Overview of S. ricini genome assembly
Final assembly of S. ricini genome was 450,479,495 bp long with 155 scaffolds. The N50 length of the assembly was approximately 21 Mb (Table 1). GC content was 34.3%. The longest scaffold length was approximately 33 Mbp. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis using BUSCO v3.0 with insecta odb9, including 1,658 BUSCOs from 42 species revealed that 97.8% of BUSCOs were completely detected in the assembled genome (1614, complete and single-copy; 8, complete and duplicated) among 1,658 tested BUSCOs (see Table S5). To the best of our knowledge, these statistic scores are the best among ever–constructed lepidopteran genome assemblies (Challis, Kumar, Dasmahapatra, Jiggins, & Blaxter, 2016; Kim et al., 2018; Triant, Cinel, & Kawahara, 2018). Low heterozygosity in S. ricini strain used for this project might be the key to the successful assembly: k-mer distribution analysis (k = 31) estimated that heterozygosity in one male individual of S. ricini was 0.0466 to 0.0472% (Table 1, see Fig. S2), considerably lower than that of the Antheraea yamamaigenome, (0.807 to 0.808%) a related species belonging to the family Saturniidae (Fig. S2; Kim et al., 2018). This might result from the difference in voltinism between S. ricini and A. yamamai : It is quite difficult to establish an inbred line of A. yamamai because A. yamamai is a univoltine species and emerge only once per year, whereas multivoltine S. ricini can generate at least six generations per year. The difference of diapause strategy mentioned above indicates that at least six times longer periods are required to establish an inbred line of A. yamamai .
Linkage analysis of thirty-five scaffolds (> 1 Mbp) revealed that the scaffolds are grouped into fourteen linkages (Table 2, Fig. S1B), which corresponds to the previous report (Yoshido, Yasukochi, & Sahara, 2011) where BAC-FISH was conducted and concluded thatS. ricini has thirteen autosomes and one Z chromosome (male: 2n = 28, female: 2n = 27). These thirty-five scaffolds counted up 443,618,927 bp, meaning that approximately 98.5% of the genome was assigned to the chromosomes (Table 2).