DOI: 10.5061/dryad.wstqjq2kr
title: A combined RAD-Seq and WGS approach reveals the genomic basis of yellow color variation in bumble bee Bombus terrestris

description: Bumble bees exhibit exceptional diversity in their segmental body
 coloration largely as a result of mimicry. In this study we sought to
 discover genes involved in this variation through studying a lab-generated
 mutant in bumble bee Bombus terrestris, in which the typical black
 coloration of the pleuron, scutellum, and first metasomal tergite is
 replaced by yellow, a color variant also found in sister lineages to B.
 terrestris. Utilizing a combination of RAD-Seq and whole-genome
 re-sequencing, we localized the color-generating variant to a single SNP
 in the protein-coding sequence of transcription factor cut. This mutation
 generates an amino acid change that modifies the conformation of a
 coiled-coil structure outside DNA-binding domains. We found that all
 sequenced Hymenoptera, including sister lineages, possess the non-mutant
 allele, indicating different mechanisms are involved in the same color
 transition in nature. Cut is important for multiple facets of development,
 yet this mutation generated no noticeable external phenotypic effects
 outside of setal characteristics. Reproductive capacity was reduced,
 however, as queens were less likely to mate and produce female offspring,
 exhibiting behavior similar to that of workers. Our research implicates a
 novel developmental player in pigmentation, and potentially caste, thus
 contributing to a better understanding of the evolution of diversity in
 both of these processes.
description: Please refer to the
 publication Rahman et al. 2021; "A combined RAD-Seq and WGS approach
 reveals the genomic basis of yellow color variation in bumble bee Bombus
 terrestris" published in Scientific Reports for detailed
 methods. This data repository contains following files:
 1. Final SNP
 dataset from publicly available wildtype <i>B. terrestris</i>
 sequencing data (1.NCBI22filtered.recode.vcf) Please refer to the methods
 section "<b>SNP comparison to other bumble bees
 and Hymenoptera"</b> 2. Final SNP
 dataset from in-house RAD-Seq <i>B. terrestris</i> sequencing
 data (2.populations.snps.vcf) Please refer to the methods section
 "<b>Analysis of RAD-Seq
 Dataset"</b> 3. Final SNP
 dataset from in-house WGS <i>B. terrestris</i> sequencing data
 (3.BterGWASSNPonlymissingrm75QC.recode.vcf) Please refer to the methods
 section "<b>Analysis of whole-genome resequencing
 dataset"</b> 4. Population/Phenotype
 Assignment file for RAD-Seq Samples (4.RAD_pheno.txt) Please
 refer to the methods section "<b>Analysis of
 RAD-Seq Dataset"</b> 5. Population/Phenotype
 Assignment file for WGS Samples (5.WGS_pheno.txt) Please refer
 to the methods section "<b>Analysis of
 whole-genome resequencing dataset"</b> 6. MAFFT alignment
 file (nexus format) from Hymenoptera protein homologs from OrthoDB
 database (6.OrthoDB_Protein_Alignment.nex) Please refer to the methods
 section "<b>SNP comparison to other bumble bees
 and Hymenoptera"</b> 7. Alignment files
 (nexus format) from SNP validation in <i>B.
 terrestris</i> (7.Terrestris_GenotypingCutSNP.nex) Please refer to
 the methods section "<b>SNP Validation using
 Sanger Sequencing"</b> 8. Alignment files
 (nexus format) from SNP validation of outgroups of <i>B.
 terrestris</i> (8.OutgroupSeqsCutSNPregion.nex) Please refer to the
 methods section "<b>SNP comparison to other bumble
 bees and Hymenoptera"</b> 9. Alignment files
 (nexus format) from SNP validation to detect possible splice
 variants <i>B.
 terrestris</i> (9.SpliceVariantFINAL.nex) Please refer to the
 methods section "<b>Gene
 annotation"</b>