Lepidoptera Comparative Genomics

The high levels of gene order synteny found amongst the Lepidoptera (Pringle et al., 2007 (link)) allows markers to be developed to cover all 31 chromosomes based on their location and non-paralogous nature in Biston betularia, Melitaea cinxia—species with 31 chromosome pairs and for which linkage maps are available, and also Bombyx mori with 28 chromosomes pairs (Ahola et al., 2014 (link); Duan et al., 2010 (link); Van’t Hof et al., 2013 (link)). The coding sequence of identified genes acquired from the B. mori database (SilkDB) was blasted against a local database to provide H. bolina-specific sequence. To create the local database, DNA extracted from a Thai female butterfly was used to create two Illumina paired end libraries (TruSeq fragment library and Nextera large-insert library), which were sequenced on the Illumina HiSeq platform. Reads were assembled using CLC Genomics Server to create a draft de novo assembly, which was used to create a custom, local nr BLAST database in Geneious Pro v. 5.6.6. Retrieved H. bolina sequence was aligned to B. mori coding sequence to infer intron/exon boundaries, so that primers could be designed to amplify intronic regions to develop informative markers, which were then sequenced through the Sanger method. Marker information is detailed in Table S1.