Antagonistic relationships between intron content and codon usage bias of genes in three mosquito species: functional and evolutionary implications

Abstract

Genome biology of mosquitoes holds potential in developing knowledge-based control strategies against vectorborne diseases such as malaria, dengue, West Nile, and others. Although the genomes of three major vector mosquitoes have been sequenced, attempts to elucidate the relationship between intron and codon usage bias across species in phylogenetic contexts are limited. In this study, we investigated the relationship between intron content and codon bias of orthologous genes among three vector mosquito species. We found an antagonistic relationship between codon usage bias and the intron number of genes in each mosquito species. The pattern is further evident among the intronless and the intron-containing orthologous genes associated with either low or high codon bias among the three species. Furthermore, the covariance between codon bias and intron number has a directional component associated with the species phylogeny when compared with other nonmosquito insects. By applying a maximum likelihood-based continuous regression method, we show that codon bias and intron content of genes vary among the insects in a phylogeny-dependent manner, but with no evidence of adaptive radiation or species-specific adaptation. We discuss the functional and evolutionary significance of antagonistic relationships between intron content and codon bias.

Keywords: Intron; codon bias; coevolution; mosquito; ortholog.

Figure 1

Scatter plots between codon bias and number of introns of 1:1:1 orthologous genes among Aedes aegypti (top), Culex quinquefasciatus (middle), and Anopheles gambiae (bottom). The x-axis represents codon bias index (SCUO), and y-axis represents number of introns of genes.

Figure 2

Number of genes associated with low (L)/high (H) intron number (INT) and/or low/high codon bias (CB) in Aedes aegypti (top row), Anopheles gambiae (middle row) and Culex quinquefasciatus (bottom row). The observed and the bootstrap experiment (BSExp) data are shown. In BSExp 1, both codon bias and intron number of the genes were randomized simultaneously, whereas either codon bias or intron number of the genes was randomized in BSExp 2 and BSExp 3, respectively. Error bars represent standard error values. The color code on the top of the graph represents the four gene groups. The abbreviation of these gene groups are as follows: LCB – low codon bias; HCB – high codon bias; LINT – low intron content; HINT – high intron content. The Yates' chi square P-values determined based on 2x2 contingency tests of the four gene groups, which remain unchanged between observed and randomized data sets, are shown for each species.

Figure 3

Distribution of intronless genes among the 1:1:1 orthologous genes among Aedes aegypti, Culex quinquefasciatus, and Anopheles gambiae. The Venn diagram shows the number and percentage of orthologous genes, which are intronless either within or between species. The significance of permanova tests between gene groups (g1 through g6) are shown to the right of the Venn diagram.

Figure 4

Hierarchical cluster patterns of codon bias (high: pink color and low: black color) and intron number (high: green color and low: black color) among orthologous genes (n = 226) among the three mosquitoes (Aedes aegypti, Aaeg; Culex quinquefasciatus, Cqui; and Anopheles gambiae, Agam) and three nonmosquito insects Drosophila melanogaster, Dmel; Apis mellifera, Amel; and Pediculus humanus, Phum). The cluster patterns of variation, in tree formats, are shown to the left and right of the corresponding self-organizing maps.