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[…] Transcripts mapping to the same location were collapsed into the one encoding the longest ORF, or, when partial- or non-overlapping, merged into a single locus. To recover all possible AATs that are encoded by the genomes but were not identified from M. persicae and D. vitifoliae de novo transcriptome assemblies, we performed BLAST searches (evalue <0.001) using an APC or AAAP transcript of M. persicae and D. vitifoliae, respectively, against their own genome databases, and those recovered, if any, were subsequently verified at the NCBI non-redundant protein database as described above. For the remaining species lacking draft genome sequences, we: 1) collapsed transcripts having the same Trinity component number into the one encoding the longest ORF, and 2) collapsed closely related transcripts into the one encoding the longest ORF if they have a pairwise synonymous substitution rate (Ks value) less than 0.25 [] determined using PAML (version 4.8; []) or if two transcripts have less than 50-bp of overlapping region, as performed in []. All chosen representative transcripts were translated into the longest protein sequences in Blast2GO Pro []. Amino acid transporters encoded by Acyrthosiphon pisum and Drosophila melanogaster genomes were annotated and previously reported []., We used DNA sequences of three protein-coding mitochondrial genes, cytochrome c oxidase subunit I (COI), cytochrome c oxidase subunit II (COII) and cytochrome b (CYTB), to resolve the phylogenetic relationship among the nine Phylloxera species and six Aphididae species as described above. COI and COII are widely used to infer insect phylogeny at a variety of hierarchy levels, from closely related species to orders, and CYTB is fast-evolving and thus useful for the phylogenetic analysis of closely-related taxa []., The DNA sequences of these t […]

Pipeline specifications

Software tools Trinity, PAML, Blast2GO
Organisms Bacteria
Diseases Cholelithiasis, Gallbladder Diseases, Calculi
Chemicals Amino Acids