Genome sequence of the Japanese oak silk moth, Antheraea yamamai: the first draft genome in the family Saturniidae

Abstract

Background Antheraea yamamai, also known as the Japanese oak silk moth, is a wild species of silk moth. Silk produced by A. yamamai, referred to as tensan silk, shows different characteristics such as thickness, compressive elasticity, and chemical resistance compared with common silk produced from the domesticated silkworm, Bombyx mori. Its unique characteristics have led to its use in many research fields including biotechnology and medical science, and the scientific as well as economic importance of the wild silk moth continues to gradually increase. However, no genomic information for the wild silk moth, including A. yamamai, is currently available.FindingsIn order to construct the A. yamamai genome, a total of 147G base pairs using Illumina and Pacbio sequencing platforms were generated, providing 210-fold coverage based on the 700-Mb estimated genome size of A. yamamai. The assembled genome of A. yamamai was 656 Mb (>2 kb) with 3675 scaffolds, and the N50 length of assembly was 739 Kb with a 34.07% GC ratio. Identified repeat elements covered 37.33% of the total genome, and the completeness of the constructed genome assembly was estimated to be 96.7% by Benchmarking Universal Single-Copy Orthologs v2 analysis. A total of 15 481 genes were identified using Evidence Modeler based on the gene prediction results obtained from 3 different methods (ab initio, RNA-seq-based, known-gene-based) and manual curation.ConclusionsHere we present the genome sequence of A. yamamai, the first genome sequence of the wild silk moth. These results provide valuable genomic information, which will help enrich our understanding of the molecular mechanisms relating to not only specific phenotypes such as wild silk itself but also the genomic evolution of Saturniidae.

A chromosome‐scale genome assembly of Antheraea pernyi (Saturniidae, Lepidoptera)

“…A combined structure‐ and homology‐based analysis identified a total of 441.75 Mb of repetitive sequences, accounting for 60.74% of the total A. pernyi genome (Table S10), which was higher than the proportion reported for A. yamamai (37.33%) (Kim et al., 2018) and B. mori (46.84%) (Kawamoto et al., 2019). The same methods were also used to identify 223.59 Mb repeat elements, accounting for 48.54% of B. mori genome (Table S10), which was nearly consistent with the reported proportion (46.84%).…”

“…Gene functional annotation is a helpful tool for interpreting the complex relationship between internal genes and external traits. We defined the models of protein‐coding genes in A. pernyi genome using full‐length transcriptome with de novo and homology‐based methods, producing a total of 21,431 protein‐coding genes (Table S11), which is also a much higher number than detected in A. yamamai (15,481) (Kim et al., 2018) and B. mori (16,880) (Kawamoto et al., 2019). Approximately 85.2% of the protein‐coding genes could be functionally annotated using at least one public database (Table S12).…”

“…Orthologous and paralogous groups from A. pernyi , B. mori (Kawamoto et al., 2019), A. yamamai (Kim et al., 2018), D. plexippus (Zhan, Merlin, Boore, & Reppert, 2011), P. xylostella (You et al., 2013), H. armigera (Pearce et al., 2017), D. melanogaster (Berlin et al., 2015), and S. frugiperda (Liu, Lan, et al., 2019) were first identified using OrthoMCL v1.4 (Li, Stoeckert, & Roos, 2003) after all‐versus.‐all BLASTP alignment. Orthologous single copy genes were aligned using MUSCLE v3.8.31 (Edgar, 2004) to develop a super‐sequence for each species using four‐fold degenerate sites.…”

“…Some of these questions can be resolved by comparative genomics analysis among A. pernyi , Antheraea yamamai (Kim et al., 2018), B. mori (Kawamoto et al., 2019; Xia et al., 2004) and other Bombycoidea species, which requires chromosome‐scale genome resources that are currently lacking. The B. mori genome was assembled onto its 28 chromosomes; thus, the genome assembly for A. pernyi should precisely cover its 49 chromosomes, which allows for further comparative analysis to better understand the lineage divergence and karyotype evolution.…”

Visible light biophotosensors using biliverdin from Antheraea yamamai

“…One of the sources to obtain a decent amount of biliverdin is silkworms and silk cocoons, in particular Antheraea yamamai (Japanese oak silkmoth). Specifically, Antheraea yamamai has been cultivated for centuries as a native in East Asia [20,21]. Mimicking the natural sunlight exposure, when light with high intensity (5000 lux) is irradiated onto Japanese oak silkmoths, the silk cocoon is colorized to be green due to the photochemical transformation to biliverdin [8,9].…”