Genome annotation was carried out by the Bioinformatics Short-term Support and Infrastructure (BILS, Sweden). BILS was provided with the chromosomal assembly of P. napi, and 45 RNA sequencing read sets representing three different tissues (head, fat body, and gut) of seven male and eight female larvae from laboratory lines that were separate from the ones used for the initial sequencing. Sequence evidence for the annotation was collected in two complementary ways. First, we queried the UniProt database (67) for protein sequences belonging to the taxonomic group of Papilionoidea (2516 proteins). To be included, proteins gathered in this way had to be supported on the level of either proteomics or transcriptomics and could not be fragments. In addition, we downloaded the UniProt/Swiss-Prot reference dataset (downloaded on 15 May 2014) (545,388 proteins) for a wider taxonomic coverage with high-confidence proteins. In addition, 493 proteins were used that were derived from a P. rapae expressed sequence tag library that was Sanger-sequenced.

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