DOI: 10.5061/dryad.np5hqc055
title: Exome capture design for the strawberry poison frog, Oophaga pumilio, in Bocas del Toro

description: 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 carotenoid
 conversion in birds, is the primary factor behind the yellow-red
 polymorphism in the Bastimentos West area. The causal genetic regions show
 evidence of selective sweeps acting locally to spread the rare phenotype.
 Our analyses suggest an evolutionary model in which selection is driving
 the formation of new morphs in a dynamic system resulting from a trade-off
 between predation avoidance, intraspecific competition, and mate choice.
description: 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/MarkerDevelopmentPopGen) to filter out sequences smaller than 150 bp and with a GC content smaller than 35% or larger than 75%. This script also masked repeats setting the parameter to “Xenopus genus” and “vertebrates”. Finally, we checked if a list of candidate color genes was present. We added the missing genes from the Oophaga pumilio or the Ranitomeya imitator genomes. The final design had 90 Mb and 115,420 regions and was sent to NimbleGene for approval.  NimbleGene made 116,121 probes that targeted 80 Mb, estimating a final coverage of 86 Mb across 110,329 transcripts.
description: # 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 showing the probe targets
 with no padding #### File: IRN1000004503_Opumilio_21Feb2020_coverage.txt
 **Description:** Estimated coverage in target regions #### File:
 Opumilio.target.noendline.fasta **Description:** Fasta file submitted as
 the primary target (what we want to extract from the whole genome) ####
 File: annotation_complete **Description:** Annotation of the transcript ##
 Access information Other publicly accessible locations of the data: *
 PRJNA760522: Sequencing generated using the probes and Illumina Sequencing
 Data was derived from the following sources: * Transcriptome from this
 article: Stuckert, A.M.M., Freeborn, L., Howell, K.A., Yang, Y., Nielsen,
 R., Richards-Zawacki, C., and MacManes, M.D. (2023). Transcriptomic
 analyses during development reveal mechanisms of integument structuring
 and color production. Evol. Ecol.
 [https://doi.org/10.1007/s10682-023-10256-2](https://doi.org/10.1007/s10682-023-10256-2).