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Figure S1. Phylogenetic tree showing relationships of Apis pisum and Drosophila melanogaster calcium channel protein sequences. Numbers at each node signify bootstrap values with 1000 replicates and the scale bar represents substitutions per site. The proteins shown in the tree (as well as GenBank accession numbers) are as follows: DmeI Alpha 1T (NP_572296), Dmel Alpha 1D (NP_602305), Dmel Alpha Cacophony (NP_511133), Dmel Ca Beta 1 (NP_523546), Dmel CG12295 (NP_610902), Dmel CG4587 (NP_001097163), Dmel CG12455 (NP_609779) and Dmel CG13762 (NP_570013).The tree was constructed using the neighbour-joining method (Saitou & Nei, 1987) available with the CLUSTALX program (Thompson et al., 1997) and displayed using TreeView (Page, 1996).

Figure S2. Phylogenetic tree showing relationships of Acythosiphon pisum and Drosophila melanogaster potassium channel protein sequences. Numbers at each node signify bootstrap values with 1000 replicates and the scale bar represents substitutions per site. The proteins shown in the tree (as well as GenBank accession numbers) are as follows: DmeI Slo (NP_524486), Dmel Slack (NP_001097259), Dmel KCNQ (NP_788300), Dmel ShaWl (NP_001097131), Dmel ShaW (NP_476721), Dmel ShaB (NP_728783), Dmel Shaker (NP_728124), Dmel ShaI (NP_524159), Dmel Ih (NP_001033947),Dmel Seizure (NP_476713),Dmel Eag (NP_511158),Dmel Egl (NP_477009),Dmel SK (NP_726988),Dmel Irk1 (NP_651131), Dmel Irk2(NP_651149) and Dmel Irk3 (NP_609903). The tree was constructed using the neighbour-joining method (Saitou & Nei, 1987) available with the CLUSTALX program (Thompson et al., 1997) and displayed using TreeView (Page, 1996).

Figure S3. Phylogenetic tree of the NMDA receptors in Drosophila melanogaster and Acyrthosiphon pisum. Tree showing relationships of A. pisum, Apis mellifera and D. melanogaster NMDA receptors protein sequences. Numbers at each node signify bootstrap values with 1000 replicates and the scale bar represents substitutions per site. The proteins shown in the tree (as well as GenBank accession numbers) are as follows: DmelNmdar1 (NP_730940), DmelNmdar2 (NP_001014716), DmelCG3814 (NP_610824), DmelCG30379 (NP_724626), AmelNmdar1 (NP_001011573), AmelNmdar2 (XP_396271), Amel CG3814 (XP_391854), AmelNmdar3 (XP_624931). The tree was constructed using the neighbour-joining method (Saitou & Nei, 1987) available with the CLUSTALX program (Thompson et al., 1997) and displayed using MEGA.

Figure S4. Phylogenetic tree of the kainate receptors in Drosophila melanogaster and Acyrthosiphon pisum. Tree showing relationships of A. pisum, Apis mellifera and D. melanogaster kainate receptors protein sequences. Numbers at each node signify bootstrap values with 1000 replicates and the scale bar represents substitutions per site. The proteins shown in the tree (as well as GenBank accession numbers) are as follows: DmeCG5621 (NP_650927), Dmel KaiRIA (NP_651982), Dmel GluRIIE (NP_001036733), DmelCG3822 (NP_650925), Dmel CG9935 (NP_651931), Dmel CG11155 (NP_651941), Dmel Clumsy (NM_078886), Dmel GluRIIC (NP_608557), Dmel GluRIIA (NP_523484), Dmel GluRIIB (NP_523485), AmelCG3822-3 (XP_392185), AmelCG3822-1(XP_394265), AmelCG3822-2 (XP_394264). The tree was constructed using the neighbour-joining method (Saitou & Nei, 1987) available with the CLUSTALX program (Thompson et al., 1997) and displayed using MEGA.

Figure S5. Phylogenetic tree of the other ionotropic receptors in Drosophila melanogaster and Acyrthosiphon pisum. Tree showing relationships of A. pisum, Apis mellifera and D. melanogaster or other forms of ionotropic glutamate receptors protein sequences. Numbers at each node signify bootstrap values with 1000 replicates and the scale bar represents substitutions per site. The proteins shown in the tree (as well as GenBank accession numbers) are as follows: DmelCG32704 (NP_727328), DmelCG15627 (NP_608863), DmelCG42315 (NP_650924), DmelCG7385 (NP_649176), DmelCG2657 (NP_001097043), DmelCG6185 (NP_648455), DmelCG11775 (NP_649833), DmelCG17152 (NP_648548), DmelCG8533 (NP_649148), DmelCG33492 (NP_995744), DmelCG15732 (NP_572795), DmeCG15324 (NP_572411), DmelCG14076 (NP_649074), DmelCG10101 (NP_649720), DmelCG10633 (NP_647962), DmelCG31718 (NP_723585), DmelCG14586 (NP_649013), DmelCG14585 (NP_649012), AmelCG32704 (XP_393270), AmelCG15627 (XP_396400), AmelCG17274 (XP_624089), AmelCG7385 (XP_624096), AmelCG6185 (XP_001123055), AmelCG7385 (XP_624096), AmelCG14076 (XP_001121834), AmelPlr2 (XP_395079). The tree was constructed using the neighbour-joining method (Saitou & Nei, 1987) available with the CLUSTALX program (Thompson et al., 1997) and displayed using MEGA.

Figure S6. Alternative splicing of exons in Acyrthosiphon pisum nAChR subunits. Comparison of alternative exons of Drosophila melanogaster and A. pisum α4 (a) and α6 (b) subunits. Aphid residues that differ from those of the orthologous Drosophila exon are underlined. The Cys-loop is marked by asterisks and loops involved in ligand binding (LpB and LpE) are indicated. (c) Putative splice variants of Apisumα7 which generate diversity in loop C (LpC) potentially affecting ACh binding and in transmembrane regions 1 and 2 (TM1 and TM2) potentially affecting ion channel properties.

Figure S7. Tree of sequence similarity showing the translated transient receptor potential sequences of Acyrthosiphon pisum and Drosophila melanogaster. A neighbour-joining tree was produced from a ClustalX alignment of the translated transient receptor potential sequences from A. pisum and D. melanogaster. D. melanogaster sequences were obtained from FlyBase (http://flybase.org), and are labelled according to their FlyBase gene symbol. Sequences from A. pisum were retrieved from the genome sequence reference assembly and putatively identified by a reciprocal TBLASTX search, using the D. melanogaster transient receptor potential sequences as the initial search queries. A. pisum sequences are labelled with the appropriate gene model reference number (with ACYPIT prefix) where available. Two additional A. pisum transient receptor potential sequences were found, and are labelled with the prefix Ap and an appropriate identity based on their similarity to D. melanogaster sequences. The partial translated sequences from the aphid genome were then aligned against the Transient Receptor Potential sequences from Drosophila using ClustalX (version 1.83). The ClustalX alignments were used to generate bootstrapped neighbour-joined trees, which were viewed using Treeview (version1.6.6) software.

Table S1. Sodium channels

Table S2. Calcium Channels

Table S3. Potassium channels

Table S4. Chloride channels

Table S5. Cyclic-gated nucleotide Channels

Table S6. Glutamate Receptors

Table S7. The Transient Receptor Potential channels of Acyrthosiphon pisum and Drosophila melanogaster.

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