DOI: 10.5061/dryad.rv15dv492
title: BigWig files for FAIRE-seq data

description: Butterfly wings exhibit a diversity of patterns which can vary between
 forewings and hindwings and spatially across the same wing. Regulation of
 morphological variation involves changes in how genes are expressed across
 different spatial scales which is driven by chromatin dynamics during
 development. How patterns of chromatin dynamics correspond to
 morphological variation remains unclear. Here we compared the chromatin
 landscape between forewings and hindwings and also across the proximal and
 distal regions of the hindwings in two butterfly species, Bicyclus anynana
 and Danaus plexippus. We found that the chromatin profile varied
 significantly between the different wing regions, however, there was no
 clear correspondence between the chromatin profile and the wing patterns.
 In some cases, wing regions with different phenotypes shared the same
 chromatin profile whereas those with a similar phenotype had a different
 profile. We also found that in the forewing, open chromatin regions were
 AT rich whereas those in the hindwing were GC rich. GC content also varied
 between the proximal and hindwing regions. These differences in GC content
 were also reflected in the transcription factor binding motifs that were
 differentially enriched between the wings and wing regions. Our results
 suggest that the chromatin landscape varies between different wing tissues
 and even spatially within the same tissue with no clear correspondence to
 phenotype. These findings may be explained by differences in how Hox genes
 cooperate with other transcription factors that show preferences for
 specific GC content and function either as activators or repressors in
 different wings or wing regions.
description: Wings from <em>Bicyclus anynana</em> and
 <em>Danaus plexippus </em>were dissected at ~22-26 hours
 post-pupation. For control input libraries (non-enriched), two whole
 forewings and two whole hindwings were pooled for each species.
 FAIRE-enriched libraries for <em>D. plexippus</em> included 3
 libraries, one prepared from whole forewings, and two from partial
 hindwings (proximal and distal regions) (Fig.1). For <em>B.
 anynana,</em> three FAIRE-enriched libraries were prepared including
 a forewing distal library, and two from partial hindwings (proximal and
 distal regions). All FAIRE-enriched libraries were prepared from 7-8
 pooled wing tissues.  Libraries were prepared by
 Genotypic Technology (India), as paired-end reads (75*2) and sequenced
 using Illumina NextSeq. Quality checking of the raw reads was performed
 using FASTQC v0.11.3 and reads which had a phred score&gt;30 were
 retained for downstream analyses. The reads were aligned to reference
 scaffolds or genomes for each species (BACs for <em>B.
 anynana</em> and the whole genome for <em>D.
 plexippus</em>) with BWA (0.7.13) using the following parameters –k
 INT, -w INT, -A INT, -B INT, -O INT, -E INT, -L INT, -U INT. The SAM files
 were converted to BAM files using SAMtools-0.1.7a and the resulting BAM
 files were converted to sorted BAM followed by removal of PCR duplicates.
 The final BAM files were then converted to BEDgraph files using
 BEDtools-2.14.3. Peaks were called with the MACS2 software using the
 aligned enriched and input (control) files with the qvalue (minimum FDR)
 cutoff to call significant peaks (Excel files S1-6). Fold-enrichment and
 log likelihood scores were calculated using the command bdgcmp script on
 the enriched and input BEDgraph files. The bdgcmp command also removes
 noise from the enriched sample relative to the control. The BEDgraph files
 were converted BigWig files using <strong>bdg2bw</strong><strong> </strong>for visualization in IGV.
description: For this experiment we only collected one replicate per
 library.