DOI: 10.5061/dryad.x3ffbg7pr
title: The genetic basis of wing spots in Pieris canidia butterflies

description: Spots in pierid butterflies and eyespots in nymphalid butterflies are
 likely non-homologous wing colour pattern elements, yet they share a few
 features in common. Both develop black scales that depend on the function
 of the gene spalt, and both might have central signalling cells.
 This suggests that both pattern elements may be sharing common genetic
 circuitry. Hundreds of genes have already been associated with the
 development of nymphalid butterfly eyespot patterns, but the genetic basis
 of the simpler spot patterns on the wings of pierid butterflies has not
 been investigated. To facilitate studies of pierid wing patterns, we
 report a high-quality draft genome assembly for Pieris canidia,
 the Indian cabbage white. We then conducted transcriptomic analyses of
 pupal wing tissues sampled from the spot and non-spot regions
 of P. canidia at 3-6h post-pupation. A total of 1,352 genes were
 differentially regulated between wing tissues with and without the black
 spot, including spalt, Krüppel-like factor 10, genes from the
 Toll, Notch, TGF-β, and FGFR signalling pathways, and several genes
 involved in the melanin biosynthetic pathway. We identified 21 genes that
 are up-regulated in both pierid spots and nymphalid eyespots and propose
 that spots and eyespots share regulatory modules despite their likely
 independent origins.
description: High Molecular weight (HMW) DNA was extracted from two female
 pupae using a phenol-chloroform method. Extracted DNA was stored in - 80°C
 before being pooled and sent for sequencing. Long reads library
 preparation and sequencing were performed at AIT Novogene, Singapore. 20GB
 of data, roughly about (70x) coverage was sequenced using the PacBio
 sequel platform. Initial genome assembly was carried
 out using canu (1) and wtdbg2 (2) assemblers separately. The two
 assemblies were merged using quickmerge (3), with the canu assembly as the
 reference, and the wtdbg2 assembly as the query. Heterozygosity in the
 contigs of the resulting assembly was purged using purge_haplotigs (4),
 and only the haploid contigs were kept. The obtained contigs were polished
 with three rounds of racon (5) and Pilon (6) using corrected PacBio long
 reads and Illumina short reads, respectively, to get the final genome
 assembly, Pcan.v1. 
 <em><strong>References</strong></em> S. Koren, B. P. Walenz, K. Berlin, J. R. Miller, N. H. Bergman, A. M. Phillippy, Canu: Scalable and accurate long-read assembly via adaptive κ-mer weighting and repeat separation. Genome Res. 27, 722–736 (2017). J. Ruan, H. Li, Fast and accurate long-read assembly with wtdbg2. Nat. Methods. 17, 155–158 (2020). M. Chakraborty, J. G. Baldwin-Brown, A. D. Long, J. J. Emerson, Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage. Nucleic Acids Res. 44, 1–12 (2016). M. J. Roach, S. A. Schmidt, A. R. Borneman, Purge Haplotigs: Allelic contig reassignment for third-gen diploid genome assemblies. BMC Bioinformatics. 19, 1–10 (2018). R. Vaser, I. Sović, N. Nagarajan, M. Šikić, Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 27, 737–746 (2017). B. J. Walker, T. Abeel, T. Shea, M. Priest, A. Abouelliel, S. Sakthikumar, C. A. Cuomo, Q. Zeng, J. Wortman, S. K. Young, A. M. Earl, Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 9 (2014), doi:10.1371/journal.pone.0112963.
description: Draft genome assembly of <em>Pieirs canidia</em> with
 its annotation in fasta and gff format respectively.