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).