RNA sequencing (RNA-seq)
Embryo-derived libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit (Illumina) and were sequenced using the Illumina HiSeq 2500 platform with 100-bp and 101-bp paired-end reads. The library for midgut-derived RNA samples was prepared using TruSeq RNA Library Prep Kit (Illumina) and sequenced using the Genome Analyser IIx System with 76-bp paired-end reads. The library for anterior silk gland- and middle silk gland-derived RNA samples were prepared using SureSelect Strand Specific RNA Library Prep Kit (Agilent) and were sequenced using the Illumina HiSeq 2500 platform with 100-bp paired-end reads. Table S3 summerizes information on the results of RNA-seq.