Tissues of silk gland, fat body, midgut, Malpighian tubules, testis and ovary were dissected on the 3rd day of fifth instar larva which is Silkworm P50T (daizo) strain. The silk gland was further subdivided into anterior silk gland, anterior part of the middle silk gland, middle part of the middle silk gland, posterior part of the middle silk gland and posterior silk gland . Each tissue was dissected from one individual and totally three biological replicates were obtained and analyzed separately. The tissues were homogenized using ISOGEN (NIPPON GENE, Tokyo, Japan) and SV Total RNA Isolation System (Promega, Madison, WI) was used for RNA extraction.　The extract total RNA samples were sequenced by Illumina Novaseq6000 (Macrogen Japan Corp., Kyoto, Japan) .

The raw RNA-seq data of the samples were trimmed by Trimmomatic-version 0.36. The trimmed RNA-seq data of each tissue was mapping to the new reference genome with new gene model by Hisat2 version 2.1.0. The each mapped data was assembled to transcript data by stringtie version 1.3.3. The transcript data was merged to one transcript data set we refer as “reference transcriptome” by the stringtie, and gtf file of the reference transcriptome had been gotten.

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