Gene Complete Sequences (FibHome) Revealed Silkworm Pedigree.

The highly repetitive and variable fibroin heavy chain () gene can be used as a silkworm identification; however, only a few complete sequences are known. In this study, we extracted and examined 264 gene complete sequences (FibHome) from a high-resolution silkworm pan-genome. The average lengths of the wild silkworm, local, and improved strains were 19,698 bp, 16,427 bp, and 15,795 bp, respectively. All sequences had a conserved 5' and 3' terminal non-repetitive (5' and 3' TNR, 99.74% and 99.99% identity, respectively) sequence and a variable repetitive core (RC). The RCs differed greatly, but they all shared the same motif. During domestication or breeding, the gene mutated with hexanucleotide (GGTGCT) as the core unit. Numerous variations existed that were not unique to wild and domesticated silkworms. However, the transcriptional factor binding sites, such as fibroin modulator-binding protein, were highly conserved and had 100% identity in the gene's intron and upstream sequences. The local and improved strains with the same gene were divided into four families using this gene as a marker. Family I contained a maximum of 62 strains with the optional (Opti-, 15,960 bp) gene. This study provides new insights into variations and silkworm breeding.