DOI: 10.5061/dryad.47d7wm3mr
title: Genome assembly and annotation of the Dark-branded Bushbrown butterfly Mycalesis mineus (Nymphalidae: Satyrinae)

description: We report a high-quality genome draft assembly of the Dark-branded
 Bushbrown, Mycalesis mineus, a member of the Satyrinae subfamily of
 nymphalid butterflies. This species is emerging as a promising model
 organism for investigating the evolution and development of phenotypic
 plasticity. Using 45.99 Gb of long-read data (N50=11.11 Kb), we assembled
 a genome size of 497.4 Mb for M. mineus. The assembly is highly contiguous
 and nearly complete (96.8% of BUSCO lepidopteran genes were complete and
 single-copy). The genome comprises 38.71% of repetitive elements and
 includes 20,967 predicted protein coding genes. The assembled genome was
 super-scaffolded into 28 pseudo-chromosomes using a closely related
 species, Bicyclus anynana, with a chromosomal-level genome as a template.
 This valuable genomic tool will advance both ongoing and future research
 focused on this model organism.
description: High molecular weight (HMW) DNA was extracted from a female
 individual.  Following the user's protocol, the Oxford Nanopore
 library was prepared using the Ligation Sequencing kit for gDNA
 (SQK-LSK114). Sequencing was performed on an FLO-PRO002 cell in the
 PromethION machine, and base calling was performed using Guppy 6.5.7.
 Initial genome assembly was performed separately using the Flye assembler
 (Kolmogorov et al., 2019) and the wtdbg2 assembler (Ruan & Li,
 2020). Flye was run with the default settings, with polisher iteration set
 to 1, while wtdbg2 was run with its default settings. For both assemblers,
 the genome size was set to 500MB, based on the genome size of the closely
 related species <em>Bicyclus anynana</em>. The two genome
 assemblies were merged using quickmerge (Chakraborty et al., 2016), with
 wtdbg2 as the reference assembly and the Flye assembly as the query.
 Purge_haplotigs were used to remove any heterozygosity in the genome. The
 genome was broken at the point of misassembly with ragtag_correct using
 the <em>B. anynana</em> genome as a reference. The final
 genome was scaffolded to chromosome level using the <em>B.
 anynana</em> genome as reference using
 Chromosome_Scaffolder.
description: # *Mycalesis mineus* genome assembly The submission contains the assembly
 and annotation files of *M. mineus* assembly. Mmineus_v0.6.fa - assembly
 Using 45.99 Gb of long-read data (N50=11.11 Kb), we assembled a genome
 size of 497.4 Mb for *Mycalesis mineus*. The assembly is highly contiguous
 and nearly complete (96.8% of BUSCO lepidopteran genes were complete and
 single-copy). The genome comprises 38.71% of repetitive elements. The
 assembled genome was super-scaffolded into 28 pseudo-chromosomes using a
 closely related species, *Bicyclus anynana,* with a chromosomal-level
 genome as a template. The current version of the assembly v0.6 has 342
 scaffolds with N50 of 17.8MB. Mmineus_v0.6.gff3 - annotation The genome
 was annotated using the Braker2 automated pipeline, which resulted in
 18,360 genes accompanied by 20,967 transcripts. The Mmineus_v0.6.gff3 file
 contains the information of the genes and transcript annotation in the
 Mmineus_v0.6.fa - assembly. Mminues_Assembly_scripts- This file contains
 the codes and steps used in assembling the genome and annotation