Comparative analysis of nuclear tRNA genes of Nasonia vitripennis and other arthropods, and relationships to codon usage bias

Abstract

Using bioinformatics methods, we identified a total of 221 and 199 tRNA genes in the nuclear genomes of Nasonia vitripennis and honey bee (Apis mellifera), respectively. We performed comparative analyses of Nasonia tRNA genes with honey bee and other selected insects to understand genomic distribution, sequence evolution and relationship of tRNA copy number with codon usage patterns. Many tRNA genes are located physically close to each other in the form of small clusters in the Nasonia genome. However, the number of clusters and the tRNA genes that form such clusters vary from species to species. In particular, the Ala-, Pro-, Tyr- and His-tRNA genes tend to accumulate in clusters in Nasonia but not in honey bee, whereas the bee contains a long cluster of 15 tRNA genes (of which 13 are Gln-tRNAs) that is absent in Nasonia. Though tRNA genes are highly conserved, contrasting patterns of nucleotide diversity are observed among the arm and loop regions of tRNAs between Nasonia and honey bee. Also, the sequence convergence between the reconstructed ancestral tRNAs and the present day tRNAs suggests a common ancestral origin of Nasonia and honey bee tRNAs. Furthermore, we also present evidence that the copy number of isoacceptor tRNAs (those having a different anticodon but charge the same amino acid) is correlated with codon usage patterns of highly expressed genes in Nasonia.

Figure 1

Clusters of tRNA genes (clusters with > 5 genes are shown) in Nasonia (filled) and honey bee (empty). Letters on top represent the amino acid the gene is cognate to, and numbers on the bottom show the intergenic distance in kb (rounded to one decimal).

Figure 2

Sequence evolution patterns of Nasonia and honey bee tRNA genes. A) Correlation in the nucleotide diversity (π value) of tRNA genes between Nasonia and honey bee. B) The average nucleotide differences (y-axis) vary among the tRNA genes of Nasonia and honey bee. Some tRNAs show the least number of nucleotide differences (highly conserved) whereas others show elevated numbers of nucleotide differences (relatively less conserved).

Figure 3

A minimum evolution phylogenetic tree of Tyr-tRNA genes of Nasonia and honey bee. The genetic distance scale is shown at the bottom.

Figure 4

Contrasting patterns of the relationship of tRNA gene abundance in Nasonia genome with the codon usage between: A) a group of 100 genes predicted to be highly expressed and B) all other genes of Nasonia. Codon usage was measured by RSCU (relative synonymous codon usage) and tRNA abundance was measured by RAIT (relative abundance of isoacceptor tRNAs).

Figure 5

Correlation patterns between RAIT (x-axis) and RSCU (y-axis) of orthologous ribosomal protein genes in N.vitripennis, A. mellifera and D. melanogaster. The specific codons that show correlation to the cognate tRNA copy number are shown at the right side of the graph.