Fig 1.
Phylogenetic topology and detoxification gene numbers of seventeen insect organisms.
The phylogenetic topology of nine Aphidinae species and eight other phytophagous insect organisms was taken from papers. The tree was rooted using five insect organisms from the Lepidoptera and Coleoptera. Gene counts are the total numbers of the ATP-binding cassette transporter, cytochrome P450 monooxygenases, glutathione S-transferases, carboxylesterase and UDP-glycosyltransferases.
Fig 2.
Analysis of three gene families (GST, CCE, P450) in two Aphidinae species and Bemisia tabaci.
These two Aphidinae species are from two different Aphidinae branches of the phylogenetic topology shown in Fig 1. M. persicae belong to tribe Macrosiphini, S. graminum belong to tribe Aphidini. These three gene families contract in Aphidinae compared with other insect organisms. (A) GST, (B) CCE, (C) P450. Genes in different species are color-coded as follows: Myzus persicae, red; Schizaphis graminum, green; B. tabaci, grey. Red stars indicate detoxification-related subfamilies.
Fig 3.
Phylogenetic relationships and gene gain-and-loss events of two subclades.
Genus- specific expansions of CYP4 and Delta occur in the genus Acyrthosiphon. Notung was used to calculate numbers of gene gain-and-loss, and numbers are presented above branches with negative and plus signs, respectively. Maximum-likelihood trees of the CYP4 and Delta genes were developed by using PhyML. (A) Gene gain-and-loss events of Delta subfamily. Most duplications occurred before formation of the genus Acyrthosiphon and are indicated in red. (B) The phylogenetic tree of the Delta subfamily in nine Aphidinae species. Clade for most of the genus Acyrthosiphon is highlighted in grey arc. (C) Gene gain-and-loss events of CYP4 subclade. Most duplications occurred after formation of the genus Acyrthosiphon and are indicated in red. (D) Phylogenetic tree of CYP4 clade in nine Aphidinae species. The clade for A. kondoi most and the clade for the genus Aphis only are highlighted in the grey arc, respectively. Red palette indicates the tribe Macrosiphini, green palette indicates the tribe Aphidini. Genes in different species are colour-coded as follows: S. graminum, green; R. padi, dark sea green; A. glycines, spring green; A. gossypii, green yellow; D. noxia, hot pink; M. persicae, pink; S. avenae, dark orange; A. pisum, red; and A. kondoi, magenta. The numbers after the aphid species names indicate numbers of Delta or CYP4 genes in the extant aphid species.
Fig 4.
Relative evolutionary rate reflected by amino acid sequence identity.
The upper line, middle line, lower line and error symbol indicate upper quartile, median, lower quartile and average of each box, respectively. (A) The amino acid sequence identity within nine Aphidinae species of eleven detoxification-related subfamilies and five detoxification families is exhibited by scatter diagram. Colors of species are the same as in Fig 3. (B) Sequence identity among nine Aphidinae species of the eleven detoxification-related subfamilies and five detoxification families is displayed by scatter diagram. (C) Sequence identity among nine Aphidinae species of eleven detoxification-related subfamilies, eleven detoxification-unrelated subfamilies and the UGT family is exhibited by box plot. Detoxification-related subfamilies are displayed in solid boxes, whereas the detoxification-unrelated subfamilies are hollow boxes. Colors of detoxification families are the same as in Fig 1.