between each X. laevis paralog from a trio with its X. tropicalis ortholog (blue and gray). The small number (eight in total) of d_S values that were >1 were eliminated to provide an appropriate scale.

Figure 3.

Clustered Image Map of genes with no paralog versus GO categories for categories with significant enrichment. Thumbnail clustered image map (CIM) of genes (top) versus categories (right) for categories with a false discovery rate (FDR) ≤0.10. Very large generic categories have been removed to improve visualization. Clustering was performed with the Genesis Client (Sturn et al. 2002; http://genome.tugraz.at/Software/GenesisCenter.html). Three major clusters can be seen. Processes involved in general metabolism (far left) include “cofactor catabolism,” “acetyl-CoA catabolism,” “aerobic respiration,” “cellular respiration,” and “tricarboxylic acid cycle.” Processes involved in nucleic acid processing (bottom right) include “RNA metabolism,” “transcription,” “nucleobase metabolism,” “DNA replication,” and “DNA metabolism.” The third cluster contains GO categories involved in nucleoside metabolism such as “nucleobase metabolism,” “pyrimidine base biosynthesis,” and “nucleobase biosynthesis.” The full-size CIM in which all genes are displayed is available as Supplemental Figure S6.