Figure S1. Wnt gene subfamilies in Metazoans. Wnt gene subfamilies are shown for the insects Drosophila melanogaster, Tribolium castaneum (Bolognesi et al., 2008), Apis mellifera and Acyrthosiphon pisum, as well as the crustacean Daphnia pulex, Human, and the cnidarian Nematostella (Kusserow et al., 2005). Wnt subfamilies are numbered horizontally with the relationships between these animals shown to the left. A dash indicates where a particular Wnt ligand has not been found and duplications are indicated by overlapping boxes of the same color. Wnt6, Wnt8/D, Wnt9 and Wnt10 may have been lost in the pea aphid.

Figure S2. TGFβ signaling pathway components. Maximum likelihood tree of TGFb ligands (A) and SMAD family (B) are shown. Aphid Med5 is not included in the phylogeny because it is annotated as a pseudogene in the current version of gene model (LOC100158761). Ap Acyrthosiphon pisum; Am Apis mellifera; Tc Tribolium castaneum; Dm Drosophila melanogaster; Hs Homo sapiens; Gg Gallus gallus. The protein sequences were aligned with MUSCLE and the phylogenetic tree was made with PhyML using following parameters: amino-acid substitution model = WAG for (A) and JTT for (B), proportion of invariable sites = 0.004 for (A) and 0 for (B), number of categories of substitution rate = 4. Statistical support for phylogenetic grouping was assessed by approximate likelihood-ratio tests based on a Shimodaira-Hasegawa-like procedure (SH-aLRT) (Anisimova and Gascuel, 2006). Pea aphid genes are marked with green closed circles.

Figure S3. A graphical representation of the sequence conservation pattern of APEZ motif, a C2H2 Zinc-finger motif highly represented in the pea aphid proteome. The sequence logo was generated from the multiple alignment of 1,053 Zinc-finger motifs derived from 115 pea aphid proteins using WebLogo (Crooks et al., 2004). Numbers on the x-axis represent the relative sequence positions in the motif. The y-axis represents the information content measured in bits. WebLogo employs a correction factor to compensate for underestimates of entropy arising from limited sequence data: error bars are twice the height of this correction.

Figure S4. Homeobox genes. (A) Bayesian phylogeny of the ANTP-class built from the homeodomain is shown. The tree includes pea aphid and Drosophila orthologues of all families except Cdx, for which the pea aphid sequence is incomplete, and Nedx and Hex, for which there is no pea aphid ortholog in the genome sequence. For clarity, the values for some Hox gene families are displayed on the right of the clades (NJ/ML/PP). (B) Bayesian phylogeny of the PRD-class built from the homeodomain is shown. The tree includes the aphid and Drosophila orthologs of all families except Vsx and Al, for which the aphid sequences are incomplete. (C) Bayesian phylogeny of the minor classes built from the homeodomain is shown. The tree includes pea aphid and Drosophila orthologs of all families except Mkx, for which there is no aphid orthologue in the genome sequence. Classes are defined by their possession of distinctive domains in addition to the homeodomain(s); the classification at this level is not based upon homeodomain sequence phylogeny. In the trees of (A), (B) and (C), support values for family-level nodes are given, with bootstrap support values for the neighbor joining and maximum likelihood methods above internal branches (NJ/ML) and posterior probabilities from the Bayesian analysis below internal branches. Species abbreviations: Chaetopterus variopedatus (Cv), Haematopota pluvialis (Hv), Cupiennius salei (Cs) and Branchiostoma floridae (Bf). Other abbreviations are same as Figure 1. Pea aphid genes showing lineage-specific duplication are marked with orange closed circles. Drosophila genes whose orthologs are missing from the pea aphid but present in other sequenced insect genomes are marked with blue open circles. Two Hox complex genes (Ftz and Zen) showing rapid evolution in the pea aphid lineage are marked with green closed circles.

Figure S5. Phylogenetic analysis of the gap gene losses in the pea aphid genome (A) A Bayesian phylogeny of Zinc finger proteins reveals that the closest hits are not Btd or Hkb orthologs. (B) Bayesian analysis of Gt proteins and related leucine zipper proteins showed that none of the pea aphid related proteins grouped with Gt orthologs. Multiple sequence alignments were carried out in ClustalX and analysed using MrBayes 3.1.2 (Ronquist and Huelsenbeck, 2003) under the GTR model with default settings. The Monte Carlo Markov Chain search was performed over 10000 generations with trees sampled every 100 generations, with 25% of the trees ‘burntin’. Abbreviations: Drosophila melanogaster (Dm), Anopheles gambiae (Ag), Tribolium castanerum (Tc), Nasonia vitripennis (Nv), Apis mellifera (Am), Drosophila virulus (Dv), A pisum (Ap), Strigamia maritima (Sm), Pediuculus humanus humanus (Phum), Drosophila pseudoscura (Dp), Crookedlegs (Crol), Huckebein (Hkb), Buttonhead (Btd). Used accession numbers: Tc-Gt, NP_001034531; Nv-Gt, NP_001128393; Dm-Gt, NP_525049; Ag-Gt, XP_321187; Sm-Gt, ABO77130; Dm-CG7786, NP_611101; Am-Gt, XP_001121066; Dv-Gt, XP_002057392; Ap-ACYPI000702, XP_001943257; Am-XP00122257, XP_00122257; Nv-XP01600732, XP_01600732; Dv-XP002049589, XP_002049589; DmHkb, NP_524221.1; DmSp1, NP_001096927; NvSp1, XP_001606079; TcSP1, NP_001034509; Ph-PHUM008270, EEB14186; Ph-PHUM001804, EEB16542; NvXP001603467, XP_001603467; AmHKb, GB30303-PA (beebase); TcXP001807455, XP_001807455; TcXP972252, XP_972252; ApXP001945146, XP_001945146; AgXP313817, XP_313817; Dvhkb, XP_002058675; dmbtd, NP_511100; Amsp1, XP_624528; NvXP001607184, XP_001607184; Ambtd, XP_001119912; agbtd, XP_311200; DmCG5669, NP_651232; Nvbtd, XP_001599101; AmXP392980, XP_392980; Dpbtd, XP_002134535; DvGJ14523, XP_002058619; Dmcrookedlegs, NP_477243; PHUM005753, EEB12166; Dppga22020, XP_002019287; apXP001950606, XP_001950606; Tcbtd, NP_001107792; PHUM002913-PA, EEB15382; PHUM001599-PA, EEB17122; PHUM006898-PA, EEB11609; Ap-ACYPI35197, ACYPI35197.

Table S1. Developmental genes of A. pisum

Table S2. Nuclear Receptors of the pea aphid

Table S3. Transcription factor-related protein motifs in insect proteomes

Table S4. Classification of all homeoboxgenes in the A. pisum genome

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