Transcriptome Analysis of Aphid Lucorum

Total RNA from whole bodies of A. lucorum was extracted using the RNA simple Total RNA Kit (Tiangen, China) according to the manufacturer’s instructions, and then sequenced with the Illumina NGS platform to generate high-throughput RNA sequencing (RNA-Seq) data. The resultant raw reads were processed by removing poor quality reads and trimming adaptors. In the absence of a reference genome of A. lucorum, the clean reads were imported into the Trinity assembler with the default parameters for de novo assembly (Grabherr et al., 2011 ). For the assembled transcripts, the TransDecoder program was used to identify candidate coding regions. Signal peptides were predicted using SignalP v3.0 (Bendtsen et al., 2004 (link)). The aphid effector sequences were retrieved from publications (Bos et al., 2010 (link); Atamian et al., 2013 (link)), and used as queries for Blast searches (E-value <1×10^–5) against A. lucorum secreted proteins. The domain component in each protein sequence was predicted using the Pfam database (Finn et al., 2016 (link)). To predict GPx domain-containing proteins in each insect, the hidden Markov model profile of GPx (PF00255) was obtained from the Pfam database, and then used to perform a HMM search against insect proteins using the HMMER program (Finn et al., 2011 (link)).