Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog Xenopus laevis

Table 2 Gene content in X. tropicalis genes within LLT-triplets compared to the reference set of all X. tropicalis genes with X. laevisorthologs.

Molecular function	Number within referenceSet	Number within LLT triplets	Expected based on reference	Over- or Under-represented (±)	p-Value
Transfer/carrier	123	46	29.11	+	0.06
Membrane traffic	165	57	39.05	+	0.107
Defense/immunity	90	10	21.3	-	0.146
Ribosomal	105	42	24.85	+	0.154
Hydrogen transporter	24	14	5.68	+	0.44
Select regulatory molecule	479	135	113.36	+	0.625
Receptor	309	57	73.13	-	0.787
Nucleodityltransferase	35	8	8.28	-	~1
Double-stranded DNA binding	10	2	2.37	-	~1
Transferase	431	91	102.00	-	~1

Genes were categorized by assigning PANTHER classification terms to our X. tropicalis gene set by HMM scanning of the peptides and then grouping the terms into high-level categories of molecular function. We were able to assign categories to 6393 genes in the reference set and to 1513 genes in the subset. Out null hypothesis is that the second copy of genes following the X. laevis tetraploidization are lost in a random fashion. None of the 10 categories shown here show significant deviation from the null hypothesis, and the remaining molecular categories all have p-values close to 1. All p-values were Bonferroni-corrected for multiple tests.

ISSN: 1741-7007