FibH Gene Complete Sequences (FibHome) Revealed Silkworm Pedigree

SIMPLE SUMMARY: The fibroin heavy chain (FibH) is the core protein of silkworm silk, and a systematic analysis of its sequence (primary structure) is essential for understanding silkworm silk fibers. However, only a few FibH sequences have been identified. The recently published high-resolution silkworm pan-genome was useful in analyzing the FibH gene systematically. In this study, we extracted the complete FibH sequences of wild silkworms, local and improved strains from the silkworm pan-genome, bringing the total number of known silkworm FibH genes to 286. We characterized in detail the FibH variation during domestication and breeding and established a silkworm pedigree based on the FibH gene sequence. Additionally, we investigated the relationship between the cis-regulatory elements of FibH gene and silk yield in wild and domesticated silkworms. Our study laid the foundation for artificial silk as well as provided guidance for silkworm breeding. ABSTRACT: The highly repetitive and variable fibroin heavy chain (FibH) gene can be used as a silkworm identification; however, only a few complete FibH sequences are known. In this study, we extracted and examined 264 FibH gene complete sequences (FibHome) from a high-resolution silkworm pan-genome. The average FibH lengths of the wild silkworm, local, and improved strains were 19,698 bp, 16,427 bp, and 15,795 bp, respectively. All FibH 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 FibH 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 FibH gene’s intron and upstream sequences. The local and improved strains with the same FibH gene were divided into four families using this gene as a marker. Family I contained a maximum of 62 strains with the optional FibH (Opti-FibH, 15,960 bp) gene. This study provides new insights into FibH variations and silkworm breeding.