Exome capture design for the strawberry poison frog, Oophaga pumilio, in Bocas del Toro

The aposematic strawberry poison frog, Oophaga pumilio, is an iconic model system for studying the evolution and maintenance of color variation. Through most of its range, this frog is red with blue limbs. However, frogs from the Bocas del Toro Province, Panama, show striking variance in color and pattern, both sympatrically and allopatrically. This observation contradicts standard models of the evolution of aposematism and has led to substantial speculation about its evolutionary and molecular causes. Since the enigma of O. pumiliophenotypic variation is partly unresolved because of its large, ∼ 6.7 Gb genome, we here sequence exomes from 347 individuals from ten populations and map a number of genetic factors responsible for the color and pattern variation. The kitgene is the primary candidate underlying the blue-red polymorphism in Dolphin Bay, where an increase in melanosomes is correlated with blue coloration. Additionally, thettc39bgene, a known enhancer of yellow-to-red carotenoi..., The initial transcriptome was 108,640,165 bp represented by 152,862 transcripts. The transcripts were mapped to the Oophaga pumilio and the Ranitomeya imitator genomes using STARlong 2.7.0d. using the following parameters: --outFilterMismatchNmax 5000, --outFilterMismatchNoverReadLmax .1, --seedSearchStartLmax 20, --seedPerReadNmax 50000, --sjdbOverhang 100 --outFilterScoreMin 0, –outFilterScoreMinOverLread 0, --outFilterMatchNminOverLread .5 --seedPerWindowNmax 1000. We removed the transcripts that did not map to these two assemblies. This resulted in 141,482 transcripts and 104,671,021 bp. Then we used transcript_filter.pl v0.2.0 to remove isoforms. We did two rounds of filtering using the following parameters: 1) minimum 80% coverage and 98% identical 2) 90% coverage, 95% identical. The isoform removal step resulted in 97 Mb. We removed most mitochondrial genes using the annotation and kept cytB. We used 6-Process Annotation (https://github.com/CGRL-QB3-UCBerkeley/MarkerDevelopmentPo..., # Exome capture design for the straweberry poison frog, Oophaga pumilio, in Bocas del Toro

Dataset DOI: [10.5061/dryad.np5hqc055](10.5061/dryad.np5hqc055)

## Description of the data and file structure

Exome capture was designed from skin transcriptome of different developmental stages of Oophaga pumilio. The target was sent to NimbleGenes to design the probes. 

### Files and variables

#### File: IRN1000004503_Opumilio_21Feb2020_capture_targets.bed

**Description:** bedfile of all the regions that we designed to capture including padding around primary regions

#### File: IRN1000004503_Opumilio_21Feb2020_predicted_no_coverage_regions.bed

**Description:** bedfile of all the regions that NimbleGene predicted to have no coverage

#### File: IRN1000004503_Opumilio_21Feb2020_coverage_summary.txt

**Description:** Summary of the expected coverage using the exome capture

#### File: IRN1000004503_Opumilio_21Feb2020_primary_targets.bed

**Description:** This file contains coordinates showi...,