DOI: 10.5061/dryad.xd2547dnr
title: Long read genome assembly of Automeris io (Lepidoptera: Saturniidae) an emerging model for the evolution of deimatic displays

description: Automeris moths are a morphologically diverse group with 145 described
 species that have a geographic range that spans from the New World
 temperate zone to the Neotropics. Many Automeris have hindwing eyespots
 that are thought to deter or disrupt the attack of potential predators,
 allowing the moth time to escape. Some species in the genus have vestigial
 eyespots or lack them completely, suggesting that this trait may provide a
 selective benefit. The Io moth (Automeris io), known for its striking
 eyespots, is the most widely studied species within the genus and is an
 emerging model system to study the evolution of deimatism, a predatory
 defense that combines visual stimuli and movement. Here we present a
 high-quality, PacBio HiFi genome assembly for Io moth to aid existing
 research on the molecular development of eyespots. Genomic research is
 needed to address questions involving antipredatory defenses and eyespot
 pattern development. BUSCO analysis for this genome shows a completeness
 of 98.4%, and N50 of 15.
description: PacBio consensus reads were used to estimate genome size and
 heterozygosity using the program K-Mer counter (KMC) v.3.2.1 (RRID:
 SCR_001245). A k-mer length of 23 (-m 23) was used to create a histogram
 of k-mer frequencies and visualized using GenomeScope 2.0
 (RRID:SCR_017014). PacBio consensus reads were assembled using the de novo
 assembler, HiFiasm v.0.16.1 r307 (RRID:SCR_021069), resulting in a 500 Mbp
 primary assembly. The assembly_stat.py script was used to assess assembly
 contiguity. BUSCO v.5.2.0 was used to assess completeness with 5,286
 putative single copy genes from the lepidoptera_odb10.2019-11-20 database
 (RRID:SCR_015008; ). Therefore, we attempted to further collapse allelic
 variation using the Purge Haplotigs pipeline was used to purge additional
 duplicates. (purge_haplotigs v.1.1.2 ). A coverage histogram was used to
 choose a minimum, median, and maximum read depth cut off value for
 purging. This was produced by mapping raw reads to the primary assembly
 using minimap v.2.21 (RRID:SCR_018550). Contigs were assigned as haplotigs
 if the 80% of the contig showed diploid-level coverage (-s 80) and
 discarded if coverage was 80% above or below the read depth cut offs (-j
 80). We used blobtools v1.0 (RRID:SCR_017618) to investigate potential
 contamination in the assembly. RepeatMasker  was used to mask repeat
 regions of the assembly, creating a soft-masked genome to be used for all
 downstream analyses. The BRAKER2 pipeline (v2.1.5; RRID:SCR_018964) with
 protein sequences from the NCBI Bombyx mori Annotation Release 101 was
 used for structural annotation. This pipeline uses programs Bamtools
 (RRID:SCR_015987;, GeneMark-EP+ (RRID:SCR_011930, DIAMOND
 (RRID:SCR_016071), and Augustus (RRID:SCR_008417). Annotation statistics
 were summarized using gFACs (RRID:SCR_022017. BUSCO v.5.2.0 was used to
 assess completeness of this annotation. Refer to original publication for
 further details. 
description: Files can be opened in a text editor or a spreadsheet
 software. 
description: # Data and supporting information for "Genome assembly for Automeris
 io (Lepidoptera: Saturniidae)" This readme file contains the list
 supporting files. Authors: Chelsea Skojec, R. Keating Godfrey, Akito Y.
 Kawahara --- ## **FILES** **readme.md** This file describes the files
 included in this supplemental material ### ***Files related to genome
 assembly*** * **full_table.tsv** BUSCO results from curated assembly using
 lepidoptera_odb10 database. Column headings Busco ID: orthologous group ID
 Status: missing or complete Sequence: sequence id Gene Start: beginning
 location of the gene Gene End: end location of the gene Strand: forward or
 reverse Score: scores are dereived from comparison of input sequences
 against a database of known orthologs Length: length of sequence OrthoDB
 url Description: url link to OrthoDB corresponding orthologous group *
 **short_summary.txt** Summary table of BUSCO results in txt format *
 **missing_busco_list.tsv** List of BUSCOs IDs not found in the assembly.
 From the lineage dataset lepidoptera_odb10 Column headings Busco ID: This
 is the Busco ID for list of BUSCOs IDs not found in the assembly. *
 **Automeris_blob_result.blobDB.json** The output of blobplot analysis from
 blobtools v1.0 in json format * **Automeris_io_blob_result.table.txt** The
 output of blobplot analysis from blobtools v1.0 ### ***Files related to
 structural annotation*** * **Automeris_io_braker2_augustus_pep.aa** A file
 containing predicted peptide sequences from the structural annotation *
 **augustus.hints.gtf** Structural annotation from the genome from braker2