De novo genome assembly

Nanopore sequenced reads with a length of at least 8 kb were used for genome assembly by the Canu v1.8¹⁴ with parameters of “maxThreads = 60 genomeSize = 636 m -nanopore-raw”. For the primary assembly, the purge_dups¹⁵ was used to remove haplotypic duplication sequences, and Pilon¹⁶ and Racon¹⁷ were used to polish the assembly. Bacterial sequences that were identified by aligning against the NCBI nt database were also removed. After removing the mitogenome and bacterial sequences, we obtained the 665 contigs with size of 648.2 Mb, which was similar to the predicted size of ~560–636 Mb. The contig N50 size was 3.2 Mb. The analysis of Hi-C data helped to anchor 337 (50.7%) contigs of 596.3 (92.0%) Mb sequence to 29 chromosomes¹⁸ (Table 1 and Fig. 2). The 328 (49.3%) un-anchored scaffolds contained 51.9 (8.0%) Mb sequence. The mitochondrial genome of 15,267 bp was also obtained (Table 2 and Fig. 3).

Characterization of the Phthorimaea operculella genome. Circos plot of chromosome level genome assembly (~648.2 Mb) and the distribution of COE, UGT, GST and P450 genes on 29 chromosomes.

Statistics of genome assembly.

The assembly of the complete mitogenome (15,269 bp) of Phthorimaea operculella. 13 protein-coding genes (ND1-ND6, ND4L, COX1-COX3, CYTB, ATP6 and ATP8) identified in the mitogenome were marked by coloured boxes.